title: neuroblastoma tumor touch imprint 32

status: Public on Aug 31 2016

type: genomic

city: Vienna

first: Clemens

last: Brunner

address: Zimmermannplatz 10

department: Tumor Biology

country: Austria

institute: Children's Cancer Research Institute

hyb_protocol: Affymetrix Cytoscan HD protocol

scan_protocol: Affymetrix Cytoscan HD protocol

data_processing:
Affymetrix fluorescence intensity raw data (cel files) were processed with the Chromosome Analysis Suite (version 2.1) with default parameters resulting in Affymetrix Cytoscan HD cychp files.
Affymetrix Cytoscan HD array fluorescence intensity raw data

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: neuroblastoma tumor tissue, tumor touch imprint

label_protocol: Affymetrix Cytoscan HD protocol

extract_protocol: gDNA was extracted from tumor touch imprint cells following the high salt method from Miller SA (1988): Proteinase K digestion at 56 °C overnight, protein precipitation with 6 M NaCl, DNA precipitation with absolute ethanol, DNA dissolved in TE buffer.

treatment_protocol: Tumor pieces were pressed gently onto a standard microscopic glass slide to generate the tumor touch imprints. The cells on the glass slides were air dried for fixation. The fixed cells were collected with a polypropylen swab and washed with phosphate buffered saline. Finally DNA was extracted from these cells.

tag: diagnosis

value: neuroblastoma


title: neuroblastoma tumor touch imprint 37


title: desmoplastic small round cell tumor touch imprint 01

source_name: desmoplastic small round cell tumor, tumor touch imprint

value: desmoplastic small round cell tumor


title: neuroblastoma tumor touch imprint 33


title: neuroblastoma tumor touch imprint 41


title: neuroblastoma tumor touch imprint 29


title: Ewing tumor touch imprint 01

source_name: Ewing tumor tissue, tumor touch imprint

value: Ewing tumor


title: medulloblastoma tumor touch imprint 01

source_name: medulloblastoma tumor tissue, tumor touch imprint

value: medulloblastoma


title: neuroblastoma tumor touch imprint 35


title: neuroblastoma tumor touch imprint 30


title: neuroblastoma tumor touch imprint 44


title: neuroblastoma tumor touch imprint 28


title: neuroblastoma tumor touch imprint 26


title: osteosarcoma tumor touch imprint 01

source_name: osteosarcoma tumor tissue, tumor touch imprint

value: osteosarcoma


title: neuroblastoma tumor touch imprint 25


title: neuroblastoma tumor touch imprint 22


title: neuroblastoma tumor touch imprint 38


title: neuroblastoma tumor touch imprint 27


title: neuroblastoma tumor touch imprint 40


title: neuroblastoma tumor touch imprint 34


title: neuroblastoma tumor touch imprint 39


title: neuroblastoma tumor touch imprint 23


title: neuroblastoma tumor touch imprint 36


title: neuroblastoma tumor touch imprint 24


title: neuroblastoma tumor touch imprint 20


title: neuroblastoma tumor touch imprint 31


title: neuroblastoma tumor touch imprint 42


title: neuroblastoma tumor touch imprint 19


title: BPEC_2hr_2Gy_Xrays_rep1

type: RNA

city: Cerdanyola del Valles

first: Mariona

last: Terradas

state: BARCELONA

address: U. Cell Biology, Fac. Biosciences

department: Cell Biology, Animal Physiology and Immunology

country: Spain

institute: Universitat Autonoma de Barcelona

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 2Gy of X-ray under a Therapax device
2GyIR_1

hyb_protocol: First, 0.6ng of labelled cRNA was fragmented at 60°C for 30 minutes following manufacturer’s instructions. Then, Agilent hybridization buffer (Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression v2 Microarray (G4851B, Agilent) for 17 hours at 65°C in a hybridization oven. Microarrays were washed using Gene Expression Wash Buffers (Agilent) following manufacturer’s instructions and recommendations.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using Profile AgilentG3_Gx_1color setting for 8x60K microarrays (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

source_name: Breast Primary Epithelial Cells, 2Gy, X-ray replicate 1

label_protocol: cRNA labelling was prepared using 0.5ug of total RNA and using the Low Input Quick Amp Labeling (Agilent) according to the manufacturer's instructions. Labeled/amplified RNA was purified using Qiagen’s RNeasy mini spin columns (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: Breast primary epithelial cells (BPECs) were obtained from normal breast tissue (Instituto Quirúrgico Barcelona) and cultured in WIT medium (Cellaria) using Corning Primaria culture flasks (Corning). Cells growing in 25cm2 flasks were maintained at 37ºC in a humidified incubator with 5% CO2 until irradiation time. Afterwards, cells were returned to the incubator for two hours.

extract_protocol: RNA collection of the samples was done at three different days in order to have biological triplicates per each sample. Total RNA for microarray analysis was isolated from cells using Trizol reagent (Ambion) and then it was treated with DNase (Qiagen) during RNA purification using RNeasy Kit (Qiagen) following manufacturers instructions. RNA integrity was analized using the Agilent 2100 Bioanalyzer (Agilent)

treatment_protocol: BPECs growing in 25cm2 flasks were irradiated with two (0.02 Gy) and ten automatic shots (0.1 Gy) under a mammography X-ray diagnostic device (SENO DMR plur, General electric). A Therapax STX 150 machine (Pantak) was used to irradiate BPECs at high doses (2Gy). After irradiation, cells were returned to the incubator and maintained for 2 hours until RNA extraction.

tag: tissue

value: Mammary Gland

tag: gender

value: female


title: BPEC_2hr_2Gy_Xrays_rep2

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 2Gy of X-ray under a Therapax device
2GyIR_2

source_name: Breast Primary Epithelial Cells, 2Gy, X-ray replicate 2


title: BPEC_2hr_0.1Gy_Xrays_rep3

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 10 automic X-ray shots (0.1Gy) under a mammography device
010GyIR_3

source_name: Breast Primary Epithelial Cells, 0.1Gy, X-ray replicate 3


title: BPEC_2hr_2Gy_Xrays_rep3

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 2Gy of X-ray under a Therapax device
2GyIR_3

source_name: Breast Primary Epithelial Cells, 2Gy, X-ray replicate 3


title: neuroblastoma tumor touch imprint 21


title: BPEC_2hr_0.02Gy_Xrays_rep2

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 2 automic X-ray shots (0.02Gy) under a mammography device
002GyIR_2

source_name: Breast Primary Epithelial Cells, 0.02Gy, X-ray replicate 2


title: BPEC_2hr_0.1Gy_Xrays_rep1

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 10 automic X-ray shots (0.1Gy) under a mammography device
010GyIR_1

source_name: Breast Primary Epithelial Cells, 0.1Gy, X-ray replicate 1


title: BPEC_2hr_0.02Gy_Xrays_rep1

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 2 automic X-ray shots (0.02Gy) under a mammography device
002GyIR_1

source_name: Breast Primary Epithelial Cells, 0.02Gy, X-ray replicate 1


title: BPEC_2hr_0.02Gy_Xrays_rep3

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 2 automic X-ray shots (0.02Gy) under a mammography device
002GyIR_3

source_name: Breast Primary Epithelial Cells, 0.02Gy, X-ray replicate 3


title: BPEC_2hr_0.1Gy_Xrays_rep2

description:
Gene expression of breast primary epithelial cells 2 hours after exposure to 10 automic X-ray shots (0.1Gy) under a mammography device
010GyIR_2

source_name: Breast Primary Epithelial Cells, 0.1Gy, X-ray replicate 2


title: neuroblastoma tumor touch imprint 43


title: BPEC_2hr_shamIR_rep3

description:
Gene expression in breast primary epithelial cells 2 hours after sham-irradiation
shamIR_3

source_name: Breast Primary Epithelial Cells, shamirradiated, replicate 3


title: C_38736_27

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

hyb_protocol: cRNA samples were hybridized to an Agilent Technologies Human Gene Expression 8x60K Microarray Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters. Each sample represents one channel of a dual-channel array.

data_processing: Expression arrays were processed using BioConductor (one color arrays, Quantile normalization). Also we combated the dataset by patient (as the “batch” variable).

source_name: prostate cancer

label_protocol: The cRNA labeling was performed according to Protocol from Agilent Technologies Inc. (Santa Clara, CA) using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer's protocol.

extract_protocol: RNA was extracted following the manufacturer's recommendations.

tag: ethnicity

value: African-American


title: BPEC_2hr_shamIR_rep2

description:
Gene expression in breast primary epithelial cells 2 hours after sham-irradiation
shamIR_2

source_name: Breast Primary Epithelial Cells, shamirradiated, replicate 2


title: HBEC3_p53_KRAS_CD24lo_CD44hi

city: Dallas

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

description: HBEC3-KTRL53 CD24lo-CD44hi

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

label: Biotin

source_name: HBEC3-KTRL53 CD24lo-CD44hi

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: Cells were grown in adherent conditions and cell pellets were harvested when cells were ~70% confluent.

extract_protocol: RNA was isolated using RNeasy mini kit (QIAGEN, Valencia, CA) and quality was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

tag: cell line

value: Human bronchial epithelial cell (HBEC) immortalized with cdk4 and hTERT

value: yes

tag: cmyc

value: no

tag: cd24hi (facs)

tag: cd44hi (facs)

tag: growth media

value: KSFM

tag: age

value: F

tag: smoker


title: HBEC3_p53_KRAS_CD24lo_CD44lo

description: HBEC3-KTRL53 CD24lo-CD44lo

source_name: HBEC3-KTRL53 CD24lo-CD44lo


title: HBEC3_p53_KRAS_CD24hi_CD44lo

description: HBEC3-KTRL53 CD24hi-CD44lo

source_name: HBEC3-KTRL53 CD24hi-CD44lo


title: HBEC3_p53_KRAS_cMYC


title: HBEC3_p53_KRAS_FBS


title: BPEC_2hr_shamIR_rep1

description:
Gene expression in breast primary epithelial cells 2 hours after sham-irradiation
shamIR_1

source_name: Breast Primary Epithelial Cells, shamirradiated, replicate 1


title: Beta-catenin KLS34 REP1

city: Durham

first: William

last: Lento

state: NC

address: 213 Research Drive

department: Medicine/Cellular Therapy

institute: Duke University

hyb_protocol: Following fragmentation, 2ug of cRNA were hybridized for 16 hr at 45C on mouse 1.0 ST Gene Array. Hybridization was performed using an Affymetrix FS450 hybridization oven.  GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

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

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.

organism: Mus musculus

source_name: sorted KLSCD34-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

extract_protocol: KLSCD34- stem cells were sorted on a FACS Aria (BD Biosciences) into buffer RLT (Qiagen) containing 2-ME and total RNA was extracted by trizol.

value: Bone marrow

tag: cell type

value: sorted KLSCD34-

tag: genotype/variation

value: Beta-catenin


title: HBEC3_p53_KRAS


title: Beta-catenin KLS34 REP2


title: Control KLS34 REP3

value: control


title: Beta-catenin KLS34 REP3


title: HBEC3_cMYC


title: HBEC3_pSRZ_pL6Z


title: Control KLS34 REP1


title: neuroblastoma tumor touch imprint 18

source_name: neuroblastoma tumor tissue, tumor touch imprint

value: neuroblastoma


title: HBEC3_pMSCV


title: HBEC3_ZEB1.1


title: SW480 p+19

city: Edinburgh

first: Romina

last: Briffa

state: Lothian

address: Crewe Road South

department: Division of Pathology

country: United Kingdom

institute: University of Edinburgh

description: Biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and quantile normalisation with Genome Studio

source_name: CRC cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrepTM RNA Amplification Kit (Ambion®, cat. no. AMIL1791)

growth_protocol: The cell lines were cultured in Dulbecco’s Modified Eagles Medium (DMEM) (Gibco®, Cat. no. 31885) supplemented with 10% Foetal Bovine Serum (FBS; PAA, Cat. no. A15-101) and 1% penicillin-streptomycin (Gibco®, Cat. no.15140-122). The cell lines were grown in a humidified incubator at 37°C, containing 5% CO2.

extract_protocol: Total RNA was extracted from the 15 CRC cell lines in duplicate.  The RNeasy MinElute Cleanup Kit (Qiagen, Cat. no. 74204) and miRNeasy Mini Kit was used, as per manufacturer's instructions.  Prior to progressing with preparation of the RNA samples for microarray analysis, the RNA integrity was further assessed with the Agilent® 2100 Bioanalyzer, using the Agilent® RNA 6000 Nano Kit (Agilent, cat. no. 5067-1511).

tag: sensitivity to 5 fu

value: less

tag: sensitivity to l-ohp

tag: sensitivity to bez235

value: insensitive


title: SW48 p+18

description: Biological replicate 2

value: high


title: LS411N p+13

description: Biological replicate 2

value: sensitive


title: SW480 p+19 tech rep

description: Technical replicate


title: T84 p+21

description: Biological replicate 2


title: HCT116 p+15 tech rep

description: Technical replicate


title: DLD1 p46

description: Biological replicate 2


title: neuroblastoma tumor touch imprint 11


title: LoVo p54

description: Biological replicate 2

value: LoVo


title: neuroblastoma tumor touch imprint 12


title: neuroblastoma tumor touch imprint 13


title: HT29 p+12

description: Biological replicate 2


title: HCT116 p+15

description: Biological replicate 2


title: neuroblastoma tumor touch imprint 10


title: SW837 p72

description: Biological replicate 2


title: Control KLS34 REP2


title: LS411N p+12

description: Biological replicate 1


title: neuroblastoma tumor touch imprint 08


title: neuroblastoma tumor touch imprint 07


title: neuroblastoma tumor touch imprint 05


title: neuroblastoma tumor touch imprint 06


title: HT29 p+19

description: Biological replicate 1


title: SW837 p78 tech rep

description: Technical replicate


title: NCI H716 p+19 tech rep

description: Technical replicate

value: NCI H716


title: Colo320DM p+7

description: Biological replicate 2


title: SW837 p78

description: Biological replicate 1


title: Colo201 p+22

description: Biological replicate 2


title: neuroblastoma tumor touch imprint 04


title: neuroblastoma tumor touch imprint 15


title: SK CO1 p+16

description: Biological replicate 2

value: SK CO1


title: NCI H508 p+10 #2

description: Biological replicate 2

value: NCI H508


title: Artificially Acclimated penguin 3

city: Bremerhaven

first: Cyril

last: Degletagne

address: Am Handelshafen

department: Functional Ecology

country: Germany

institute: Alfred Wegener Institute

description: Gene expression data in pectoralis muscle from an artificially acclimated penguin

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Arrays in a Genechip hybridization oven 640 (Affymetrix). GeneChips were washed and stained with streptavidin-phycoerythrin (Invitrogen Corporation, CA, USA) in a fluidic 450 (Affymetrix) according to the manufacturer’s instruction.

scan_protocol: The arrays were scanned with a confocal laser (Genechip scanner 3000, Affymetrix).

data_processing: The data were analyzed with the MAXRS method dedicated to heterologous hybridization analysis on high density microarrays (Degletagne et al., 2010). They were then normalized by using the quantile method implemented in the limma Bioconductor package.

organism: Aptenodytes patagonicus

source_name: Muscle sample biopsy from juvenile penguin captured just before it undergone its first immersion to cold water subjected to experimental immersions in cold water (8°C) to simulate acclimatization to marine life.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: 3 penguins juveniles captured just before they undergone their first immersion to cold water and that moulted in captivity are subjected to experimental immersions in cold water (8°C) to simulate acclimatization to marine life. The protocol consisted in a ten successive immersions (5 hours every 2 days) in a water tank (1.2m width, 2.0m long, 1.0m deep).

extract_protocol: Total RNA was extracted using TriReagent procedure (Invitrogen, Cergy Pontoise, France) following the manufacturer's instructions.

treatment_protocol: Penguins were anaesthetized by isoflurane inhalation, and approximately 100mg of pectoralis muscle was surgically excised, frozen in liquid nitrogen and kept at -80°C until molecular analysis.

value: Female

tag: developmental stage

value: juvenile

value: pectoralis muscle


title: HCT116 p53(-/-) p+12

description: Biological replicate 2


title: Artificially Acclimated penguin 1


title: NCI H716 p+19

description: Biological replicate 2


title: FACS sorted E17.5 lung epithelial tip biological replicate 5

city: Cambridge

first: Emma

middle: Louise

last: Rawlins

address: Tennis Court Road

department: Gurdon Institute

institute: University Of Cambridge

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Bioconductor

source_name: Tip epithelial progenitor cells from E17.5 developing lung

label_protocol: Standard Affymetrix protocol using Ovation RNA Amplification Kit V2 and FL-Ovation Biotin V2 (NuGEN)

growth_protocol: Timed matings of Id2-CreER/+heterozygotes  with Rosa26R-fGFP/fGFP homozygotes. Noon on day of plug = E0.5.

extract_protocol: Total RNA using Qaigen RNEasy Mini Kit as per manufacturer's instructions

treatment_protocol: Lungs were dissected from E11.5 embryos and tip epithelium was microdissected following a 5 minute treatment with 16U/ml dispase. For E17.5 cells, pregnant females were injected with 150 micrograms per gram body weight at E16.5.  E17.5 embryos were dissected and GFP+ lungs selected under GFP-dissecting microscope. Lungs were dissociated to single cells using trypsin/EDTA and GFP+ cells isolated by flow cytometry.

value: Lung epithelial tip progenitor cells

tag: cell isolation

value: Cells FACs-sorted from embryonic lung

tag: embryo genotype

value: Id2-CreER; Rosa26R-fGFP


title: FACS sorted E17.5 lung epithelial tip biological replicate 4


title: neuroblastoma tumor touch imprint 02

tag: diagnosis


title: neuroblastoma tumor touch imprint 17


title: Colo201 p+8

description: Biological replicate 1


title: neuroblastoma tumor touch imprint 16


title: neuroblastoma tumor touch imprint 14


title: T84 p21 tech rep

description: Technical replicate


title: FACS sorted E17.5 lung epithelial tip biological replicate 3


title: NCI H716 p+20

description: Biological replicate 1


title: Microdissected E11.5 lung epithelial tip biological replicate 2

source_name: Tip epithelial progenitor cells from E11.5 developing lung

value: Cells microdissected from embryonic lung


title: Microdissected E11.5 lung epithelial tip biological replicate 5


title: FACS sorted E17.5 lung epithelial tip biological replicate 1


title: Microdissected E11.5 lung epithelial tip biological replicate 4


title: LoVo p53 tech rep

description: Technical replicate


title: Microdissected E11.5 lung epithelial tip biological replicate 1


title: neuroblastoma tumor touch imprint 03


title: Artificially Acclimated penguin 2

tag: gender

value: Male

tag: tissue


title: HCT116p53(-/-) p+12

description: Biological replicate 1

tag: cell line


title: Microdissected E11.5 lung epithelial tip biological replicate 3


title: HCT116 p+18

description: Biological replicate 1


title: NCI H508 p+10 #1

description: Biological replicate 1


title: SK CO1 p+18

description: Biological replicate 1


title: LoVo p53

description: Biological replicate 1


title: FACS sorted E17.5 lung epithelial tip biological replicate 2


title: Colo320DM p+9

description: Biological replicate 1


title: SW480 p+9

description: Biological replicate 1


title: z-f

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

institute: TULANE UNIVERSITY

description: This sample is p53-null HCT116 cells treated with INZ.  It is the third of three biological replicates.

hyb_protocol: Hybridization was performed by Arraystar Inc. (Rockville, MD), following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Arraystar Inc. (Rockville, MD), 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 2.5.26 (Roche NimbleGen, Inc.).

label_protocol: Labeling was performed by Arraystar Inc. (Rockville, MD), following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 0.1 mg/ml streptomycin at 37°C in a 5% CO2 humidified atmosphere.
Cells were plated in 10-cm cell culture dishes and were treated with 4μM INZ at 70% confluency and harvested at 18 hours post treatment

extract_protocol: Total RNA was extracted using TriZol  (Invitrogen, USA). RNA quality was confirmed by agarose electrophoresis and only those samples showing no degradation (ratios approaching 2:1 for the 28S and 18S bands) were sent to Arraystar Inc. (Rockville, MD)

tag: genotype

value: p53 null


title: Ovol2_GE_16

city: Tsukuba

first: Kuniya

last: Abe

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

country: Japan

institute: RIKEN

description: Primordial germ cells of mouse E16.5 female embryos_rep2

hyb_protocol: One ug of Cy3-labelled cRNA was fragmented following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A) for 16hours 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 immediately subjected to a microarray scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner) using one color scan setting for 8x60k array slides ( Scan resolution 5um).

data_processing: Agilent Feature Extraction and GeneSpring software was used for data processing.

source_name: Female Primordial germ cells, E16.5, replicate2

label_protocol: Twenty five nanogram of total RNA was labeled with Cy3-CTP with a Quick Amp Labeling Kit (Agilent Technologies). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: Total RNAs were extracted from samples using an AllPrep DNA/RNA Micro Kit (Qiagen, Hilden, Germany). The quality of RNA samples was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: cell types

value: embryonic germ cells


title: Ovol2_GE_15

description: Primordial germ cells of mouse E16.5 female embryos_rep1

source_name: Female Primordial germ cells, E16.5, replicate1


title: Ovol2_GE_14

description: Primordial germ cells of mouse E13.5 female embryos_rep2

source_name: Female Primordial germ cells, E13.5, replicate2


title: z-d

description: This sample is p53-null HCT116 cells treated with INZ.  It is the first of three biological replicates.


title: DLD-1 p36

description: Biological replicate 1

value: less


title: z-c

description: This sample is p53-null HCT116 cells treated with DMSO.  It is the third of three biological replicates.

source_name: HCT116 p53-/- DMSO


title: SW48 p+7

description: Biological replicate 1

value: high

value: insensitive


title: T84 p21

description: Biological replicate 1


title: Ovol2_GE_13

description: Primordial germ cells of mouse E13.5 female embryos_rep1

source_name: Female Primordial germ cells, E13.5, replicate1


title: z-e

description: This sample is p53-null HCT116 cells treated with INZ.  It is the second of three biological replicates.


title: Ovol2_GE_12

description: Primordial germ cells of mouse E16.5 male embryos_rep2

source_name: Male Primordial germ cells, E16.5, replicate2


title: Ovol2_GE_10

description: Primordial germ cells of mouse E13.5 male embryos_rep2

source_name: Male Primordial germ cells, E13.5, replicate2


title: MDA-MB-468 RNA harvested at 24 hours treatment

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

description: 24 hour (+) .AVG_Signal

data_processing:
The data for each series were normalized using quantile normalization with IlluminaGUI in R
raw probe level expression data were background subtracted and log2 transformed; normalized data were background subtracted, log2 transformed, quantile normalized across the series

source_name: MDA-MB-468 cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: MDA-MB-468 cells were grown in DMEM supplemented with 10% FBS, 2.5 μg/mL amphotericin B and 25 μg/mL gentamicin.

extract_protocol: RNA was isolated from cell cultures using the QIAGEN Rneasy Plus kit (Qiagen, Valencia, CA) in accordance with the prescribed protocol provided with the kit. RNA quantity and quality was assessed by the nanodrop 3000 spectrophotometer.

treatment_protocol: cell cultures were treated with the targeted antioxidant CAT-SKL at 1uM concentration for the time duration indicated in the sample title and name

value: breast cancer cell line derived from metastatic breast cancer

tag: treated with

value: CAT-SKL at 1uM for 24hrs


title: z-a

description: This sample is p53-null HCT116 cells treated with DMSO.  It is the first of three biological replicates.


title: Ovol2_GE_09

description: Primordial germ cells of mouse E13.5 male embryos_rep1

source_name: Male Primordial germ cells, E13.5, replicate1


title: neuroblastoma tumor touch imprint 09

value: neuroblastoma


title: z-5

description: This sample is wild-type p53 harboring HCT116 cells treated with INZ.  It is the second of three biological replicates.

value: Wild-type p53


title: Ovol2_GE_11

description: Primordial germ cells of mouse E16.5 male embryos_rep1

source_name: Male Primordial germ cells, E16.5, replicate1


title: Ovol2_GE_08

description: Primordial germ cells of mouse E8.5 embryos_rep2

source_name: Primordial germ cells, E8.5, replicate2


title: MDA-MB-468 RNA harvested at 30 hours treatment

description: 30 hour (+) .AVG_Signal

value: CAT-SKL at 1uM for 30hrs


title: z-2

description: This sample is wild-type p53 harboring HCT116 cells treated with DMSO.  It is the second of three biological replicates.

source_name: HCT116 p53+/+ DMSO


title: MDA-MB-468 RNA harvested at 6 hours treatment

description: 6 hour (+) .AVG_Signal

value: CAT-SKL at 1uM for 6hrs


title: z-6

description: This sample is wild-type p53 harboring HCT116 cells treated with INZ.  It is the third of three biological replicates.


title: MDA-MB-468 RNA harvested at 18 hours treatment

description: 18 hour (+) .AVG_Signal

value: CAT-SKL at 1uM for 18hrs


title: Ovol2_GE_07

description: Primordial germ cells of mouse E8.5 embryos_rep1

source_name: Primordial germ cells, E8.5, replicate1


title: MDA-MB-468 RNA harvested at 12 hours treatment

description: 12 hour (+) .AVG_Signal

value: CAT-SKL at 1uM for 12hrs


title: Ovol2_GE_06

description: Embryonic ectoderm of mouse E8.5 embryos_rep2

source_name: Embryonic Ectoderm, E8.5, replicate 2

value: embryonic tissue


title: z-4

description: This sample is wild-type p53 harboring HCT116 cells treated with INZ.  It is the first of three biological replicates.


title: MDA-MB-468 RNA harvested at 0 hours treatment

description: 0 hour (+) .AVG_Signal

value: CAT-SKL at 1uM for 0hrs


title: Ovol2_GE_05

description: Embryonic ectoderm of mouse E8.5 embryos_rep1

source_name: Embryonic Ectoderm, E8.5, replicate 1


title: Ovol2_GE_02

description: Mouse ES cells_J1_cultured in 2i_rep2

source_name: mESC, J1 in 2i, replicate 2

value: stem cells


title: z-3

description: This sample is wild-type p53 harboring HCT116 cells treated with DMSO.  It is the third of three biological replicates.


title: Ovol2_GE_04

description: Epiblast of mouse E6.5 embryos_rep2

source_name: Epiblast, E6.5, replicate 2


title: Flight_002

first: Akira

last: Higashibata

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

description: Gene expression in ground control

hyb_protocol: The labeled cRNA (1.65 µg/sample) was hybridized to a microarray using the Agilent Gene Expression Hybridization Kit at 65°C for 17 hours.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1.
Microarray data were analyzed using Gene Spring software (Agilent Technologies). Normalized data were produced by Normalize to 75 percentile sift protocol’’ and baseline to median of control sample protocol’’. Arrays were filtered on expression (20-100)th percentile in raw data.

organism: Caenorhabditis elegans

source_name: Space flight sample, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: Approximately 10000 mixed stage worms were cultured in C. elegans mentenace medium (CeMM). During transporting the worms to the International Space Station, it took 2 days at 12 degree. The worms were cultured at 18 degree for 8 days in internatioal space station. To recover the sample, it took 1day at 18 degree. The recovered worms were frozen by liquid N2 on the earth.

extract_protocol: RNA was prepared using ISOGEN (Nippon Gene, Tokyo, Japan) following the manufacturer's recommendations. The residual DNA was eliminated by treating with DNase I (Takara Bio, Shiga, Japan) during an isolation process of total RNA. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The worms were washed by M9 buffer.

tag: strain

value: N2 wild type

tag: Stage

value: Mix stage


title: z-1

description: This sample is wild-type p53 harboring HCT116 cells treated with DMSO.  It is the first of three biological replicates.


title: Flight_003

description: Gene expression in ground control

source_name: Space flight sample, replicate 3


title: z-b

description: This sample is p53-null HCT116 cells treated with DMSO.  It is the second of three biological replicates.

value: p53 null


title: Flight_001

description: Gene expression in ground control

source_name: Space flight sample, replicate 1


title: Ovol2_GE_03

description: Epiblast of mouse E6.5 embryos_rep1

source_name: Epiblast, E6.5, replicate 1


title: Ovol2_GE_01

description: Mouse ES cells_J1_cultured in 2i_rep1

source_name: mESC, J1 in 2i, replicate 1


title: Ground_001

description: Gene expression in space flight

source_name: Ground control sample,replicate 1


title: Ground_003

description: Gene expression in space flight

source_name: Ground control sample,replicate 3


title: 1G control_4days_rep1

description: Gene expression in artificial 1G control on orbit

source_name: artificial 1G control for 4days on orbit, replicate 1

growth_protocol: The worms were cultured at 20 degree for 4 days in internatioal space station (ISS). The 2 mL of M9 cholesterol buffer suspended 9,000 of the hatched L1 larvae and the 12 mL of S-basal media suspended E. coli (OD600=5) were separately packed into a monolayer polyethylene bag. The experiment was activated once onboard the ISS by reintroducing worms to bacterial food.

treatment_protocol: The worms were washed by M9 buffer. The worms were homoginaized with four rounds of 20-secound beating at 5000rpm in a MicroSmash MS-100 bead beater (Tomy seiko,Tokyo JAPAN).

value: Adult


title: Old_normal_fed_1 [L6 dorsal root ganglia]

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505C with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028279_D_F_20100603) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: L6DRG, old, normal fed, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 120 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from tissues using the miRNeasy Mini Kit (QIAGEN).

value: L6 dorsal root ganglia

value: Fischer 344

value: male


title: ground control_4days_rep3

description: Gene expression in ground control

source_name: ground 1G control for 4days, replicate 3


title: Old_CR_fed_1 [L6 dorsal root ganglia]

source_name: L6DRG, old, CR, replicate1


title: 1G control_4days_rep2

source_name: artificial 1G control for 4days on orbit, replicate 2


title: Old_normal_fed_4 [L6 dorsal root ganglia]

source_name: L6DRG, old, normal fed, replicate2


title: Ground_002

description: Gene expression in space flight

source_name: Ground control sample,replicate 2


title: Old_CR_fed_8 [L6 dorsal root ganglia]

source_name: L6DRG, old, CR, replicate4


title: ica_SM_rep2

city: Pohang

first: Ildoo

last: Hwang

address: Chungam-ro

department: Department of life science

country: South Korea

institute: POSTECH

description: gene expression of the inflorescence stem in ica at 6th silique

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.13.0 (R2011b)

organism: Arabidopsis thaliana

source_name: ica, uppermost 1 cm of vegetative nodes in the inflorescence stems, replicate 2

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Seeds were germinated on 1/2 B5 medium containing 1% sucrose and 0.8% w/v agar under fluorescent light (16-h light/8-h dark) at 23 oC. Young seedlings were then transferred to soil and grown until the experiment.

extract_protocol: Total RNA was isolated from the inflorescence stem at the stage of the sixth silique development in Col-0 and ica using TRIZOL reagent (Thermo Fisher scientific, http://www.thermofisher.com/) according to the manufacturer’s instructions. RNA samples were freed of DNA contamination using DNAfree (Ambion, http://www.invitorgen.com/ambion). cDNA was synthesized using the ImProm-II reverse transcription system(Promega, http://www.promega.com/). The integrity of RNA was checked using bioanalyzer (Agilent Technologies, http://www.agilent.com/).

value: inflorescence stem

value: 6th silique

tag: ecotype

value: ica


title: Old_normal_fed_5 [L6 dorsal root ganglia]

source_name: L6DRG, old, normal fed, replicate3


title: Young_normal_fed_5 [L6 dorsal root ganglia]

source_name: L6DRG, young, normal fed, replicate2


title: ground control_4days_rep1

description: Gene expression in ground control

source_name: ground 1G control for 4days, replicate 1


title: Old_CR_fed_2 [L6 dorsal root ganglia]

source_name: L6DRG, old, CR, replicate2


title: Col-0_SM_rep2

description: gene expression of the inflorescence stem in Col-0 at 6th silique

source_name: Col-0, uppermost 1 cm of vegetative nodes in the inflorescence stems, replicate 2

value: wildtype


title: ground control_4days_rep2

description: Gene expression in ground control

source_name: ground 1G control for 4days, replicate 2


title: ica_SM_rep1

source_name: ica, uppermost 1 cm of vegetative nodes in the inflorescence stems, replicate 1


title: Young_normal_fed_9 [L6 dorsal root ganglia]

source_name: L6DRG, young, normal fed, replicate4


title: microG_4days_rep3

description: Gene expression in microG

source_name: microgravity for 4days, replicate 3


title: Young_normal_fed_6 [L6 dorsal root ganglia]

source_name: L6DRG, young, normal fed, replicate3


title: Old_CR_fed_5 [L6 dorsal root ganglia]

source_name: L6DRG, old, CR, replicate3


title: microG_4days_rep1

description: Gene expression in microG

source_name: microgravity for 4days, replicate 1


title: Col-0_SM_rep1

source_name: Col-0, uppermost 1 cm of vegetative nodes in the inflorescence stems, replicate 1


title: Canine Atopic Dermatitis Patient 19

city: Warszawa

first: Alicja

last: Majewska

address: Nowoursynowska 159

department: Department of Physiology Sciences

country: Poland

institute: Warsaw University of Life Sciences-SGGW Faculty of Veterinary Medicine

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

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

organism: Canis lupus familiaris

source_name: whole blood

growth_protocol: not applicable

extract_protocol: Total RNA extracted using Rneasy Protect Animal Blood Kit following manufacturer's instructions (Qiagen, USA)

treatment_protocol: Blood collection into Rneasy Protect Animal Blood Tubes  (Qiagen, USA).

tag: disease state

value: atopic dermatitis

source_name: common reference sample composed of total RNAs isolated from whole blood from 13 healthy dogs

tag: sample type

value: reference

value: healthy


title: Old_normal_fed_7 [L6 dorsal root ganglia]

source_name: L6DRG, old, normal fed, replicate4


title: 1G control_4days_rep3

source_name: artificial 1G control for 4days on orbit, replicate 3


title: microG_4days_rep2

description: Gene expression in microG

source_name: microgravity for 4days, replicate 2


title: Young_normal_fed_4 [L6 dorsal root ganglia]

source_name: L6DRG, young, normal fed, replicate1


title: Old_CR_fed_2 [bladder]

source_name: bladder body, old, CR, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling 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.

value: bladder body


title: neuroblastoma tumor touch imprint 01

source_name: neuroblastoma tumor tissue, tumor touch imprint

value: neuroblastoma


title: Canine Atopic Dermatitis Patient 16

label_protocol: according to the manufacturer's protocol


title: Old_CR_fed_8 [bladder]

source_name: bladder body, old, CR, replicate4


title: Old_CR_fed_5 [bladder]

source_name: bladder body, old, CR, replicate3


title: Old_normal_fed_4 [bladder]

source_name: bladder body, old, normal fed, replicate2


title: Old_normal_fed_7 [bladder]

source_name: bladder body, old, normal fed, replicate4


title: Canine Atopic Dermatitis Patient 17


title: Canine Atopic Dermatitis Patient 20


title: Canine Atopic Dermatitis Patient 14


title: Canine Atopic Dermatitis Patient 13


title: Old_CR_fed_1 [bladder]

source_name: bladder body, old, CR, replicate1


title: Old_normal_fed_5 [bladder]

source_name: bladder body, old, normal fed, replicate3


title: Canine Atopic Dermatitis Patient 11


title: Canine Atopic Dermatitis Patient 12


title: Canine Atopic Dermatitis Patient 15


title: Canine Atopic Dermatitis Patient 10


title: Canine Atopic Dermatitis Patient 18


title: Old_normal_fed_1 [bladder]

source_name: bladder body, old, normal fed, replicate1


title: Young_normal_fed_6 [bladder]

source_name: bladder body, young, normal fed, replicate3


title: 11465_C dried neonatal bloodspot

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

hyb_protocol: Standard protocol defined by Illumina for HM450K

data_processing: Data normalization was performed using ChAMP in R (version 3.2.0). To minimize technical variation, all multiply-mapped probes, as well as probes containing SNPs in either the target CpG or the 10 bases of probe closest to the target CpG site (Price et al. 2013; Illumina annotation) were removed from subsequent analysis. This excluded 91,058 probes from analysis, leaving 394,454 probes prior to calculating differential methylation. Differential methylation analysis was done using A-clustering algorithm followed by estimation of methylation difference by Generalized estimation equation (GEE) from Sofer et al, 2013.

label: Cy5 and Cy3

source_name: genomic DNA from dried neonatal bloodspot

extract_protocol: DNA was isolated from one third of each dried bloodspot with Qiagen EZ1 Advanced using the DNA Investigator reagents and protocol.  The “Stains on Fabric” preprocessing and Trace (tip-dance) instrument protocol were used for the isolation. DNA was quantified by UV spectrometry using the DropSense96 Microplate Spectrophotometer (Trinean) and the purity assessed based on the A260/A280 and A260/A230 ratios. The methylation protocol began with bisulphite treatment of 250 ng of starting material using the EZ-96 Methylation Kit (Zymo Reasearch) using the standard protocol for Infinum.  Bisulphite treated DNA was then enzymatically fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip

value: Female

tag: conception type

value: IVF-Frozen embryo transfer (FZ)

value: dried peripheral neonatal blood


title: 11340_C dried neonatal bloodspot

scan_protocol: Standard protocol defined by Illumina for HM450K


title: Young_normal_fed_9 [bladder]

source_name: bladder body, young, normal fed, replicate4


title: Canine Atopic Dermatitis Patient 8

source_name: whole blood

source_name: common reference sample composed of total RNAs isolated from whole blood from 13 healthy dogs


title: 10695_C dried neonatal bloodspot

label_protocol: Standard protocol defined by Illumina for HM450K


title: Canine Atopic Dermatitis Patient 7


title: 11580_C dried neonatal bloodspot


title: skin_wt_treated_24h_rep3

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

hyb_protocol: End labeled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays for 16 h at 45°C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturers´ protocol.

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing:
Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probe set were summarized by GeneSpring's ExonRMA16 algorithm after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: skin, wt, stressed, 24h

label_protocol: Synthesis of biotin labeled cDNA was performed on three replicates of each experimental group according to the manufacturers´ protocol (WT Plus Reagent Kit; Affymetrix, Inc, Palo Alto, CA). Briefly, 100 ng of total RNA were converted to cDNA. After amplification by in vitro transcription and 2nd cycle synthesis, cDNA was fragmented and biotin labeled by terminal transferase.

growth_protocol: We used B6.129-AhRtm1Bra/J (Schmidt et al.(1996) PNAS 93:6731), or mice with conditional deletion of AhR in keratinocytes and Langerhans cells (LC) (Kadow et al. ( 2011) J. Immunol 197:3104;Jux et al. (2009) J. Immunol. 182:6709 (referred to as AhR-KO, AhRΔK5, or AhRΔLC, respectively). Animal housing was specific pathogen free, with a 12/12 hour light dark cycle, and access to food and water ad libitum.

extract_protocol: Total RNA from epidermal sheets was isolated using my Budget RNAmagic (Bio Budget Technologies GmbH, Krefeld, Germany) according to the manufacturer’s instructions. Additionally, the total RNA was cleaned up using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany). Total RNA preparations were checked for RNA integrity by Agilent 2100 Bioanalyzer quality control. All samples in this study showed high quality RNA Integrity Numbers (RIN; mean). RNA was further analyzed by photometric Nanodrop measurement and quantified by fluorometric Qubit RNA assays (LifeTechnologies, Darmstadt, Germany).

treatment_protocol: AHR-KO (-/-) and WT (+/+) littermates were mechanically stressed on the shaved back skin by tape-stripping (5 times with Tegaderm3 M film).

tag: genetic background

tag: genotype/variation

value: AhR+/+

tag: treatment

value: mechanical stress

tag: time

value: female

value: skin


title: Canine Atopic Dermatitis Patient 9


title: 11452_C dried neonatal bloodspot


title: Young_normal_fed_5 [bladder]

source_name: bladder body, young, normal fed, replicate2

value: Fischer 344

value: male


title: 11048_C dried neonatal bloodspot


title: 10831_C dried neonatal bloodspot


title: Young_normal_fed_4 [bladder]

source_name: bladder body, young, normal fed, replicate1


title: Canine Atopic Dermatitis Patient 6


title: skin_wt_treated_24h_rep1


title: skin_wt_treated_24h_rep2


title: Canine Atopic Dermatitis Patient 3


title: Canine Atopic Dermatitis Patient 4


title: 10587_C dried neonatal bloodspot


title: 10829_C dried neonatal bloodspot


title: 11165_C dried neonatal bloodspot


title: 10894_C dried neonatal bloodspot


title: skin_ko_treated_24h_rep3

source_name: skin, ko, stressed, 24h

value: AhR-/-


title: Canine Atopic Dermatitis Patient 2


title: 10511_C dried neonatal bloodspot


title: 10292_C dried neonatal bloodspot


title: Canine Atopic Dermatitis Patient 5


title: Canine Atopic Dermatitis Patient 1


title: skin_ko_treated_24h_rep2


title: skin_wt_treated_6h_rep3

source_name: skin, wt, stressed, 6h


title: Healthy Dog Patient 8


title: 10347_C dried neonatal bloodspot


title: skin_wt_treated_6h_rep1


title: skin_ko_treated_24h_rep1


title: Healthy Dog Patient 7


title: 10389_C dried neonatal bloodspot


title: Healthy Dog Patient 6


title: skin_wt_treated_6h_rep2


title: 10447_C dried neonatal bloodspot


title: Healthy Dog Patient 5


title: skin_ko_treated_6h_rep2

source_name: skin, ko, stressed, 6h


title: 10141_C dried neonatal bloodspot


title: Healthy Dog Patient 4


title: Healthy Dog Patient 3


title: skin_ko_treated_6h_rep3


title: skin_ko_treated_6h_rep1


title: Healthy Dog Patient 2


title: skin_wt_untreated_0h_rep3

source_name: skin, wt, unstressed, 0h

value: unstressed


title: skin_wt_untreated_0h_rep1


title: 10136_C dried neonatal bloodspot


title: skin_ko_untreated_0h_rep2

source_name: skin, ko, unstressed, 0h


title: skin_wt_untreated_0h_rep2


title: 11127_C dried neonatal bloodspot

value: Male


title: 11381_C dried neonatal bloodspot


title: 11177_C dried neonatal bloodspot


title: skin_ko_untreated_0h_rep3


title: 10947_C dried neonatal bloodspot


title: Healthy Dog Patient 1


title: 11368_C dried neonatal bloodspot


title: skin_ko_untreated_0h_rep1


title: ESCs-shPaf1 knockdown replicate 3

first: Alexandros

last: Strikoudis

address: 550 First Avenue, Smilow 1303

department: Pathology

institute: NYU Medical Center

description: Gene expression data from mouse ESCs under shPaf1 knockdown

hyb_protocol: Following fragmentation/lableling, 10 ug of labeled ssDNA was added to a hybridization cocktail outlined in Affymetrix Genechip WT Terminal Labeling kit (part#900671). The cocktail-sample mixture was heated to 99°C for 5 minutes, cooled for 5 mins at 45°C, and centrifuge for 1 minute according to the protocol. The mix was injected into the array chips and hybridized for 16 hr at 45°C at 60RPM in the Genechip 645 Hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics 450 Station according to the Genechip Expression Wash, Stain, and Scan protocol (part# 7022731, revision 3).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Agilent GeneSpring 12 software. Gene level expression was summarized using ExonRMA16 algorithm and then quantile normalized.

source_name: ESC shPaf1

label_protocol: cDNA was generated from 125ng of total RNA according to the Ambion WT Expression protocol (Life technologies, part#441974). The subsequent cDNA was fragmented and labeled according to the protocol of the Affymetrix Genechip WT Terminal Labeling kit (part#900671).

growth_protocol: Embryonic stem cells (ESCs), cultured in LIF-containing ESC growth medium on gelatin coated plates. ESC strain used: Nanog-GFP (NG4) reporter ESC line (129/Sv) Original ESC line reference: Schaniel, C., et al. (2009). Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells 27(12): 2979-2991.

extract_protocol: RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: We used pLKO.1-based backdone lentiviruses expressing shControl, shPhf5a or shPaf1 hairpins to transduce the ESCs. Cells were selected with puromycin (2μg/mL) for 72h. RNA was extracted using RNeasy kit (Qiagen) and hybridized on Affymetrix microarrays.

value: mouse embryonic stem cells

value: Nanog-GFP (NG4) reporter ESC line


title: ESCs-shPaf1 knockdown replicate 1


title: 11600_C dried neonatal bloodspot


title: 10649_C dried neonatal bloodspot


title: 10821_C dried neonatal bloodspot


title: 10667_C dried neonatal bloodspot


title: 10890_C dried neonatal bloodspot


title: 10743_C dried neonatal bloodspot


title: 10729_C dried neonatal bloodspot


title: 10612_C dried neonatal bloodspot


title: ESCs-shControl knockdown replicate 1

description: Gene expression data from mouse ESCs under shControl knockdown

source_name: ESC shControl


title: ESCs-shPhf5a knockdown replicate 3

description: Gene expression data from mouse ESCs under shPhf5a knockdown

source_name: ESC shPhf5a


title: ESCs-shPhf5a knockdown replicate 2


title: SAH patients

city: Shatin

first: Kwok Chu

last: Wong

address: Prince of Wales Hospital

department: Surgery

country: Hong Kong

institute: The Chinese University of Hong Kong

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip miRNA 3.0 Arrays (Affymetrix) and scanned at the Core Laboratory,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The signal values obtained were analyzed with Affymetrix miRNA Expression Console (Affymetrix, Santa Clara, CA) for data normalization with RMA algorithm. The noise signals were filtered with Detection Above the Background (DABG)

source_name: 20 SAH patients pooled sample

label_protocol: RNA was generated from miRNAeasy Serum/Plasma Kit and then poly A tailing and labeled with FlashTag™ Biotin HSR RNA Labeling Kit

growth_protocol: Serums were prepared by adding 20% w/v CaCl2 (Sigma, St. Louis, MO) was added into the plasma samples to a ratio of 1:100 followed by clotting overnight and centrifugation.

extract_protocol: Total RNA was isolated from pooled serum samples using the miRNeasy Serum/Plasma Kit following the manufacturer’s instructions

value: SAH

value: Serum


title: Healthy controls

source_name: 20 healthy donors pooled sample

value: Healthy


title: ESCs-shControl knockdown replicate 2


title: ESCs-shPaf1 knockdown replicate 2


title: ESCs-shControl knockdown replicate 3


title: 10460_C dried neonatal bloodspot

source_name: genomic DNA from dried neonatal bloodspot


title: 10443_C dried neonatal bloodspot


title: 10359_C dried neonatal bloodspot


title: 11651_B dried neonatal bloodspot

value: Female

value: IVF-Fresh embryo transfer (FH)


title: ESCs-shPhf5a knockdown replicate 1


title: 11420_B dried neonatal bloodspot

value: dried peripheral neonatal blood


title: 10555_C dried neonatal bloodspot

value: IVF-Frozen embryo transfer (FZ)


title: 10208_C dried neonatal bloodspot


title: 11029_B dried neonatal bloodspot


title: 11629_B dried neonatal bloodspot


title: 10055_C dried neonatal bloodspot


title: 10869_B dried neonatal bloodspot


title: 11283_B dried neonatal bloodspot


title: 10846_B dried neonatal bloodspot


title: 10402_B dried neonatal bloodspot


title: 11387_B dried neonatal bloodspot


title: 11016_B dried neonatal bloodspot


title: 10843_B dried neonatal bloodspot


title: 11541_B dried neonatal bloodspot


title: 10156_B dried neonatal bloodspot


title: 10046_B dried neonatal bloodspot


title: 10117_B dried neonatal bloodspot


title: 10350_B dried neonatal bloodspot


title: 10453_C dried neonatal bloodspot


title: 10133_B dried neonatal bloodspot


title: 10231_B dried neonatal bloodspot


title: 11598_B dried neonatal bloodspot


title: 11378_B dried neonatal bloodspot


title: 11624_B dried neonatal bloodspot


title: 11034_B dried neonatal bloodspot


title: 11458_B dried neonatal bloodspot


title: 11359_B dried neonatal bloodspot


title: 10601_B dried neonatal bloodspot


title: 10697_B dried neonatal bloodspot


title: 10344_B dried neonatal bloodspot


title: 10932_B dried neonatal bloodspot


title: 10346_B dried neonatal bloodspot


title: 10558_B dried neonatal bloodspot


title: 11002_B dried neonatal bloodspot


title: 10706_B dried neonatal bloodspot


title: 10653_A dried neonatal bloodspot

value: IUI


title: 10432_B dried neonatal bloodspot


title: 10798_B dried neonatal bloodspot


title: 10882_B dried neonatal bloodspot


title: 10101_B dried neonatal bloodspot


title: 10006_B dried neonatal bloodspot


title: 10434_B dried neonatal bloodspot


title: 10255_A dried neonatal bloodspot


title: 11414_A dried neonatal bloodspot


title: 11523_A dried neonatal bloodspot


title: 11066_A dried neonatal bloodspot


title: 11691_A dried neonatal bloodspot


title: 10225_A dried neonatal bloodspot


title: 11508_A dried neonatal bloodspot


title: 11067_A dried neonatal bloodspot


title: 10010_A dried neonatal bloodspot


title: 10716_A dried neonatal bloodspot


title: 11998_A dried neonatal bloodspot


title: 10863_A dried neonatal bloodspot


title: 11981_A dried neonatal bloodspot


title: Fish_5_Control

city: St. John's

first: Khalil

last: Eslamloo

state: Newfoundland and Labrador

address: 0 Marine Lab Rd.

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: For each array, 3 µg of labelled aRNA of one individual, 3 µg of labelled aRNA of the common reference and 2 µl of LNA blocker (Genisphere, Hatfield, Pennsylvania, USA) were mixed in a formamide-based hybridization buffer (Genisphere) and hybridized to the array overnight (~ 16 h) at 42˚C. The detailed protocols for hybridizations and washing were described in Booman et al. (2011, Mar Biotechnol, 13:733-50).

scan_protocol: Arrays were scanned at a resolution of 5 μm using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (v4.0; Perkin Elmer, Woodbridge, ON) with photomultiplier tube (PMT) set to balance fluorescence signal between channels.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 3 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene.

organism: Gadus morhua

source_name: Macrophages, PBS, individual fish 5

label_protocol: Macrophages exposed to 50 µg/ml pIC or PBS (control) for 24 h (pIC and PBS treatments for each of 6 individuals) were used for microarray analysis, using a common reference design and the Atlantic cod 20K oligonucleotide microarray platform. The mRNA of each sample was amplified and then labelled using 1 µg of DNase-treated and column-purified RNA and Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion®, Carlsbad, CA, USA), according to the kit’s procedure. A common reference was prepared using a pool of all 12 samples (15 µg aRNA from each sample). The experimental samples (pIC and control) were labelled with Cy5 (GE Healthcare, Buckinghamshire, UK), whereas the common reference samples were labelled with Cy3 (GE Healthcare), based on the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from TRIzol-lysed samples, following the manufacturer’s instructions, and RNA pellets were dissolved in 50 µl Dnase/Rnase-free water. The RNA samples were treated with Dnase-I (Qiagen, Mississauga, Ontario, Canada) for removing any residual genomic DNA contamination, and then purified using RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacturer’s instructions.  The high-purity RNA samples (e.g. A260/230 and A260/280 ratios > 1.8) with tight 18S and 28S ribosomal RNA bands were used for the microarray analysis.

treatment_protocol: [cell isolation and stimulation] Each fish was netted and immediately euthanized with an over-dose of MS222 (400 mg/L; Syndel Laboratories, Vancouver, BC). Each fish was then dissected, and the head kidney was removed and minced through 100 µm nylon cell strainers. The cell suspension (in L-15) was centrifuged on a discontinuous 25/51% Percoll gradient (GE Healthcare, Uppsala, Sweden) at 300 × g for 40 min at 4 ˚C, and the macrophage-enriched interface was collected. The resulting macrophage-rich suspension was washed twice in L-15 by centrifuging at 300 × g for 15 min at 4 ˚C. Thereafter, the cells seeded into 35 mm culture plates. The cells were allowed to adhere overnight (16 h) at 10˚C, and then the non-adherent cells were removed by washing the culture plates 3 times with L-15. The isolated macrophages from each individual were incorporated in all experimental groups. Macrophages were exposed to either 50 µg/ml pIC or PBS (control) at 24 h post-isolation. The stimulated and non-stimulated macrophages were harvested using TRIzol at 24 h post-stimulation

tag: individual

value: fish 5

tag: cell type

value: Macrophage-like cells isolated from fish head kidney

tag: developmental stage

value: Pre-adult

tag: agent

value: PBS

source_name: pool of RNAs from all 12 samples involved in the microarray experiment

value: Juvenile

value: common reference


title: 10291_A dried neonatal bloodspot

tag: gender

tag: tissue


title: 10058_A dried neonatal bloodspot


title: Fish_2_Control

source_name: Macrophages, PBS, individual fish 2

value: fish 2


title: 20025_D dried neonatal bloodspot

value: Unassisted (NAT)


title: Fish_3_Control

source_name: Macrophages, PBS, individual fish 3

value: fish 3


title: 10512_A dried neonatal bloodspot

value: Male


title: Fish_1_Control

source_name: Macrophages, PBS, individual fish 1

value: fish 1


title: 20018_D dried neonatal bloodspot


title: 20020_D dried neonatal bloodspot


title: 20022_D dried neonatal bloodspot


title: 20023_D dried neonatal bloodspot


title: Fish_4_Control

source_name: Macrophages, PBS, individual fish 4

value: fish 4


title: 20019_D dried neonatal bloodspot

value: Female


title: Fish_6_pIC

source_name: Macrophages, pIC, individual fish 6

value: fish 6

value: pIC


title: Fish_3_pIC

source_name: Macrophages, pIC, individual fish 3


title: Fish_4_pIC

source_name: Macrophages, pIC, individual fish 4


title: Fish_5_pIC

source_name: Macrophages, pIC, individual fish 5


title: 20021_D dried neonatal bloodspot

value: dried peripheral neonatal blood


title: 20015_D dried neonatal bloodspot


title: 20017_D dried neonatal bloodspot


title: Fish_6_Control

source_name: Macrophages, PBS, individual fish 6


title: 20016_D dried neonatal bloodspot


title: Fish_2_pIC

source_name: Macrophages, pIC, individual fish 2


title: Fish_1_pIC

source_name: Macrophages, pIC, individual fish 1


title: 20009_D dried neonatal bloodspot


title: 20012_D dried neonatal bloodspot


title: 20011_D dried neonatal bloodspot


title: 20014_D dried neonatal bloodspot


title: 20027_D dried neonatal bloodspot


title: 20013_D dried neonatal bloodspot


title: 10374_A dried neonatal bloodspot

value: IUI


title: 20024_D dried neonatal bloodspot


title: 20007_D dried neonatal bloodspot


title: 20005_D dried neonatal bloodspot


title: 20006_D dried neonatal bloodspot


title: 20010_D dried neonatal bloodspot


title: 20008_D dried neonatal bloodspot


title: 20026_D dried neonatal bloodspot


title: 20002_D dried neonatal bloodspot


title: 20042_D dried neonatal bloodspot


title: setdb1 mutant ovaries, biological replicate 2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: standard Affymetrix FS450 protocol, AGCC

scan_protocol: standard Affymetrix GCS3007G scanner protocol

data_processing: Affymetrix Expression Console and GeneSpring GX, PLIER

organism: Drosophila melanogaster

source_name: Drosophila ovaries at the same developmental stage.

label_protocol: biotin, standard Affymetrix 3' IVT express kit protocol

growth_protocol: Flies were incubated at 25C and collected within 5 days of hatching

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

treatment_protocol: Flies were fed with yeast and dissected the next day in PBS.

value: ovary

tag: genotype

value: setdb1 mutant

tag: age

value: less than 5 days


title: bam mutant ovaries, biological replicate 1

value: bam mutant


title: setdb1 mutant ovaries, biological replicate 1


title: bam mutant ovaries, biological replicate 2


title: 20003_D dried neonatal bloodspot


title: 20004_D dried neonatal bloodspot


title: setdb1 mutant ovaries, biological replicate 3


title: 20000_D dried neonatal bloodspot


title: bam mutant ovaries, biological replicate 3


title: 20032_D dried neonatal bloodspot


title: 20037_D dried neonatal bloodspot


title: 20039_D dried neonatal bloodspot


title: 20033_D dried neonatal bloodspot


title: 20040_D dried neonatal bloodspot


title: 20041_D dried neonatal bloodspot


title: 20038_D dried neonatal bloodspot


title: Neural retina day 12 culture control 1 (DMSO)

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: Murasakicho 1-1

institute: Biohistory Research Hall

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was hybridized using Gene Expression Hybridization kit (Agilent) and washed using Gene Expression Wash Buffers Pack (Agilent).

scan_protocol: Hybridization signals were scanned using SureScan Microarray Scanner (G2600D)

data_processing: The signal intensities were converted to a numerical form using Agilent Feature Extraction.

organism: Gallus gallus

source_name: Embryonic neural retina

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Amp Labeling kit, one color (Agilent), according to the manufacturer's instructions.

growth_protocol: Neural retina tissues were isolated from E8 (stage 33) chicken embryos, dissociated by using 0.125% Trypsin at 37 °C for total of 20 min, and plated on 3.5 cm diameter dishes at the cell density of 1.5 x106 per dish in Dulbecco-modified Eagle’s MEM containing 10% fetal bovine serum.

extract_protocol: Cells were solubilized by using Trizol (Thermo-Fischer) for RNA analysis.

treatment_protocol: γ-secretase inhibitor DAPT was dissolved in DMSO and added to cultures at day 2 with the final concentrations 10 μM (samples 3 and 4) or the same volume of DMSO (samples 1 and 2). Culture media were refreshed at intervals of two days with new addition of DAPT or DMSO, and RNAs were extracted on day 12 of cultures.

value: DMSO


title: Neural retina day 12 culture control 2 (DMSO)


title: Neural retina day 12 culture DAPT 1

value: DAPT


title: 20035_D dried neonatal bloodspot


title: 20031_D dried neonatal bloodspot


title: Neural retina day 12 culture DAPT 2


title: 20034_D dried neonatal bloodspot


title: Hela cell_siBtf_ADR_8hr_rep3

city: Shanghai

first: Hanshao

last: Liu

address: No.1239 Siping Rd.

country: China

institute: Tongji University

description: gene expression after knock down Btf followed with ADR 8hr treatment Hela cell

hyb_protocol: Equal quantities of purified cRNA from each sample were applied to a Whole Human Genome (WHG) 4×44 oligonucleotide slide (Agilent Technologies, Santa Clara, CA) and hybridized for 17h at 65°C.

scan_protocol: After hybridization, the arrays were washed with wash buffers provided by Agilent and were then scanned on an Agilent G2565A Microarray Scanner System using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (Agilent Technologies, Santa Clara, CA) was used to quantify the intensities of microarray images. Raw data were exported into GeneSpring GX10 software (Agilent Technologies, Santa Clara, CA) for quantile normalization and further analysis. Significance in mRNA levels was determined by an unpaired T-test for data with unequal variance (Welch) using the Benjamini–Hochberg correction (P value<0.05 or < 0.01)

source_name: Hela cell,siRNA Btf,ADR 8hr,replicate 3

label_protocol: Total RNA (2 µg) was used to initiate cDNA synthesis and to label cRNA, following the manufacturer’s protocol (Agilent Technologies, Santa Clara, CA). Labeled cRNAs were purified with RNeasy Mini Kits (QIAGEN, GmBH, Germany) and then fragmented to 60-100 nucleotides with a fragmentation buffer provided by Agilent.

growth_protocol: Hela cells are cultured in Dulbecco’s modified Eagle’s medium with 10% heat-inactivated fetal bovine serum, 100 U/ml penicillin, 100U/ml streptomycin and 2 mM L-glutamine

extract_protocol: Total RNA was isolated from cells using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s protocol. RNA quality was evaluated with a 2100 Bioanalyzer using the RNA 6000 Pico LabChip kit (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Cells are transfected with scrambled siRNA or siRNA Btf, then Cells are treated with 2 µg/ml adriamycin for 8 hrs or not.

tag: cell line

value: Hela

tag: knock down

value: siRNA Btf


title: 20030_D dried neonatal bloodspot

source_name: genomic DNA from dried neonatal bloodspot

value: Unassisted (NAT)


title: P241-PCOS

city: Seoul

first: Do Kyeong

last: Song

address: 911-1 Mokdong, Yangchoen-Ku

institute: Ewha Womans University School of Medicine

description: miRNA in women with PCOS

hyb_protocol: desalted labeled RNA were hybridized to the Agilent miRNA expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Peripheral blood on the third day of the menstrual cycle

label_protocol: Desalted Labeled RNA were prepared from 100ng total RNA Agilent’s miRNA Complete Labeling and Hyb Kit

extract_protocol: Total RNA was extracted from 200 μl of serum samples using the Exosomal miRNA Purification kit (Genolution, Seoul, Korea).

value: serum

value: female


title: after stimulation, biological rep 5

city: Houston

first: Hao

last: Zhao

address: 7455 Fannin St

institute: The University of Texas MD Anderson Cancer Center

description: Gene expression data of melanoma cell line after IFN-gamma stimulation

hyb_protocol: Hybridization was processed by using Affymetrix GeneChip Hybridization, Wash and Stain Kit (Cat. # 900720). Briefly, array was pre-hybridized for 30 min at 45°C to block non-specific binding, then hybridization cocktail with cRNA sample was applied to array and incubated for 16 hrs at 45°C. The array was then washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450.

scan_protocol: Array scanning and image accquisition was done with Affymetrix GeneChip Scanner 3000 7G under the control of Affymetrix GeneChip Command Console Software (AGCC) v4.3

data_processing: The data were normalized and log2-transformed using the RMA method from the affy bioconductor package

source_name: melanoma cell line after interferon-gamma stimulation

label_protocol: cRNA labelling was performed with Affymetrix GeneChip 3' IVT PLUS Reagent Kit (Cat. # 902416). Briefly, Biotin-labeled cRNAs were prepared by in vitro transcription and purified with magnetic pruification beads. Labeled cRNA yield and quality were accessed with NanoDrop Spectrophotometer.

growth_protocol: Cells were maintained in DMEM/high glucose with10% FBS, 10mM HEPES, 1mM sodium pyruvate, 1x insulin-transferrin-selenium additive, 55μM β-mercaptoethanol, 20 μg/ml gentamicin.  Cells were fed twice a week and subculture when they are 90% confluent by splitting 1:2 - 1:4 generally.

extract_protocol: Total RNA was extracted with Qiagen Rneasy Plus Mini Kit (Cat. # 74134). All samples were performed quality test and only samples with RNA integrity number (RIN) > 8.0 were used for microarray analysis.

treatment_protocol: Cells were plated in 6-well plates with 80% confluence at the time of treatment. Fresh medium with or without 10 U/ml human IFN-γ was added to cells for overnight (16 hrs).

value: skin

value: melanoma


title: 20036_D dried neonatal bloodspot

value: Male


title: after stimulation, biological rep 4


title: after stimulation, biological rep 3


title: 20028_D dried neonatal bloodspot


title: P82-PCOS

description: miRNA in women with PCOS


title: P998-PCOS

description: miRNA in women with PCOS


title: P334-PCOS

description: miRNA in women with PCOS


title: 20029_D dried neonatal bloodspot


title: after stimulation, biological rep 1


title: before stimulation, biological rep 6

description: Gene expression data of melanoma cell line before IFN-gamma stimulation

source_name: melanoma cell line before interferon-gamma stimulation


title: before stimulation, biological rep 5


title: Hela cell_scramble_ADR_0hr_rep3

description: gene expression after ADR 0hr treatment Hela cell

source_name: Hela cell,scramble siRNA,ADR 0hr,replicate 3

value: scramble siRNA


title: P459-PCOS

description: miRNA in women with PCOS


title: 20001_D dried neonatal bloodspot

value: dried peripheral neonatal blood


title: after stimulation, biological rep 6


title: KET7 Post

city: Cork

first: Anand

last: Gururajan

address: Western Road

department: Anatomy & Neuroscience

country: Ireland

institute: University College Cork

description:
Hy3: 1_Exiqon_K7POST.txt
Hy5: 0_Exiqon_K7POST.txt
Non-Responder

hyb_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: KET Post Tx Non-Responder

label_protocol: 400 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Denmark) following the procedure described by the manufacturer.  This project was run with a dual colour setup and LOWES normalization so the reference RNA comprised a pool of RNA containing all samples in equal amounts.

growth_protocol: Not applicable.

extract_protocol: RNA extracted using manufacturer's intstruction.

treatment_protocol: Patients were either treated with electroconvulsive therapy or ketamine infusions.

tag: disease state

value: MDD

value: KET

value: post-treatment

tag: response

value: non-responder

value: blood

source_name: Reference

tag: reference composition


title: after stimulation, biological rep 2


title: Hela cell_siBtf_ADR_8hr_rep2

source_name: Hela cell,siRNA Btf,ADR 8hr,replicate 2


title: Hela cell_siBtf_ADR_0hr_rep3

description: gene expression after knock down Btf followed with ADR 0hr treatment Hela cell

source_name: Hela cell,siRNA Btf,ADR 0hr,replicate 3


title: ECT6 Post

description:
Hy3: 1_Exiqon_E6POST.txt
Hy5: 0_Exiqon_E6POST.txt
Non-Responder

source_name: ECT Post Tx Non-Responder

value: ECT

value: a pool of RNA containing all samples in equal amounts


title: ECT23 Post

description:
Hy3: 1_Exiqon_E23POST.txt
Hy5: 0_Exiqon_E23POST.txt
Non-Responder


title: P329-PCOS

description: miRNA in women with PCOS


title: Hela cell_scramble_ADR_8hr_rep3

description: gene expression after ADR 8hr treatment Hela cell

source_name: Hela cell,scramble siRNA,ADR 8hr,replicate 3

value: Hela


title: before stimulation, biological rep 4


title: before stimulation, biological rep 3


title: Hela cell_siBtf_ADR_0hr_rep2

source_name: Hela cell,siRNA Btf,ADR 0hr,replicate 2

value: siRNA Btf


title: P685-PCOS

description: miRNA in women with PCOS


title: P2024-control

description: miRNA in control subjects


title: before stimulation, biological rep 1


title: KET19 Post

description:
Hy3: 1_Exiqon_K19POST.txt
Hy5: 0_Exiqon_K19POST.txt
Non-Responder


title: ECT1 Post

description:
Hy3: 1_Exiqon_E1POST.txt
Hy5: 0_Exiqon_E1POST.txt
Non-Responder


title: before stimulation, biological rep 2


title: P701-control

description: miRNA in control subjects


title: adj. normal kidney sample, patient 13_K851_NN

city: Berlin

first: Klaus

last: Jung

address: Schumannstr. 20/21

department: Dept. of Urology

institute: University Hospital Charité

hyb_protocol: cRNA were hybridized on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained according to the standard Affymetrix protocol

scan_protocol: After hypridisation the GeneChips were scanned according to the standard Affymetrix protocol

data_processing: Affymetrix Expression Console Software with default analysis settings were used to generate corresponding MAS5 CHP files. The CHP-files were analysed by Genespring (vers.12.6) software (normalisation: shift to 75 percentile; baseline transformation: median of all samples)

source_name: kidney

label_protocol: Biotinylated cRNA were prepared and fragmentated  according to the standard Affymetrix protocol

extract_protocol: Isolation according to the instruction using RNeasyMini Kit (Qiagen, Hilden, Germany; Cat.no. 74104)

treatment_protocol: Immediate stabilization of tissue after surgery in RNAlater RNA Stabilization Reagent (Qiagen, Hilden, Germany; Cat.no. 76104)

tag: metastasis

tag: Sex

value: male


title: ECT5 Post

description:
Hy3: 1_Exiqon_E5POST.txt
Hy5: 0_Exiqon_E5POST.txt
Non-Responder

tag: treatment


title: ECT25 Post

description:
Hy3: 1_Exiqon_E25POST.txt
Hy5: 0_Exiqon_E25POST.txt
Non-Responder

tag: time


title: P878-control

description: miRNA in control subjects

value: serum


title: ECT2 Post

description:
Hy3: 1_Exiqon_E2POST.txt
Hy5: 0_Exiqon_E2POST.txt
Non-Responder

tag: individual


title: KET16 Post

description:
Hy3: 1_Exiqon_K16POST.txt
Hy5: 0_Exiqon_K16POST.txt
Responder

source_name: KET Post Tx Responder

value: responder


title: P478-control

description: miRNA in control subjects

value: female


title: P658-control

description: miRNA in control subjects


title: KET8 Post

description:
Hy3: 1_Exiqon_K8POST.txt
Hy5: 0_Exiqon_K8POST.txt
Responder


title: adj. normal kidney sample, patient 12_K779_NN


title: Hela cell_scramble_ADR_0hr_rep2

source_name: Hela cell,scramble siRNA,ADR 0hr,replicate 2


title: Hela cell_scramble_ADR_8hr_rep2

source_name: Hela cell,scramble siRNA,ADR 8hr,replicate 2


title: primary ccRCC, patient 12_K779_NC

value: ccRCC

tag: tumor staging

tag: grading


title: Hela cell_siBtf_ADR_8hr_rep1

source_name: Hela cell,siRNA Btf,ADR 8hr,replicate 1


title: P1024-control

description: miRNA in control subjects


title: Hela cell_scramble_ADR_ohr_rep1

source_name: Hela cell,scramble siRNA,ADR 0hr,replicate 1


title: P238-control

description: miRNA in control subjects

source_name: Peripheral blood on the third day of the menstrual cycle


title: Hela cell_scramble_ADR_8hr_rep1

source_name: Hela cell,scramble siRNA,ADR 8hr,replicate 1


title: P424-control

description: miRNA in control subjects


title: WAT_HFDcornoil_rep4

city: Gothenburg

first: Nikulkumar

middle: Kirtilal

last: Soni

state: Vastra Gotaland

address: Kemivagen 10

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.18.0). It was vst transformed and quantile normalized.

source_name: high fat diet corn oil

label_protocol: standard as recommended by illumina

extract_protocol: Total RNA from skeletal muscle of these selected animals was purified using the RNeasy® Plus Universal Mini kit (Qiagen Nordic, Sollentuna, Sweden) by following the manufacturer's instruction carefully. The extracted RNA was quantified by NanoDrop 2000c UV-Vis Spectrophotometer (Thermo Scientific, USA) and the quality of the RNA was estimated by RNA 6000 Nano LabChip for Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).

tag: strain

value: white adipose tissue


title: primary ccRCC, patient 13_K851_NC


title: WAT_HFDEPADHA_rep4

source_name: high fat diet EPA/DHA

tag: gender


title: KET6 Post

description:
Hy3: 1_Exiqon_K6POST.txt
Hy5: 0_Exiqon_K6POST.txt
Responder

tag: tissue


title: adj. normal kidney sample, patient 11_K770_NN


title: primary ccRCC, patient 10_K765_NC


title: P1430-PCOS

description: miRNA in women with PCOS


title: P1372-control

description: miRNA in control subjects


title: Hela cell_siBtf_ADR_0hr_rep1

source_name: Hela cell,siRNA Btf,ADR 0hr,replicate 1


title: KET15 Post

description:
Hy3: 1_Exiqon_K15POST.txt
Hy5: 0_Exiqon_K15POST.txt
Responder

source_name: Reference


title: adj. normal kidney sample, patient 10_K765_NN


title: KET11 Post

description:
Hy3: 1_Exiqon_K11POST.txt
Hy5: 0_Exiqon_K11POST.txt
Responder


title: KET9 Post

description:
Hy3: 1_Exiqon_K9POST.txt
Hy5: 0_Exiqon_K9POST.txt
Responder


title: primary ccRCC, patient 11_K770_NC


title: KET10 Post

description:
Hy3: 1_Exiqon_K10POST.txt
Hy5: 0_Exiqon_K10POST.txt
Responder


title: HUVECS exposed to PCB_11

city: Lexington

first: Banrida

last: Wahlang

state: KY

address: 900 S Limestone Street Rm 559

department: UK Superfund Research Center

institute: University of Kentucky

description: MicroRNA profile data

hyb_protocol: 450ng of biotin labeled RNA was hybridized to Affymetrix GeneChip® miRNA 4.0 Arrays at 48 °C and 60 rpm for 16-18 h.

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: HUVECS exposed to PCB

label_protocol: 500 ng of total RNA was labeled using Affymetrix Flashtag Biotin HSR RNA Labeling kit (P/N 901910, Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Human umbilical vein endothelial cells (HUVECs, 10-donor pool) were obtained from Lifeline Cell Technology (Walkersville, MD, USA). Cells were maintained in VascuLife Basal Medium supplemented with components of the VascuLife VEGF LifeFactors Kit (containing Vascular Endothelial Growth Factor, 2% fetal bovine serum and other appropriate life factors) and 1% antimicrobial supplement (penicillin, streptomycin and amphotericin B). Cells were passaged and maintained according to the company instructions.

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

treatment_protocol: Cells were exposed to either DMSO (control vehicle) or the PCB mixture, Aroclor 1260

tag: cell type

value: human umblical vein endothelial cells (HUVECs)

tag: exposed to

value: PCB mixture, Aroclor 1260


title: HUVECS exposed to PCB_9

description: MicroRNA profile data


title: HUVECS exposed to PCB_10

description: MicroRNA profile data


title: HUVECS exposed to PCB_12

description: MicroRNA profile data


title: WAT_controldiet_rep4

source_name: low fat diet


title: KET12 Post

description:
Hy3: 1_Exiqon_K12POST.txt
Hy5: 0_Exiqon_K12POST.txt
Responder

value: MDD


title: adj. normal kidney sample, patient 9_K594_NN

tag: age


title: HUVECs exposed to DMSO_3

description: MicroRNA profile data

source_name: HUVECs exposed to DMSO

value: DMSO (control)


title: WAT_HFDcornoil_rep3


title: adj. normal kidney sample, patient 8_K470_NN


title: primary ccRCC, patient 9_K594_NC


title: primary ccRCC, patient 8_K470_NC


title: adj. normal kidney sample, patient 7_K458_NN


title: primary ccRCC, patient 7_K458_NC


title: HUVECs exposed to DMSO_2

description: MicroRNA profile data


title: KET5 Post

description:
Hy3: 1_Exiqon_K5POST.txt
Hy5: 0_Exiqon_K5POST.txt
Responder

value: KET

value: post-treatment


title: WAT_HFDEPADHA_rep3


title: WAT_controldiet_rep3


title: KET18 Post

description:
Hy3: 1_Exiqon_K18POST.txt
Hy5: 0_Exiqon_K18POST.txt
Responder

value: blood


title: HUVECs exposed to DMSO_4

description: MicroRNA profile data


title: adj. normal kidney sample, patient 6_K417_NN


title: WAT_controldiet_rep2


title: KET17 Post

description:
Hy3: 1_Exiqon_K17POST.txt
Hy5: 0_Exiqon_K17POST.txt
Responder

value: ECT


title: WAT_HFDEPADHA_rep2


title: WAT_HFDcornoil_rep2


title: WAT_HFDcornoil_rep1


title: ECT11 Post

description:
Hy3: 1_Exiqon_E11POST.txt
Hy5: 0_Exiqon_E11POST.txt
Responder

source_name: ECT Post Tx Responder

value: a pool of RNA containing all samples in equal amounts


title: adj. normal kidney sample, patient 5_K319_NN


title: Old_soleus_muscle_4

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

institute: Toyohashi University of Technology

description: miRNA expression in old soleus muscle

hyb_protocol: The labeled miRNAs were hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 55 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner G2505C with the Scan Control software (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 019118_D_F_20100604) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 0.1 ug RNA using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA containing miRNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).

value: soleus muscle

value: 25-28 months

value: Fischer 344


title: ECT22 Post

description:
Hy3: 1_Exiqon_E22POST.txt
Hy5: 0_Exiqon_E22POST.txt
Responder


title: ECT8 Post

description:
Hy3: 1_Exiqon_E8POST.txt
Hy5: 0_Exiqon_E8POST.txt
Responder


title: ECT4 Post

description:
Hy3: 1_Exiqon_E4POST.txt
Hy5: 0_Exiqon_E4POST.txt
Non-Responder

source_name: ECT Post Tx Non-Responder

value: non-responder


title: KET13 Post

description:
Hy3: 1_Exiqon_K13POST.txt
Hy5: 0_Exiqon_K13POST.txt
Non-Responder

source_name: KET Post Tx Non-Responder


title: Old_soleus_muscle_3

description: miRNA expression in old soleus muscle

value: male


title: WAT_HFDEPADHA_rep1


title: ECT19 Post

description:
Hy3: 1_Exiqon_E19POST.txt
Hy5: 0_Exiqon_E19POST.txt
Responder

value: responder


title: ECT20 Post

description:
Hy3: 1_Exiqon_E20POST.txt
Hy5: 0_Exiqon_E20POST.txt
Responder


title: ECT12 Post

description:
Hy3: 1_Exiqon_E12POST.txt
Hy5: 0_Exiqon_E12POST.txt
Responder


title: HUVECs exposed to DMSO_1

description: MicroRNA profile data


title: Young_soleus_muscle_3

description: miRNA expression in young soleus muscle

value: 6-7 months


title: Young_soleus_muscle_2

description: miRNA expression in young soleus muscle


title: primary ccRCC, patient 5_K319_NC

source_name: kidney

value: ccRCC


title: Young_soleus_muscle_4

description: miRNA expression in young soleus muscle


title: ECT9 Post

description:
Hy3: 1_Exiqon_E9POST.txt
Hy5: 0_Exiqon_E9POST.txt
Responder


title: WAT_controldiet_rep1

value: white adipose tissue


title: Old_soleus_muscle_1

description: miRNA expression in old soleus muscle


title: adj. normal kidney sample, patient 4_K296_NN


title: Old_soleus_muscle_2

description: miRNA expression in old soleus muscle


title: Young_soleus_muscle_1

description: miRNA expression in young soleus muscle


title: primary ccRCC, patient 4_K296_NC

value: female


title: primary ccRCC, patient 3_K285_NC


title: adj. normal kidney sample, patient 3_K285_NN


title: BAT_controldiet_rep4

value: brown adipose tissue


title: BAT_HFDcornoil_rep3


title: primary ccRCC, patient 6_K417_NC


title: adj. normal kidney sample, patient 2_K282_NN


title: BAT_HFDcornoil_rep4


title: primary tumor, patient 2_K282_NC

value: sarcoma


title: ECT10 Post

description:
Hy3: 1_Exiqon_E10POST.txt
Hy5: 0_Exiqon_E10POST.txt
Responder

value: MDD


title: BAT_controldiet_rep3


title: BAT_HFDEPADHA_rep4


title: BAT_controldiet_rep2


title: BAT_HFDEPADHA_rep3


title: ECT21 Post

description:
Hy3: 1_Exiqon_E21POST.txt
Hy5: 0_Exiqon_E21POST.txt
Responder

value: post-treatment


title: BAT_HFDcornoil_rep2


title: ECT3 Post

description:
Hy3: 1_Exiqon_E3POST.txt
Hy5: 0_Exiqon_E3POST.txt
Responder

value: blood


title: KET8 Pre

description:
Hy3: 1_Exiqon_K8PRE.txt
Hy5: 0_Exiqon_K8PRE.txt
Baseline Responder

source_name: KET Pre Tx Responder

value: KET

value: pre-treatment


title: adj. normal kidney sample, patient 1_K235_NN


title: KET13 Pre

description:
Hy3: 1_Exiqon_K13PRE.txt
Hy5: 0_Exiqon_K13PRE.txt
Baseline Non-Responder

source_name: KET Pre Tx Non-responder

value: a pool of RNA containing all samples in equal amounts


title: KET6 Pre

description:
Hy3: 1_Exiqon_K6PRE.txt
Hy5: 0_Exiqon_K6PRE.txt
Baseline Responder


title: Old_EDL_muscle_3

description: miRNA expression in old EDL muscle

value: EDL muscle

value: 25-28 months


title: Old_EDL_muscle_1

description: miRNA expression in old EDL muscle

value: Fischer 344


title: Old_EDL_muscle_4

description: miRNA expression in old EDL muscle

value: male


title: KET16 Pre

description:
Hy3: 1_Exiqon_K16PRE.txt
Hy5: 0_Exiqon_K16PRE.txt
Baseline Responder

value: responder


title: BAT_HFDEPADHA_rep2


title: Young_EDL_muscle_3

description: miRNA expression in young EDL muscle

value: 6-7 months


title: Young_EDL_muscle_4

description: miRNA expression in young EDL muscle


title: primary ccRCC, patient 1_K235_NC

value: ccRCC


title: Old_EDL_muscle_2

description: miRNA expression in old EDL muscle


title: KET17 Pre

description:
Hy3: 1_Exiqon_K17PRE.txt
Hy5: 0_Exiqon_K17PRE.txt
Baseline Responder


title: adj. normal kidney sample, patient 14


title: KET19 Pre

description:
Hy3: 1_Exiqon_K19PRE.txt
Hy5: 0_Exiqon_K19PRE.txt
Baseline Non-Responder

value: non-responder


title: BAT_HFDcornoil_rep1


title: Young_EDL_muscle_2

description: miRNA expression in young EDL muscle


title: adj. normal kidney sample, patient 13

value: female


title: primary ccRCC, patient 14


title: Spleen_HFDcornoil_rep4

extract_protocol: Total RNA from skeletal muscle of these selected animals was purified using the RNeasyÂ® Plus Universal Mini kit (Qiagen Nordic, Sollentuna, Sweden) by following the manufacturer's instruction carefully. The extracted RNA was quantified by NanoDrop 2000c UV-Vis Spectrophotometer (Thermo Scientific, USA) and the quality of the RNA was estimated by RNA 6000 Nano LabChip for Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).

value: spleen


title: BAT_HFDEPADHA_rep1

value: brown adipose tissue


title: primary ccRCC, patient 13


title: BAT_controldiet_rep1


title: Spleen_HFDEPADHA_rep4


title: KET11 Pre

description:
Hy3: 1_Exiqon_K11PRE.txt
Hy5: 0_Exiqon_K11PRE.txt
Baseline Responder

value: MDD


title: primary ccRCC, patient 12


title: adj. normal kidney sample, patient 12


title: Young_EDL_muscle_1

description: miRNA expression in young EDL muscle


title: Non-SS patient-2

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

description: non-Sjögren’s syndrome

hyb_protocol: 7.5 µg fragmented and labeled aRNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlasTM fluidics station.

scan_protocol: Array Strip was scanned in the GeneAtlasTM imaging station.

data_processing: The robust multichip average (RMA) method was used background correction and normalization by quantile.

source_name: Minor salivary glands of the lower lip

label_protocol: 10 ng of total RNA was labeled using a GeneAtlasTM 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

extract_protocol: After fresh tissues were homogenized by TissueLyser, total RNA was extracted by ISOGEN.

value: Minor salivary glands of the lower lip

value: Female


title: adj. normal kidney sample, patient 11


title: Spleen_controldiet_rep4


title: KET10 Pre

description:
Hy3: 1_Exiqon_K10PRE.txt
Hy5: 0_Exiqon_K10PRE.txt
Baseline Responder

value: KET

value: blood


title: KET5 Pre

description:
Hy3: 1_Exiqon_K5PRE.txt
Hy5: 0_Exiqon_K5PRE.txt
Baseline Responder

value: pre-treatment

value: a pool of RNA containing all samples in equal amounts


title: KET18 Pre

description:
Hy3: 1_Exiqon_K18PRE.txt
Hy5: 0_Exiqon_K18PRE.txt
Baseline Responder


title: Spleen_controldiet_rep3


title: Spleen_HFDEPADHA_rep3


title: adj. normal kidney sample, patient 10


title: KET12 Pre

description:
Hy3: 1_Exiqon_K12PRE.txt
Hy5: 0_Exiqon_K12PRE.txt
Baseline Responder


title: KET7 Pre

description:
Hy3: 1_Exiqon_K7PRE.txt
Hy5: 0_Exiqon_K7PRE.txt
Baseline Non-Responder


title: KET9 Pre

description:
Hy3: 1_Exiqon_K9PRE.txt
Hy5: 0_Exiqon_K9PRE.txt
Baseline Responder


title: primary ccRCC, patient 11


title: Spleen_HFDcornoil_rep3


title: Spleen_HFDcornoil_rep2


title: SS patient-2

description: primary Sjögren’s syndrome


title: Spleen_controldiet_rep2


title: ECT20 Pre

description:
Hy3: 1_Exiqon_E20PRE.txt
Hy5: 0_Exiqon_E20PRE.txt
Baseline Responder

source_name: ECT Pre Tx Responder

value: ECT


title: ECT8 Pre

description:
Hy3: 1_Exiqon_E8PRE.txt
Hy5: 0_Exiqon_E8PRE.txt
Baseline Responder


title: Non-SS patient-1

description: non-Sjögren’s syndrome


title: primary ccRCC, patient 7


title: Spleen_HFDEPADHA_rep2


title: adj. normal kidney sample, patient 9


title: adj. normal kidney sample, patient 8


title: primary ccRCC, patient 9


title: Spleen_controldiet_rep1


title: primary ccRCC, patient 10


title: Spleen_HFDcornoil_rep1


title: Mouse-PCP+Caspofungi-rep4

city: Bethesda

first: Joseph

middle: A.

last: Kovacs

state: MD

address: 10 Center Dr

department: CCMD

institute: NIH

description: CD40L-KO mouse lung

hyb_protocol: Labeled cDNA was hybridized for 18 hours to the GeneChip Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA) following the manufacturer's directions.  Arrays were stained and washed in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix 7G

data_processing:
Data were processed using Partek software. RMA background correction with quantile normalization
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: Mouse lung, infected with PCP and treated with caspofungin

label_protocol: cDNA was fragmented and labeled using Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: CD40L-KO mice (B6;129S2-Tnfsf5tm1Imx/J), which are highly susceptible to Pneumocystis  infection, were obtained from The Jackson Laboratory (Bar Harbor, ME) and subsequently bred at the NIH.   All Pneumocystis-infected mice in each study were co-housed in a single cage with a P. murina infected seeder mouse.

extract_protocol: After sacrifice, the lungs were removed and sections were placed in PBS for quantitation of Pneumocystis burden, RNALater (QIAGEN, Valencia, CA) for gene expression studies.  Total RNA was isolated from lung tissues using RNeasy Mini kit (QIAGEN) following the manufacturer's instructions. RNA quality was evaluated using RNA 6000 Nano LabChip (Agilent 2100 Bioanalyzer, Santa Clara, CA). Double stranded cDNA was synthesized from 150 ng of total RNA, which was then transcribed in vitro to make cRNA followed by sense strand cDNA synthesis using WT Expression Kit (Ambion).

treatment_protocol: Mice with PCP were treated with 30 µg/kg dose of caspofungin administered intraperitoneally once daily for 9 days.  Untreated mice with PCP and uninfected mice served as controls.

value: lung


title: primary ccRCC, patient 8

value: male


title: Mouse-PCP+Caspofungi-rep3

description: CD40L-KO mouse lung

value: infected with PCP and treated with caspofungin


title: adj. normal kidney sample, patient 7


title: adj. normal kidney sample, patient 6


title: SS patient-1

description: primary Sjögren’s syndrome


title: Spleen_HFDEPADHA_rep1


title: ECT10 Pre

description:
Hy3: 1_Exiqon_E10PRE.txt
Hy5: 0_Exiqon_E10PRE.txt
Baseline Responder

value: responder


title: ECT1 Pre

description:
Hy3: 1_Exiqon_E1PRE.txt
Hy5: 0_Exiqon_E1PRE.txt
Baseline Non-Responder

source_name: ECT Pre Tx Non-responder


title: ECT5 Pre

description:
Hy3: 1_Exiqon_E5PRE.txt
Hy5: 0_Exiqon_E5PRE.txt
Baseline Non-Responder


title: ECT25 Pre

description:
Hy3: 1_Exiqon_E25PRE.txt
Hy5: 0_Exiqon_E25PRE.txt
Baseline Non-Responder


title: ECT21 Pre

description:
Hy3: 1_Exiqon_E21PRE.txt
Hy5: 0_Exiqon_E21PRE.txt
Baseline Responder


title: ECT6 Pre

description:
Hy3: 1_Exiqon_E6PRE.txt
Hy5: 0_Exiqon_E6PRE.txt
Baseline Non-Responder


title: Mouse-PCP+Caspofungi-rep2

description: CD40L-KO mouse lung


title: ECT3 Pre

description:
Hy3: 1_Exiqon_E3PRE.txt
Hy5: 0_Exiqon_E3PRE.txt
Baseline Responder


title: Mouse-PCP-rep3

description: CD40L-KO mouse lung

source_name: Mouse lung, infected with PCP

value: infected with PCP


title: primary ccRCC, patient 6

value: ccRCC


title: Mouse-PCP+Caspofungi-rep1

description: CD40L-KO mouse lung


title: Mouse-Uninfected-rep4

description: CD40L-KO mouse lung

source_name: Mouse lung, uninfected with PCP

value: uninfected with PCP


title: ECT9 Pre

description:
Hy3: 1_Exiqon_E9PRE.txt
Hy5: 0_Exiqon_E9PRE.txt
Baseline Responder


title: ECT19 Pre

description:
Hy3: 1_Exiqon_E19PRE.txt
Hy5: 0_Exiqon_E19PRE.txt
Baseline Responder


title: primary ccRCC, patient 5