title: HuEx_30_SK-N-MC


title: HuEx_35_TC-71

status: Public on Aug 01 2015

type: RNA

city: Bethesda

first: Eric

middle: C

last: Polley

state: MD

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

country: USA

institute: National Cancer Institute

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.  Wash and stain were performed on Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned on Affymetrix GeneChip scanner 3000 7G.

data_processing: Probe set summarization and normalization with the core annotated probes was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R package aroma.affymetrix.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human cell line

label_protocol: Total RNA (100 ng) was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol.  Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

extract_protocol: Cells were grown in flasks to approximately 70% confluency, detached with trypsin, and then total RNA extracted using Qiagen miRNeasy mini-kit according to manufacturers instructions. Quality of RNA was assessed using an Agilent 2100 Bioanalyzer and all samples were of good quality with RIN# > 8.

tag: type

value: Ewing Sarcoma


title: HuEx_38_SK-LMS-1

value: Leiomyosarcoma


title: HuEx_27_SAOS-2

value: Osteosarcoma


title: HuEx_20_MHM-8

value: Sarcoma


title: HuEx_2_A-673


title: HuEx_17_Hu09


title: Control WLSSD LSW 3

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 µm resolution

data_processing: Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer’s protocol and recommendations.  Data processing was conducted using R package Limma.

organism: Pimephales promelas

source_name: ovary tissue,fish in water control

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: Sexually mature adult fathead minnows (5-6 month old) were obtained from an on-site aquatic culture facility at the US EPA Mid-Continent Ecology Division, Duluth, MN, USA. Fish were held under a 16:8 light:dark photoperiod fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3), and dissolved oxygen (mean ± SD; 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups.

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

treatment_protocol:
To initiate a typical experiment, four males and four females were placed together in a glass test tank holding 10 L of Lake Superior water (4 µM filtered, UV sterilized) or test chemical dissolved in Lake Superior water, which was continuously renewed at a rate of about 45 mL/min. There were two such tanks for each treatment condition. The animals were held at 25 +/- 0.5 °C under a 16:8 L:D photoperiod, and were fed brine shrimp to satiation twice per day.
chemical abbreviations: BPA, bisphenol-A; EE2, 17a-ethynyl estradiol; FAD, fadrozole; FLU, flutamide; GEM, Gemfibrozil; KTC, ketoconazole; PRO,prochloraz; RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine; TB, 17 -trenbolone; TNT, 2,4,6-trinitrotoluene; TRI,trilostane; VIN, vinclozolin; WLSSD, effluent from Western Lake Superior Sanitary District

tag: tissue

value: ovary

tag: age (month)

tag: treatment

value: in water control

tag: treatment duration

tag: experiment

value: WLSSD

tag: sampling date

tag: scan date

tag: rna date

tag: rna person

value: rnaL

tag: chip id


title: Control WLSSD LSW-1


title: Control WLSSD LSW-5


title: Control WLSSD LSW-4


title: HuEx_23_RD-ES


title: Control VZ PHASE3 96h B

value: rnaB


title: Control VZ PHASE3 96hp A

value: post-96 h


title: Control WLSSD LSW-2


title: Control VZ PHASE3 96h D


title: Control VZ PHASE3 96h C


title: HuEx_18_MES-SA

value: Uterine Sarcoma


title: HuEx_24_Rh30

value: Rhabdosarcoma


title: Control VZ PHASE3 96hp D


title: HuEx_15_Hs 913.T

value: Fibrosarcoma


title: HuEx_10_ES-7


title: Control VZ PHASE3 96hp B


title: HuEx_12_EW8


title: HuEx_16_HT-1080


title: HuEx_19_MES-SA Dx5


title: WT Adult pancreas reg VP3_4C

type: SRA

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description:
4cutter 4C sequencing
processed data file: AC_4C_1214_WT_VP1_raw.txt.gz
raw data file is available on sample GSM1841836

library_source: genomic

data_processing:
Library strategy: 4C-seq
Read files were quality-checked with FastQC.
Convert BAM files to FASTQ using bedtools v2.20.1 where needed
Transform to Illumina FASTQ using NGSQCToolkit v2.3
Convert and process (map, calculate cis interactions) FASTQ files using 4cseqpipe
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: Processed data files are 4cseqpipe mapped files for each original FASTQ/BAM file. They allow to generate figures for interactions around the viewpoints with 4cseqpipe

molecule: genomic DNA

organism: Mus musculus

source_name: pancreas

extract_protocol:
Preparation of 4C samples was performed as described (van de Werken, 2012) with some modifications. Freshly collected tissues were incubated with collagenase (0.0065% collagenase I in 10% FBS/PBS for cortex, and 1.33 mg/ml collagenase P in HBSS for pancreas) for 40 min at 37ºC in a shaker. The resulting cell suspension was filtered through a 40-μm cell strainer in order to get a single cell preparation. Cells were centrifuged at 1,100 rpm for 5 min at RT and the cell pellet was resuspended in 10 ml of fixing solution containing 2% formaldehyde in 10% FBS/PBS. After 10 min, 0.125 M glycine was added to stop fixation and the mixture was incubated for 5 min at RT. Cells were pelleted and nuclei isolated upon incubation in cold lysis buffer in the following conditions: For the brain, 10 min in 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 + protease inhibitors cocktail; for the pancreas, 40 min in 50 mM Tris pH 7.5, 50 mM NaCl, 5 mM EDTA, 1% NP40, 2% TX-100 + protease inhibitors cocktail. Proper lysis was determined by methyl green-pyronin staining.
4C-seq libraries were amplified using long primers with 18-21 bp homology to the bait sequence and Illumina paired-end adapter flanks. HindIII and CvIQ (NEB) were used as as first and second cutters, respectively for preparation of the 6-cutter libraries. DpnII and CvIQ (NEB) were used as first and second cutters, respectively for preparation of the 4-cutter libraries.  Pairs of samples were sequenced together thus the raw and processed data files are shared among samples. The 4cseqpipe software identifies the viewpoints and the possible cut points out of the raw data files and flags them in the processed files.

tag: strain

tag: age

value: 8-10 week old


title: SA1 +/-  Adult pancreas reg VP3_4C

description:
4cutter 4C sequencing
processed data file: AC_4C_1214_HT_VP1_raw.txt.gz
raw data file is available on sample GSM1841837


title: HuEx_1_A-204

value: Rhabdoid Tumor


title: HuEx_11_ES-8


title: Control VZ PHASE3 192h A


title: HuEx_14_HOS


title: HuEx_21_OHS


title: Control VZ PHASE3 48hp D


title: 2102EP in vitro

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

country: Germany

institute: University Hospital Düsseldorf

description: Embryonal carcinoma-like cell line

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor R. Normalized values were tranformed into log2-values.

source_name: 2102EP in vitro

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

extract_protocol:
RNA was extracted with Trizol reagent (Sigma-Aldrich) as already published (Nettersheim et al., 2012, Pubmed ID: 22489004), followed by clean-up  treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
TCam-2 and 2102EP cells were cultivated as published (Nettersheim et al., 2013, PubMed ID: 24386123)
TCam-2 and 2102EP cells were xenografted in CD1 nude mice as published previously (Nettersheim et al., 2012, Pubmed ID: 22489004)

value: CD1 nude

value: 6 weeks at start of xenografting

tag: cell line


title: Control VZ PHASE3 48hp C


title: Control VZ PHASE3 48h C


title: Control VZ PHASE3 48h D


title: Control VZ PHASE3 48h B


title: Control VZ PHASE3 24h B


title: Control VZ PHASE3 24hp D

value: post-24 h


title: Control VZ PHASE3 24h A


title: Control VZ PHASE3 24hp A


title: Control VZ PHASE3 48hp A


title: Control VZ PHASE3 24h D


title: Control VZ PHASE3 24h C


title: Control VZ PHASE3 48h A


title: Control VZ PHASE3 192hp C

value: post-192 h


title: Control VZ PHASE3 192hp A


title: HuEx_13_G-401


title: Control VZ PHASE3 192h B


title: Control VZ PHASE3 192hp D


title: Control VZ PHASE3 192hp B


title: Control VZ PHASE3 192h C


title: Control VZ PHASE3 24hp C


title: Control VZ PHASE3 96h A


title: Control VZ ATC 8h D

value: 8 h


title: Control VZ PHASE3 192h D


title: Control VZ ATC 4h D

value: 4 h


title: Control VZ ATC 8h C

value: ovary


title: Control VZ ATC 8h A

value: in water control


title: Control VZ ATC 4h C


title: Control VZ ATC 2h B

value: 2 h


title: Control VZ ATC 4h B

value: rnaL


title: Control VZ ATC 2h A


title: Control VZ ATC 4h A


title: Control VZ ATC 12h C


title: Control VZ ATC 1h B

value: 1 h


title: Control TRI PHASE3 96hp C

value: post-96 h

value: rnaA


title: Control TRI PHASE3 96hp D


title: Control VZ ATC 12h A


title: Control VZ ATC 12h D


title: Control VZ ATC 1h D


title: Control TRI PHASE3 96h D


title: Control VZ ATC 2h D


title: Control VZ ATC 2h C


title: Control TRI PHASE3 96h C


title: Control TRI PHASE3 96hp B


title: Control VZ ATC 8h B


title: Control TRI PHASE3 96h A


title: Control VZ PHASE3 24hp B

value: rnaB


title: Control TRI PHASE3 48hp D


title: Control TRI PHASE3 96h B


title: Control VZ PHASE3 96hp C


title: Control VZ ATC 1h A


title: Control TRI PHASE3 48hp C


title: Control TRI PHASE3 48hp A


title: Control TRI PHASE3 48h C


title: Control TRI PHASE3 48h B


title: Control TRI PHASE3 48hp B


title: Control TRI PHASE3 96hp A


title: Control TRI PHASE3 24h E


title: Control TRI PHASE3 24hp C


title: Control TRI PHASE3 24h B


title: Control TRI PHASE3 192hp C


title: Control TRI PHASE3 24hp D


title: Control TRI PHASE3 24hp B


title: Control TRI PHASE3 24hp A


title: Control TRI PHASE3 24h A


title: Control TRI PHASE3 24h C


title: Control TRI PHASE3 24h D


title: Control TRI PHASE3 192hp D


title: Control TRI PHASE3 48h A


title: Control TRI ATC 8h D


title: Control TRI PHASE3 192h B


title: Control VZ PHASE3 48hp B


title: Control TRI PHASE3 192hp A


title: Control TRI ATC 8h B


title: Control TRI PHASE3 192h C


title: Control TRI PHASE3 192h A


title: Control TRI ATC 4h C


title: Control TRI ATC 8h A


title: Control TRI ATC 2h B


title: Control TRI ATC 4h D


title: Control TRI ATC 1h D


title: Control TRI ATC 2h C


title: Control TRI ATC 2h D


title: Control TRI ATC 4h A


title: Control TRI ATC 8h C


title: Control TRI ATC 2h A


title: Control TRI ATC 1h A


title: Control TRI ATC 1h B


title: Control TRI ATC 12h C


title: Control TRI ATC 4h B


title: Control TRI ATC 12h D


title: Control TRI ATC 1h C


title: Control TB-TCC 4

value: rnaJ


title: Control TB-TCC 5


title: Control TB-TCC 3


title: Control TB Phase3 96hp 6

value: 96 h post


title: Control TRI ATC 12h B


title: Control TB-TCC 2


title: Control TB Phase3 96hp 7


title: Control TB Phase3 96hp 4


title: Control TRI PHASE3 192h D


title: Control TB Phase3 96hp 3


title: Control TB Phase3 96hp 5


title: Control TB Phase3 96hp 1


title: Control TB Phase3 96hp 2


title: Control TB-TCC 1


title: Control TB Phase3 96h 4


title: Control TRI PHASE3 192hp B


title: Control TB Phase3 96h 6


title: Control TB Phase3 96h 5


title: Control TB Phase3 96h 1


title: Control TRI ATC 12h A


title: TOL-9

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_2.txt
Sample name: TOL9_13492_1_2

hyb_protocol: cRNA samples were hybridized to a Agilent Technologie Human Gene Expression 8x60K Microarray during 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters (protocol GE2_107_Sep09 and Grid: 028004_D_F_20110819).

data_processing:
Data extraction of median feature intensity without background subtraction was peformed with Feature Extraction software v10.7.1.1 (gMedianSignal or rMedianSignal column)(Agilent Technologies). In order to remove systemic signal intensity bias between each array, median feature intensity were normalized with the function lowess (Locally weighted scatterplot smoothing) method, and then spots with half of the samples for each group exhibiting signal less than the mean of all median signals were removed (threshold: 96.95). 30, 371spots were kept out of 58,717.
Each sample represents one channel of a dual-channel array.

source_name: Purified B lymphocytes

label_protocol: The cRNA labeling and hybridizations were 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. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA were extracted and purified from human B using the RNeasy microkit following the manufacturer’s instructions (Qiagen). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE), and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Venous blood samples were collected in EDTA vacutainers and processed for analysis within 4 hours. Peripheral Blood Mononuclear Cells (PBMC) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and frozen in 10% DMSO diluted human plasma (Sigma-Aldrich, St Louis, MO). Then total B cells were purified from PBMC by negative selection on magnetic columns according to the manufacturer’s instructions (B cell isolation Kit II, Miltenyi Biotech, Gladbach, Germany).

tag: disease

value: TOL

tag: cell type

value: B cell


title: Control VZ ATC 1h C


title: Control TB Phase3 96h 3


title: Control TB Phase3 48hp 4

value: 48 h post


title: Control TB Phase3 48hp 5


title: Control TB Phase3 48hp 6


title: Control TB Phase3 96h 2


title: TOL-6

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_2.txt
Sample name: TOL6_13491_1_2


title: TOL-5

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_4.txt
Sample name: TOL5_13491_2_4


title: Control TB Phase3 48hp 3


title: TOL-7

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_1.txt
Sample name: TOL7_13492_1_1


title: TOL-8

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_4.txt
Sample name: TOL8_13491_1_4


title: Control TB Phase3 48hp 2


title: Control TB Phase3 48hp 1


title: Control TB Phase3 48h 7


title: TOL-3

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_3.txt
Sample name: TOL3_13491_2_3


title: Control TB Phase3 48h 8


title: TOL-10

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_1.txt
Sample name: TOL10_13491_2_1


title: TOL-4

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_3.txt
Sample name: TOL4_13492_1_3


title: TOL-2

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_2.txt
Sample name: TOL2_13492_2_2


title: Control TB Phase3 48h 5


title: Control TB Phase3 48h 6


title: Control TB Phase3 48h 2


title: STA-9

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_3.txt
Sample name: STA9_13492_2_3

value: STA


title: STA-5

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_1.txt
Sample name: STA5_13492_2_1


title: STA-8

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_1.txt
Sample name: STA8_13492_2_1


title: STA-4

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_2.txt
Sample name: STA4_13491_2_2


title: Control TB Phase3 24hp 5

value: 24 h post


title: Control TB Phase3 24hp 6


title: TOL-1

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_2.txt
Sample name: TOL1_13491_2_2


title: Control TB Phase3 48h 1


title: Control TB Phase3 48h 3


title: Control TB Phase3 48h 4


title: STA-12

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_3.txt
Sample name: STA12_13492_2_3


title: Control TB Phase3 24hp 3


title: STA-2

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_3.txt
Sample name: STA2_13491_1_3


title: STA-6

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_4.txt
Sample name: STA6_13491_2_4


title: STA-11

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_4.txt
Sample name: STA11_13492_2_4


title: STA-7

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_2.txt
Sample name: STA7_13492_2_2


title: STA-3

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_4.txt
Sample name: STA3_13492_1_4


title: Control TB Phase3 24hp 1


title: Control TB Phase3 24hp 2


title: Control TB Phase3 24hp 4


title: Control TB Phase3 24h 5


title: Control TB Phase3 24h 6


title: Control TB Phase3 24h 7


title: HV-8

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_1.txt
Sample name: HV8_13492_1_1

value: HV


title: HV-9

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_1.txt
Sample name: HV9_13491_2_1


title: STA-10

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_2.txt
Sample name: STA10_13492_1_2


title: Control TB Phase3 24h 4


title: STA-1

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_3.txt
Sample name: STA1_13492_1_3


title: Control TB Phase3 24hp 7


title: Control TB Phase3 24h 2


title: HV-6

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_2_4.txt
Sample name: HV6_13492_2_4


title: Control TB Phase3 24h 1


title: HV-2

description:
Raw data file: US82400123_252800413492_S01_GE2_107_Sep09_1_4.txt
Sample name: HV2_13492_1_4


title: Control TB Phase3 192hp 5

value: 192 h post


title: HV-4

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_2_3.txt
Sample name: HV4_13491_2_3


title: Control TB Phase3 192hp 2

value: ovary


title: Control TB Phase3 192hp 4

value: in water control


title: Control TB Phase3 192hp 3


title: HV-3

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_2.txt
Sample name: HV3_13491_1_2


title: HV-10

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_1.txt
Sample name: HV10_13491_1_1


title: Degenerating-9d-rep1

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

country: Japan

institute: Okayama University

description:
Gene expression in regeneration siphons 9 days after excision
9d-1

hyb_protocol: A set of fluorescently labeled cRNA targets (1.5ug for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.

scan_protocol: Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.

data_processing: The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.5 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default condition of the software. Some probes which were judged beyond analysis by Feature Extraction 10.5 software were eliminated from the following analysis.

organism: Ciona intestinalis

source_name: regenerating siphon 9 days

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng total RNA using the Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Animals were obtained by collection from marine environments nearly Woods Hole, MA., USA

extract_protocol: Total RNA was extracted from five or six siphones and purified using RNAeasy micro kit (QIAGEN) following the manufacturer's protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Regenerating oral siphons were compared to control siphons. For regenerating oral siphons, the entire siphon was removed from animals, and allowed to regenerate for 3, 6, or 9 days.  After regeneration was complete, the regenerated siphons were removed from the animals and used for RNA extraction. For control animals, the entire oral siphon was removed and used for RNA.

value: regenerating siphon

tag: days

value: 9 days


title: Control TB Phase3 24h 3


title: HV-7

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_4.txt
Sample name: HV7_13491_1_4


title: HV-5

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_3.txt
Sample name: HV5_13491_1_3


title: HV-1

description:
Raw data file: US82400123_252800413491_S01_GE2_107_Sep09_1_1.txt
Sample name: HV1_13491_1_1


title: Control TB Phase3 192hp 1


title: Control TB Phase3 192h 7


title: Control TB Phase3 192h 8


title: Degenerating-6d-rep1

description:
Gene expression in regeneration siphons 6 days after excision
6d-1

source_name: regenerating siphon 6 days

value: 6 days


title: Control TB Phase3 192h 4


title: Degenerating-3d-rep2

description:
Gene expression in regeneration siphons 3 days after excision
3d-2

source_name: regenerating siphon 3 days

value: 3 days


title: Control TB Phase3 192h 5


title: Degenerating-6d-rep2

description:
Gene expression in regeneration siphons 6 days after excision
6d-2


title: Control TB Phase3 192h 3


title: Control TB Phase3 192h 2


title: Degenerating-9d-rep2

description:
Gene expression in regeneration siphons 9 days after excision
9d-2


title: Control-rep2

description:
Gene expression in intact siphons
C-2

source_name: intact siphon

value: intact siphon

value: control


title: Control TB Phase3 192h 6


title: Control-rep1

description:
Gene expression in intact siphons
C-1


title: Leaf-treated HepG2,biological rep3

city: Onna-son, Kunigami-gun

first: Nurhanani

last: Razali

state: Okinawa

address: 1919-1 Tancha

department: Membranology

institute: Okinawa Institute of Science and Technology Graduate University (OIST)

description: Gene expression profiles in HepG2 cells treated with the methanol leaf extract of T. indica

hyb_protocol: Following fragmentation, 1 µg of cRNA were hybridized for 16 h at 45 °C on Human Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 under standard condition.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: CEL. files for each array were generated using the Affymetrix GeneChip Operating Software (GCOS) and were further analysed using Partek Genomics Suite software. Gene expression profiling was performed using arrays of HuGene-1_0-st-v1. A custom CDF (HuGene-1_0-st-v1.r3.cdf) with Entrez based gene definitions was used to annotate the arrays. The raw fluorenscence intensity values were normalized applying quantile normalization, while background correction was performed with Robust Multiarray Average (RMA). Probe set summarization was performed with Median Polish.

source_name: Leaf-treated HepG2 cells for 24h

label_protocol: Biotinylated cRNA (antisense RNA) were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix)

growth_protocol: HepG2 cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% foetal bovine serum, 1% penicillinand 1% streptomycin. Cells were maintained in humifified air with 5% CO2 at 37°C

extract_protocol: Extraction of tcRNA was performed using RNeasy Mini Kit (Qiagen) and DNase I treatement was done on the extracted tcRNA using RNase-free DNase set (Qiagen) according to manufacturer's protocols.

treatment_protocol: The cells were seeded and treated with the IC20 concentration of the methanol leaf extract of T. indica for 24 h. Folloing this, cells were trypsinized and precipitated by centrifugation at 130 x g for 5 min. Cells were washed with PBS before tcRNA was extracted from the cells.

tag: types of treatment

value: T. indica leaf-treated


title: Leaf-treated HepG2,biological rep2


title: Control TB Phase3 192h 1

tag: tissue


title: Control TB-EE2 2

tag: age (month)

value: rnaL


title: Control TB-EE2 4

tag: treatment


title: Untreated HepG2,biological rep1

source_name: Untreated HepG2 cells

value: Untreated


title: Degenerating-3d-rep1

description:
Gene expression in regeneration siphons 3 days after excision
3d-1


title: Untreated HepG2,biological rep2


title: Leaf-treated HepG2,biological rep1


title: Control TB-BPA 4

tag: treatment duration


title: Control TB-BPA 6

tag: experiment


title: Control TB-EE2 1

tag: sampling date


title: Untreated HepG2,biological rep3


title: Control TB-BPA 5

tag: scan date


title: VE-Cad neg Scf-GFP pos_3

city: Dallas

first: Bo

last: Zhou

state: TX

address: 5323 Harry Hines Blvd.

department: Children's Research Institute

institute: University of Texas Southwestern Medical Center

hyb_protocol: 2.5 µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Raw data were processed with the Expression Console (Affymetrix) for RMA summarization and Quantile normalization

source_name: FACS-sorted VE-cadherein negative Scf-GFP positive cells

label_protocol: cDNA was fragmented and biotinylated using the Encore Biotin Module (NuGEN) according to the manufacturer’s instructions..

growth_protocol: 5,000 bone marrow VE-Cad negative Scf-GFP positive cells from Scf-GFP knockin heterozygous mice were double-sorted into Trizol (Invitrogen). 5,000 whole spleen cells from Scf-GFP knockin heterozygous mice were sorted into Trizol (Invitrogen).

extract_protocol: Total RNA was extracted, amplified, and sense strand cDNA was generated using the Ovation Pico WTA System V2 (NuGEN) according to the manufacturer’s instructions.

treatment_protocol: Mice were untreated.

tag: cell population


title: VE-Cad neg Scf-GFP pos_2

value: VE-cadherein negative Scf-GFP positive cells


title: Control TB-BPA 2

tag: rna date

tag: rna person


title: Unfractionated spleen cells_2

source_name: Unfractionated spleen cells

tag: strain

value: Unfractionated spleen cells


title: In vitro derived with RA CD103+CD11b+ cDC 3

city: Palo Alto

first: Eugene

middle: C.

last: Butcher

state: CA

address: 3801 Miranda Avenue

department: Pathology

institute: Stanford School of Medicine

description: Transcriptional profiling of sorted CD103+CD11b+ cDC from day 5 culture of sorted pre-uDC from bone marrow adult male in complete IMDM media with Flt3L and GMCSF and RA

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Mouse Exon 1.0 ST Arrays and scanned by Expression Analysis, Inc.

scan_protocol: Array scanning was performed by Expression Analysis, Inc. according to the manufacturer's instruction

data_processing: GeneSpring GX 12.6 and Partek Genomic Suite (6.6) were used for processing and analyzing the data. Genespring preprocessing and default normalization (RMA-16) was applied to each dataset.

label: Biotin

source_name: Sorted pre-uDC from bone marrow adult male and cultured in vitro for 5 day in complete IMDM media with Flt3L and GMCSF and RA

label_protocol: Single-stranded cDNA was generated from amplified cRNA (using Ambion WT Expression Kit) and then fragmented/labeled with the Affymetrix GeneChip WT Terminal Labeling and Controls Kit, performed by Expression Analysis, Inc.

growth_protocol: For the in vitro derived samples, sorted pre-uDC were cultures with Flt3L and GM-CSG with or without RA in complete IMDM media for 5 days

extract_protocol: Total RNA was isolated from sorted cells using Trizol-chloroform following the protocol from Immgen.org .  Briefly, add 500ul of trizol to each sample and incubate at room temperature for 5 min. Freeze at -80C for at least 1 hr to indefinitely.  Thaw trizol  at room temp,  add 100ul of chloroform to the mixture was shake vigorously for approximately 15 sec, incubate 2-3 min at room temp and centrifuge for 15 at 12,000g at 4C.  Transfer the aqueous phase to a fresh tube and add 1 ul of glycol blue to each sample and then 250um of isoproponol. Incubate at -80C for 1 hr to indefinitely.  Centrifuge for 20 min at 12,000 g at 4C and then remove supernatant.  Wash with 500um cold 75% ethanol and centrifuge for 15 min at 7,400g at 4C.  Pipette off ethanol and resuspend RNA pellet in 14ul nuclease-free water.  Incubate at room temp for 2-3 min.  Quantify RNA using bioanalyzer.

value: In vitro derived CD103+CD11b+ cDC

tag: age

value: adult

tag: gender

value: male


title: Control KTC TNT 0-24h 6h 2

value: 6 h

value: rnaC

tag: chip id


title: Control TB-BPA 1

value: ovary

value: in water control


title: Control KTC TNT 0-24h 6h 4


title: Control KTC TNT 0-24h 6h 3


title: Unfractionated spleen cells_1


title: Control TB-BPA 3


title: In vitro derived with RA CD103+CD11b- cDC 3

description: Transcriptional profiling of sorted CD103+CD11b- cDC from day 5 culture of sorted pre-uDC from bone marrow adult male in complete IMDM media with Flt3L and GMCSF and RA

tag: cell type

value: In vitro derived CD103+CD11b- cDC


title: In vitro derived with RA CD103+CD11b+ cDC 2


title: In vitro derived with RA CD103+CD11b+ cDC 1


title: VE-Cad neg Scf-GFP pos_1


title: Control KTC TNT 0-24h 6h 1


title: In vitro derived without RA CD103+CD11b+ cDC 3

description: Transcriptional profiling of sorted CD103+CD11b+ cDC from day 5 culture of sorted pre-uDC from bone marrow adult male in complete IMDM media with Flt3L and GMCSF

source_name: Sorted pre-uDC from bone marrow adult male and cultured in vitro for 5 day in complete IMDM media with Flt3L and GMCSF


title: In vitro derived with RA CD103+CD11b- cDC 1


title: In vitro derived with RA CD103+CD11b- cDC 2


title: In vitro derived without RA CD103+CD11b- cDC 2

description: Transcriptional profiling of sorted CD103+CD11b- cDC from day 5 culture of sorted pre-uDC from bone marrow adult male in complete IMDM media with Flt3L and GMCSF


title: Control KTC TNT 0-24h 30m 4

value: 30 min


title: In vitro derived without RA CD103+CD11b- cDC 1


title: Control KTC TNT 0-24h 4h 1

value: 4 h


title: In vitro derived without RA CD103+CD11b+ cDC 2


title: Control KTC TNT 0-24h 4h 3


title: Control KTC TNT 0-24h 30m 3


title: J-778-T

city: Chengdu

first: Wen-Jian

last: Meng

state: Sichuan Province

address: No. 37, Guoxue Street

department: Department of Gastrointestinal Surgery

country: China

institute: West China Hospital, Sichuan University

hyb_protocol: Biotinylated RNA was hybridized 16 hrs at 45°C with rotation (60rpm) into individual Affymetrix GeneChip miRNA 1.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Microarrays were scanned in a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing:
For microarray analysis quality control, log2 normalization and analysis of differentially expressed genes was performed using the miRNA QC tool software. The raw array data (.txt files) was analyzed by unpaired t-test using GeneSpring Software 10.0 (Agilent technologies).
Probe group file: miRNA-1_0-st.pgf
Meta-probeset file: miRNA-1_0-st.mps
The miRNAs with fold change (FC)≥1.0 and P<0.05 were selected as significantly differential expression.

source_name: Colonic cancer mucosa from patient with solitary colorectal cancer

label_protocol: 300ng of purified RNA were labelled with biotin.

growth_protocol: Colorectal cancerous and matched normal mucosa dissected during surgery.

extract_protocol: All samples were snap frozen in liquid nitrogen and histologically confirmed. Total RNA were extracted from all the samples by using Trizol. Then, RNA Spike Control Oligos, and poly(A) tails were added to each RNA sample.

treatment_protocol: Not applicable.

value: Colonic cancer mucosa

tag: patient disease

value: solitary colorectal cancer (CRC)


title: J-775-T


title: Control KTC TNT 0-24h 30m 1


title: Control KTC TNT 0-24h 4h 2


title: In vitro derived without RA CD103+CD11b- cDC 3


title: J-774-T


title: J-772-T


title: Bone marrow pre-mucosal DC 3

description: Transcriptional profiling of sorted pre-uDC from bone marrow

source_name: C57Bl/6, male, 10-14 days old

value: Bone marrow pre-mucosal DC

value: 10-14 days old


title: Control KTC TNT 0-24h 30m 2


title: Control KTC TNT 0-24h 2h 3

value: 2 h


title: In vitro derived without RA CD103+CD11b+ cDC 1


title: Control KTC TNT 0-24h 2h 4


title: Control KTC TNT 0-24h 24h 3


title: Bone marrow pre-mucosal DC 1


title: Control KTC TNT 0-24h 2h 2


title: Control KTC TNT 0-24h 2h 1


title: Control KTC TNT 0-24h 24h 4


title: Control KTC TNT 0-24h 24h 2


title: J-771-T


title: Bone marrow pre-mucosal DC 2


title: J-768-T


title: J-682-T

source_name: Rectal cancer tissue from patient with solitary colorectal cancer

value: Rectal cancer tissue


title: J-778-N

data_processing:
Data was preprocessed by log2 transformation, and the normalization was performed by quantile normalization algorithm by miRNA QC tool.
For microarray analysis quality control, log2 normalization and analysis of differentially expressed genes was performed using the miRNA QC tool software. The raw array data (.txt files) were analyzed by unpaired t-test using GeneSpring Software 10.0 (Agilent Technologies).
The miRNAs with fold change (FC)≥1.0 and P<0.05 were selected as significantly differential expression.
Probe group file: miRNA-1_0-st.pgf
Meta-probeset file: miRNA-1_0-st.mps

source_name: Normal colonic mucosa from patient with solitary colorectal cancer

value: normal colonic mucosa


title: J-775-N


title: J-774-N


title: J-771-N


title: Control KTC TNT 0-24h 1h 4

source_name: ovary tissue,fish in water control

value: 1 h


title: Control KTC TNT 0-24h 24h 1


title: Control KTC TNT 0-24h 1h 3


title: J-682-N

source_name: Normal rectal mucosa from patient with solitary colorectal cancer

value: normal rectal mucosa


title: Control RDX 0-5mgL 21d 3

value: rnaX


title: Control RDX 0-5mgL 21d 4


title: J-656-N

source_name: Normal rectal mucosa from patient with synchronous colorectal cancer

value: synchronous colorectal cancer (CRC)


title: J-406-N


title: J-680-N

source_name: Normal colonic mucosa from patient with synchronous colorectal cancer


title: Control PRO PHASE3 48hp C

value: post-48 h

value: rnaB


title: Control PRO PHASE3 48hp A

value: ovary

value: in water control


title: Control PRO PHASE3 48hp D


title: Control KTC TNT 0-24h 1h 2

value: rnaC


title: Control PRO PHASE3 96hp G

value: post-96 h


title: Control PRO PHASE3 96hp E


title: Control RDX 0-5mgL 21d 2


title: J-779-N


title: J-779-T

data_processing: For microarray analysis quality control, log2 normalization and analysis of differentially expressed genes was performed using the miRNA QC tool software. The raw array data (.txt files) was analyzed by unpaired t-test using GeneSpring Software 10.0 (Agilent technologies). The miRNAs with fold change (FC)≥1.0 and P<0.05 were selected as significantly differential expression.

source_name: Rectal cancer mucosa from patient with synchronous colorectal cancer

value: rectal cancer mucosa


title: J-613-N


title: Control RDX 0-5mgL 21d 1


title: J-768-N

value: solitary colorectal cancer (CRC)


title: J-680-T

source_name: Colonic cancer mucosa from patient with synchronous colorectal cancer

value: colonic cancer mucosa


title: Control PRO PHASE3 48hp B


title: Control PRO PHASE3 96h C


title: Control PRO PHASE3 96h G


title: J-613-T


title: J-406-T


title: Control TB-EE2 3

value: rnaL


title: Control PRO PHASE3 96h A


title: Control PRO PHASE3 96h F


title: Control PRO PHASE3 96h D


title: Control PRO PHASE3 96h B


title: Control PRO PHASE3 48hp F


title: Control PRO PHASE3 24hp F

value: post-24 h


title: Control PRO PHASE3 48hp E


title: Control PRO PHASE3 24hp D


title: HFF-CHX,uninfect,IFNY

city: Cambridge

first: Emily

middle: E

last: Rosowski

state: MA

address: 77 Massachusetts Ave, 68-258d

department: Biology

institute: MIT

hyb_protocol: Following fragmentation, 5 ug of cDNA from samples were hybridized on GeneChip Mouse Genome 430A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.  Data was then normalized, setting all data to have a minimum value of 50.

source_name: HFF, CHX pre-treated 1hr40min, uninfected, IFNgamma treated 1hr

label_protocol: Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.

growth_protocol: 1.5-2x105 HFFs were grown in 12-well plates (BD Biosciences) at 37C, 5% CO2.  An RH 1-1 type I parasite strain was maintained in vitro by serial passage on monolayers of HFFs.

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

treatment_protocol: HFFs were pre-treated (or not) with 50ug/ml CHX for 40min.  Parasites were syringe lysed, washed at least once with PBS, and added to HFFs (still in the presence of CHX) for one hours.  Media was replaced (+/- CHX) on uninfected cell samples.  Cells were then stimulated with 100U/ml human IFN-γ for one hour (still in the presence of CHX).  Media was replaced (+/- CHX) on unstimulated cell samples.  CHX treatment inhibited IFN-γ induced protein expression without causing the cells to appear sick.

value: Human foreskin fibroblasts

tag: parasite strain

tag: treated

value: yes

tag: infection

value: no

tag: stimulated


title: HFF-untreat,RH,IFNY

source_name: HFF, untreated, RH infected 1hr, IFNgamma treated 1hr

tag: tissue


title: HFF-CHX,RH,IFNY

source_name: HFF, CHX pre-treated 40min, RH infected 1hr, IFNgamma treated 1hr


title: HFF-untreat,RH,unstim

source_name: HFF, untreated, RH infected 2hr, unstimulated


title: J-656-T


title: Control PRO PHASE3 48hp G

tag: age (month)

tag: treatment

tag: treatment duration

tag: experiment


title: Control PRO PHASE3 24hp E

tag: sampling date

tag: scan date

tag: rna date


title: HFF-CHX,RH,unstim

source_name: HFF, CHX pre-treated 40min, RH infected 2hr, unstimulated


title: Chinese Spring rep3

city: Yokohama

first: Yeonju

last: Jung

state: Kanagawa

address: Maioka-cho 641-12

department: Yokohama City University

institute: Kihara Institute for Biological Research

hyb_protocol: Hybridizations were performed at 60°C for 17 h in a hybridization chamber (Agilent Technologies).

scan_protocol: The hybridized microarrays were scanned using a DNA microarray scanner (Agilent Technologies) and signal intensities were detected from the obtained digital images using Feature Extraction software (Agilent Technologies)

data_processing: Raw fluorescence intensities (raw signal intensity > 1.0 threshold) were transformed to log scale (base 2) using GeneSpring GX software (v12.6; Agilent Technologies). For normalization, transformed signals were shifted to the 75th percentile for all arrays and to the median for all probes. Quality control was performed as follows: (1) weakly hybridized probe spots were removed using a cut-off value of the raw signal intensity in all microarray slides of <20%; (2) only probes flagged as ‘detected’ in at least one of the 10 samples were chosen; (3) repeatable probes were chosen using coefficient of variation >50%.

organism: Triticum aestivum

source_name: two-weeks old seedling

label_protocol: 500 ng of RNA were labelled using the Agilent Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies, Santa Clara, CA) with cyamine 3-cytidine 5C-triphosphate (CTP)

growth_protocol: All plants were grown in a growth chamber maintained at 22°C and 40% relative humidity, with a 16 h light (6000 lux; 64,560 fc) and 8 h dark cycle.

extract_protocol: RNA was prepared using Plant RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

tag: sample type

value: parental line


title: Chinese Spring rep2


title: HFF-untreat,uninfect,IFNY

source_name: HFF, untreated, uninfected, IFNgamma treated 1hr


title: Control PRO PHASE3 96h E

tag: rna person


title: Control PRO PHASE3 24hp C

tag: chip id


title: HFF-untreat,uninfect,unstim

source_name: HFF, untreated, uninfected, unstimulated


title: HFF-CHX,uninfect,unstim

source_name: HFF, CHX treated 2hr40min, uninfected, unstimulated


title: Control PRO PHASE3 24hp B


title: Natural hexaploid 3 rep2

source_name: two-leaves seedling

value: hexaploid


title: Natural hexaploid 3 rep3


title: Chinese Spring rep1


title: Control PRO PHASE3 48h D


title: Control PRO PHASE3 48h G


title: Control PRO PHASE3 48h C


title: Control PRO PHASE3 24hp A


title: Natural hexaploid 3 rep1


title: Control KTC TNT 0-24h 4h 4

value: 4 h


title: Natural hexaploid 2 rep1


title: Natural hexaploid 2 rep2


title: Control PRO PHASE3 48h F


title: Control PRO PHASE3 48h B


title: Natural hexaploid 2 rep3


title: WT 30 mM MeOH vs WT 1

city: Bielefeld

first: Lennart

middle: Hendrik

last: Leßmeier

address: Universitätsstr. 25

institute: Bielefeld University

description: Cultivation in mCGXII minimal medium 100 mM glucose compared to growth with additional 30 mM methanol

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was performed with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.).

organism: Corynebacterium glutamicum

source_name: WT in mCGXII 100 mM glucose 30 mM methanol

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: C. glutamicum and C. glutamicum Tol1 were cultured in LB medium for overnight and inoculated into 50 mL LB complex medium or 50 mL mCGXII medium with 100 mM of glucose at the initial O.D. of 1. Cells were harvested in the early exponential growth phase (O.D. between 6 and 8).

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini   Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: Methanol was added from the beginning of the growth.

tag: genotype

value: wildtype

tag: strain

tag: growth phase

value: Early exponential phase of growth

source_name: WT in mCGXII 100 mM glucose


title: Control PRO PHASE3 192hp C

source_name: ovary tissue,fish in water control

value: ovary

value: post-192 h

value: rnaB


title: Natural hexaploid 1 rep1


title: Natural hexaploid 1 rep2


title: Tol1 120 mM MeOH vs Tol1 1

description: Cultivation in mCGXII minimal medium 100 mM glucose compared to growth with additional 120 mM methanol

source_name: Tol1 in mCGXII 100 mM glucose 120 mM methanol

source_name: Tol1 in mCGXII 100 mM glucose


title: WT 30 mM MeOH vs WT 2


title: WT 30 mM MeOH vs WT 3


title: Tol1 120 mM MeOH vs Tol1 2


title: Natural hexaploid 1 rep3


title: Control PRO PHASE3 48h E

value: in water control


title: Control PRO PHASE3 192hp F


title: Control PRO PHASE3 48h A


title: Control PRO PHASE3 24hp G


title: Control PRO PHASE3 192hp D


title: Tol1 vs WT in LB 2

description: Cultivation in LB complex medium. Sample taken in early exponentional phase of growth. Comparison of the methanol tolerant strain Tol1 with the C. glutamicum WT.

source_name: Tol1 in LB

source_name: WT in LB


title: Control PRO PHASE3 192hp G


title: Control PRO PHASE3 192hp B


title: Control PRO PHASE3 24h D


title: Control PRO PHASE3 24h C


title: Control PRO PHASE3 192hp A


title: Tol1 vs WT in LB 1


title: Snails injected with PGN replicate 2

city: Albuquerque

first: Si-Ming

last: Zhang

state: NM

address: Castetter Hall

institute: University of New Mexico

description: Biological replicate 2 of 4

hyb_protocol: All procedures for labeling were performed based on Protocol of Two-color microarray-based gene expression analysis (version 6.6). A total of 300 ng of the purified C-3 and C-5 labeled cRNA was added to 10x hybridization buffer and incubated at 60oC for 30 min to fragment RNA. A total of 40 μl of hybridization sample were added to each gasket chamber of an Agilent hybridization gasket slide. After all eight gasket chambers on the slide were filled with hybridization samples, the gasket slide was covered with a microarray slide printed with eight identical arrays (Agilent). The assembled hybridization chamber was placed in a hybridization oven at 65oC for 17 hours (rotating at 10xg).

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and LOWESS normalization.

organism: Biomphalaria glabrata

source_name: APO

label_protocol: All procedures for labeling were performed based on Protocol of Two-color microarray-based gene expression analysis (version 6.6). All chemicals used were purchased from Agilent or recommended by Agilent. A total of 200 ng RNA were used as starting sample. Spike A (cyanine dye Cy-3) and Spike B (cyanine dye Cy-5) mix were added to the RNA sample of experimental group and universal reference RNA (URR), respectively. URR consisted of 80% from the PBS-injected group (control) and 20% from the three experimental groups. The 12 samples from the three groups contributed equally. cDNA amplification and labeling reaction with C3 and C5 were conducted at 42oC for 2 hours. The labeled complementary RNA (cRNA) was purified using RNeasy Mint Kit (Qiagen). The cRNA was quantified to determine the concentration and specific-label activity using a NanoDrop spectrophotometer.

growth_protocol: Adult Salvador strain (schistosome-resistant) B. glabrata, measuring 10-10.5 mm in shell diameter, were used for the experiments.

extract_protocol: RNA extraction was done  using Triz (Invitrogen)

treatment_protocol: Three crude (i.e., not highly purified) PAMPs from commercial sources were utilized: lipopolysaccharide (LPS) from the bacterium Escherichia coli O127-B8 (Sigma), peptidoglycan (PGN) from E. coli O111-B4 (Invitrogen), and fucoidan (FUC) from the brown alga Fucus vesiculosus (Sigma). All three chemicals were dissolved 1/3 mammalian-strength phosphate buffered saline (PBS) (Kodak, Rochester, NY) at a concentration of 1 mg/ml (LPS and PGN) or 10 mg/ml (FUC). Individual snails were injected with 5 μl of each PAMP or with PBS (control) through a hole in the shell and into a hemolymph sinus anterior to the digestive gland on the left side. At 24 hours post-injection, the pericardial sac was removed, and the anterior pericardial wall (or APO) was dissected. 20 APO was pooled as a sample and stored in Trizol (Invitrogen) for subsequent RNA extraction.  For each treatment, 4 replicates (80 APO) were used.

tag: agent

value: PGN

tag: age

value: Adult

tag: size

value: anterior pericardial wall

value: Salvador strain

source_name: Universal Reference RNA [80% from the PBS-injected group (control) and 20% from the three experimental groups]


title: Control PRO PHASE3 24h B

tag: tissue


title: Snails injected with PGN replicate 3

description: Biological replicate 3 of 4


title: Control PRO PHASE3 24h G

tag: age (month)


title: Snails injected with PGN replicate 4

description: Biological replicate 4 of 4


title: Control PRO PHASE3 24h F

tag: treatment


title: J-772-N

source_name: Normal colonic mucosa from patient with solitary colorectal cancer

value: normal colonic mucosa

tag: patient disease

value: solitary colorectal cancer (CRC)


title: Control PRO PHASE3 24h E

tag: treatment duration

tag: experiment


title: Control PRO PHASE3 96hp A

value: post-96 h

tag: sampling date

tag: scan date


title: Snails injected with FUC replicate 1

description: Biological replicate 1 of 4

value: FUC


title: Snails injected with PGN replicate 1

description: Biological replicate 1 of 4


title: Snails injected with FUC replicate 3

description: Biological replicate 3 of 4


title: TamR-8 replicate 3

city: Odence

first: Henrik

last: Ditzel

address: J.B. Winsløws Vej 25

country: Denmark

institute: University of Southern Denmark

description: Test

data_processing:
Primers leading to more than one peak in their melting characteristics were identified and annotated via melting curve analysis performed in R.
We applied a signal-dependent non-linear normalization method similar to that described by Workman et al. in 2002. The offset amounts were calculated by fitting cubic-spline to the entire dataset and were added to the raw data to obtain desired target distributions. Our normalization approach offered 20% reduction in replicate standard error of means.
As a next step, we used limma from Bioconductor package to identify miRNAs with altered expression between tamoxifen-resistant and -sensitive cell lines.
Raw Cp values were normalized as above. Log-fold changes of miRNA expression were computed relative to MCF-7 cell line using Limma package in R.

label: SYBR green

label_protocol: MiRNA qPCR profiling was conducted using miRCURY LNA Univeral RT microRNA PCR system (Exiqon, Denmark) as per manufacturer's istructions.  In brief, 50 ng total RNA was reverse-transcribed in 40 µl reactions on a Bio-RAD S1000 Thermal Cycler (60 min at 42˚C, followed by heat-inactivation of the reverse transcriptase for 5 min at 95˚C). From the resulting cDNA, 32.5 µl was used for a SYBR green master mix and run in 10 µl real-time amplification on microRNA Ready-to-use PCR, Human panel I+II, V2.R plates (Exiqon, product number 203608) on a Roche LightCycler® 480 real-time PCR system. The applied PCR settings were: 10 min at 95˚C, 40 amplification cycles (95˚C/10 sec, 60˚C/1 min, ramp rate 1.6˚C/sec). For each cell line, three biological replicates were analyzed.

growth_protocol: MCF-7 and TamR cell lines were grown in a culture of MCF-7/S0.5 cells inclubated with tamoxifen. The cells were grown in a standard phenol-red-free DMEM:F12 (1:1) medium (Gibco, 21041-025) supplied with 1% heat-inactivated FBS (Gibco, 10270-106), 6 ng/ml insulin (Sigma, I6634) and 2.5 mM glutamax (Gibco, 35050). The standard medium for the TamR cell lines was supplied with 1 µM tamoxifen (Sigma, T5648). MCF-7/S0.5 and the TamR cell lines were passaged once per week and seeded in 1x105 and 1.4x105/T25 flasks, respectively. The cell lines were cultured at 37oC and 5% CO2 and kept at low passage numbers throughout the experiments (<10 passages).

extract_protocol: Total RNA from cell line cultures was extracted and purified using TRIzol(Invitrogen) and EtOH precipitated.

tag: cell line


title: Control PRO PHASE3 96hp B

tag: rna date

tag: rna person


title: Control PRO PHASE3 192h B

tag: chip id


title: Snails injected with PBS (control) replicate 3

description: Biological replicate 3 of 4

value: PBS (control)

tag: strain


title: Snails injected with FUC replicate 2

description: Biological replicate 2 of 4


title: Control KTC TNT 0-24h 1h 1

value: 1 h

value: rnaC


title: Control PRO PHASE3 192h G


title: Control PRO PHASE3 192h D


title: TamR-8 replicate 2

description: Test


title: Snails injected with LPS replicate 4

description: Biological replicate 4 of 4

value: LPS


title: Snails injected with LPS replicate 3

description: Biological replicate 3 of 4


title: Snails injected with LPS replicate 2

description: Biological replicate 2 of 4


title: Snails injected with LPS replicate 1

description: Biological replicate 1 of 4


title: Snails injected with FUC replicate 4

description: Biological replicate 4 of 4


title: Control PRO PHASE3 96hp C


title: Snails injected with PBS (control) replicate 4

description: Biological replicate 4 of 4


title: Control PRO PHASE3 96hp F


title: Control PRO PHASE3 192h C


title: Control PRO PHASE3 24h A


title: Control PRO PHASE3 192h A


title: Control PRO 24h 6h 4

value: 6 h

value: rnaJ


title: Snails injected with PBS (control) replicate 2

description: Biological replicate 2 of 4


title: Control PRO PHASE3 192h F

value: ovary


title: TamR-4 replicate 3

description: Test


title: TamR-4 replicate 2

description: Test


title: Control PRO PHASE3 192h E

value: rnaB


title: Snails injected with PBS (control) replicate 1

description: Biological replicate 1 of 4


title: TamR-4 replicate 1

description: Test


title: TamR-1 replicate 1

description: Test


title: Control PRO 24h 6h 1

value: in water control


title: Control PRO 24h 6h 2


title: Control PRO 24h 24h 4


title: Control PRO 24h 24h 3


title: TamR-8 replicate 1

description: Test


title: TamR-1 replicate 3

description: Test


title: matched normal breast tissues 3

city: Taizhou

first: Feilin

last: Cao

state: Zhejiang

address: No.150 Ximen Road

department: Department of Surgical Oncology, Taizhou Hospital,

institute: Wenzhou Medical University

description: lncRNA and mRNA expression

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (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 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: matched normal breast tissues

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

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: Paired TNBC tissues and adjacent normal breast tissues from every subject were snap-frozen in liquid nitrogen immediately after resection and stored at -80 °C until use.

value: matched normal breast tissues

tag: gender

value: Female


title: Control PRO 24h 24h 2

data_processing: Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer’s protocol and recommendations.  Data processing was conducted using R package Limma.


title: MCF-7 replicate 3

description: Control


title: TNBC tissue 3

description: lncRNA and mRNA expression

source_name: TNBC tissue

value: TNBC  tissue


title: matched normal breast tissues 1

description: lncRNA and mRNA expression


title: Control PRO 24h 6h 3


title: TNBC tissue 2

description: lncRNA and mRNA expression


title: matched normal breast tissues 2

description: lncRNA and mRNA expression


title: Control PRO 24h 24h 1


title: 6h_4

city: JBSA FT SAM HOUSTON

first: Phillip

middle: Dalton

last: Bowman

address: 3698 CHAMBERS PASS STE B

department: DCR

institute: US Army Institute of Surgical Research

description: Gene expression after 6h after dosing with 200 nM CDDO

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65¡C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (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 10.7.1.1 (Agilent) using default parameters to obtain background subtracted  spatially detrended Processed Signal intensities as the raw data. A flat file with the greenbackground subtracted pixel intenities was prepared and analyzed with BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) version 4.4.0 stable.The data table presents the unfiltered normalized log transformed expression value for each Agilent probe.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were confirmed with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Fourth population doubling level pooled, mixed gender human umbilical vein endothelial cell (Lifeline Cell Technology, Frederick, MD) were grown until confluent.

extract_protocol: RNA was extracted by Tri Reagent l (Moleculare Research Center, Cincinnati, OH 45212) following the manufacturer's instructions.

treatment_protocol: Confluent in MCDB 131 Medium (Gibco, Long Island, NY) with endothelial supplements supplied by ATCC (Manassas, VA) in 12 well multiplates. They were Confluent cells were dosed with CDDO-IM (200 nM) in DMSO for 0.5, 1,3,6 and 24 hr with DMSO used as control with a 6 hr exposure to this vehicle.

tag: cell type

value: HUVEC

value: 10 Pooled mixed gender

value: newborn


title: Control PRO 24h 12h 4


title: 24h_3

description: Gene expression after 24h after dosing with 200 nM CDDO

tag: age


title: MCF-7 replicate 2

description: Control


title: MCF-7 replicate 1

description: Control


title: 24h_2


title: 24h_1


title: 6h_2


title: 6h_3


title: TNBC tissue 1

description: lncRNA and mRNA expression


title: Control PRO 24h 12h 3


title: ES-4-rep2 [miRNA]

city: Bethesda

first: Eric

last: Polley

address: 9609 Medical Center Drive, Rm 5W118

institute: National Cancer Institute

hyb_protocol: Samples were hybridized for 16 hrs to NanoString human miRNA probeset, which contains probe pairs specific for each miRNA with different fluorescent barcode labels. The probe pair consists of a Reporter Probe, which carries the fluorescent signal on its 5' end, and a Capture Probe which carries a biotin on its 3' end.  After hybridization, excess probes are washed away using a two step magnetic bead-based purification on the nCounter™ Prep Station and are immobilized in the cartridge for data collection.

scan_protocol: Data Collection is carried out in the nCounter Digital Analyzer. Digital images are processed and the barcode counts are tabulated in a RCC format.

data_processing: Data were analyzed using custom R scripts

label: fluorescence

source_name: Ewing Sarcoma

label_protocol: Total RNA (100 ng) was ligated to unique oligonuceotide tag to increase the length of the short miRNA for subsequent detection in a single reaction without amplification using NanoString kit following manufacturer’s suggested protocol.

growth_protocol: Immortalized human cell lines derived from sarcoma's were purchased from ATCC or provided by Memorial Sloan Kettering Cancer Center , Children's Oncology Group, and Pediatric Preclinical Testing Program, and grown in their recommended media supplemented with  10-20% fetal bovine serum. Flasks of cells in media were maintained in incubators with 95% air and 5% CO2 at 37 degrees C, and passaged as the cells reached 70-90% confluency.

extract_protocol: Cells were grown in flasks to approximately 70% confluency, detatched with trypsin, and then total  RNA (including miRNA) extracted  using Qiagen miRNeasy  mini-kit according to manufacturers instructions. Quality of RNA was assessed using an Agilent 2100 Bioanalyzer and all samples were of good quality with RIN# > 8.

value: human Ewing Sarcoma cell line


title: 24h_4


title: 3h_4

description: Gene expression after 3h after dosing with 200 nM CDDO


title: 3h_3


title: Control PRO 24h 12h 1

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

institute: US EPA

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.


title: A-204-rep2 [miRNA]

source_name: Rhabdoid Tumor

value: human Rhabdoid Tumor cell line


title: Control KTC Phase3 96h 5

value: rnaL


title: Control PRO 24h 12h 2


title: Hs 819.T [miRNA]

source_name: Chonodrosarcoma

value: human Chonodrosarcoma cell line


title: 1h_1

description: Gene expression after 1h after dosing with 200 nM CDDO


title: Hs 93.T [miRNA]

source_name: Fibrosarcoma

value: Hs 93.T

value: human Fibrosarcoma cell line


title: Hs 414.T [miRNA]


title: 6h_1


title: 0.5h_2

description: Gene expression after 0.5h after dosing with 200 nM CDDO


title: 3h_2


title: 1h_2


title: 3h_1


title: Control KTC Phase3 96h 4


title: 1h_4


title: 1h_3


title: DMSO_3

description: Gene expression after 6hr DMSO


title: Control KTC Phase3 96h 1


title: 0.5h_1


title: 0.5h_4


title: Hs 729 [miRNA]

source_name: Rhabdosarcoma

value: human Rhabdosarcoma cell line


title: Hs 132.T [miRNA]

source_name: Spindle Cell Sarcoma

value: human Spindle Cell Sarcoma cell line


title: Control KTC Phase3 96h 2

value: ovary


title: DMSO_4

description: Gene expression after 6hr DMSO


title: Control KTC Phase3 96h 3


title: Rh28 PX11/LPAM [miRNA]

value: Rh28 PX11/LPAM


title: Control KTC Phase3 8d-8dp 5

value: in water control

value: 8 d exposure, 8 d depuration


title: Control KTC Phase3 8d-8dp 4


title: DMSO_1

description: Gene expression after 6hr DMSO


title: KHOS-312H [miRNA]

source_name: Osteosarcoma

value: human Osteosarcoma cell line


title: Control KTC Phase3 8d-8dp 2

source_name: ovary tissue,fish in water control


title: Hs 706.T [miRNA]

source_name: Giant Cell Sarcoma

value: human Giant Cell Sarcoma cell line


title: Control KTC Phase3 8d-8dp 3


title: DMSO_2

description: Gene expression after 6hr DMSO

value: HUVEC


title: Pimary mPTECs on cultur dish_Day 3_rep1

city: Tainan

first: Ming-Jer

last: Tang

address: 82-0735, 7F, Department of Physiology, No.1 University Road, National Cheng-Kung University Medical College, Tainan, Taiwan

department: Department of Physiology

country: Taiwan

institute: National Cheng Kung University

description: Gene expression of mPTECs after  3 day culture

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mPTECs, Day 3, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The freshly isolated mPTECs were cultured on dishes and maintained in DMEM/F12 medium supplemented with 1 × insulin-transferrin-selenium, 1 × MEM non-essential amino acids, 0.1 M hydrocortisone (Invitrogen), 100 IU/ml penicillin, 100 μg/ml streptomycin, and 1% FBS. The cultures were incubated for 1 or 3 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA, obtained from the mPTECs, were purified using TRIzol reagent (Invitrogen-Molecular Probes, Carlsbad, CA) according to the manufacturer’s instructions. RNA obtained from freshly isolated mPTECs and mPTECs cultured on culture dishes for one and three days were purified and quantified by OD260nm by a ND-1000 spectrophotometer (Nanodrop Technology, Wilmington, DE, USA) then qualitied by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) with RNA 6000 nano labchip kit.

treatment_protocol: The freshly isolated mPTECs were cultured on dishes for 0, 1, and 3 days.

value: kidney

value: male

value: mPTEC

value: 1 month


title: KHOS-240S [miRNA]


title: Pimary mPTECs on cultur dish_Day 1_rep1

description: Gene expression of mPTECs after  1 day culture

source_name: mPTECs, Day 1, replicate 1


title: Pimary mPTECs on cultur dish_Day 0_rep1

description: Gene expression of freshly isolated mPTECs

source_name: mPTECs, Day 0, replicate 1


title: 9h_DRG_2

city: Nantong

first: Shiying

last: Li

state: Jiangsu

address: 19 Qixiu Road

institute: Nantong University

description: Gene expression after 9hr in DRG

hyb_protocol: Total RNA was amplified and labeled using a Low Input Quick Amp Labeling Kit (Agilent technologies). Labeled cRNA were further purified by RNeasy Mini kit. The quality of the labeled cRNA was again verified, and the absolute concentration was measured using a Nanodrop ND1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

scan_protocol: The arrays were scanned by Agilent Microarray Scanner (Agilent Technologies) and the subsequent data compiled with Agilent feature extraction software.

data_processing: Array normalizations and error detection were performed using Silicon Genetics’ GeneSpring GX Version 10.0 (Agilent Technologies) via the enhanced Agilent feature extraction import preprocessor. Values of poor quality intensities and low dependability were removed according to a “filter on flags” feature

organism: Rattus norvegicus

source_name: DRG, 9hr, replicate 2

label_protocol: Qualified total RNA was amplified and labeled with a Low Input Quick Amp Labeling Kit (Agilent technologies). After further purification with RNeasy Mini kit (Qiagen, Valencia, CA), the labeled cDNA was quantified by determining the absorbance at 260 nm with a Nanodrop ND1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE)

growth_protocol: Twenty-four Sprague-Dawley (SD) rats (180–220 g) were provided by the Experimental Animal Center of Nantong University and randomly divided into four groups (six per group) to undergo sciatic neurectomy.

extract_protocol: Total RNA was extracted from DRG samples with Trizol kit (Life technologies, Carlsbad, CA) as per the manufacturer’s protocols. RNA quality of each sample was determined using an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA). Qualified total RNA was purified using RNeasy Mini Kit (QIAGEN, GmBH, Germany)

treatment_protocol: Each animal was anaesthetized by an intraperitoneal injection of complex narcotics (85 mg/kg trichloroac etaldehyde monohydrate, 42 mg/kg magnesium sulfate, 17 mg/kg sodium pentobarbital), and the sciatic nerve was identified and lifted through an incision on the lateral aspect of the mid-thigh of the left hind limb. A 1 cm long segment of sciatic nerve was then resected at the site just proximal to the division of tibial and common peroneal nerves, and the incision sites were then closed. To minimize discomfort and possible painful mechanical stimulation, the rats were housed in temperature- and humidity-controlled large cages with sawdust bedding after surgery. Animals were allowed free access to water and food. Animal experimentation was carried out in accordance with the NIH Guidelines for the care and use of laboratory animals (http://oacu.od.nih.gov/regs/index.htm) and ethically approved by the Administration Committee of Experimental Animals, Jiangsu Province, China (Approval ID: SYXK(SU)2007-0021).

value: DRG

tag: time

value: sciatic nerve resection


title: 9h_DRG_1

description: Gene expression after 9hr in DRG

source_name: DRG, 9hr, replicate 1

tag: tissue


title: ES-6 [miRNA]

value: human Ewing Sarcoma cell line


title: 9h_DRG_3

description: Gene expression after 9hr in DRG

source_name: DRG, 9hr, replicate 3


title: ES-2 [miRNA]


title: 6h_DRG_3

description: Gene expression after 6hr in DRG

source_name: DRG, 6hr, replicate 3


title: 6h_DRG_2

description: Gene expression after 6hr in DRG

source_name: DRG, 6hr, replicate 2


title: Control KTC Phase3 8d-8dp 1

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 µm resolution

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

tag: age (month)

value: rnaL


title: 6h_DRG_1

description: Gene expression after 6hr in DRG

source_name: DRG, 6hr, replicate 1

tag: treatment


title: 3h_DRG_3

description: Gene expression after 3hr in DRG

source_name: DRG, 3hr, replicate 3


title: Control KTC Phase3 8d-1dp 5

value: 8 d exposure, 1 d depuration


title: 3h_DRG_1

description: Gene expression after 3hr in DRG

source_name: DRG, 3hr, replicate 1


title: 3h_DRG_2

description: Gene expression after 3hr in DRG

source_name: DRG, 3hr, replicate 2


title: Control KTC Phase3 8d-1dp 3


title: 0.5h_DRG_2

description: Gene expression after 0.5hr in DRG

source_name: DRG, 0.5hr, replicate 2


title: 0.5h_DRG_3

description: Gene expression after 0.5hr in DRG

source_name: DRG, 0.5hr, replicate 3


title: 0.5h_DRG_1

description: Gene expression after 0.5hr in DRG

source_name: DRG, 0.5hr, replicate 1


title: CHLA-258 [miRNA]

source_name: Ewing Sarcoma


title: CHLA-32 [miRNA]


title: CHA-59 [miRNA]

source_name: Osteosarcoma


title: CHLA-25 [miRNA]


title: Control KTC Phase3 8d-1dp 2

source_name: ovary tissue,fish in water control


title: JJ012 [miRNA]

source_name: Chondrosarcoma

value: human Chondrosarcoma cell line


title: Control KTC Phase3 8d-1dp 1

value: ovary


title: TamR-1 replicate 2

description: Test


title: control biological replicate 3

city: Portland

first: Tamilla

last: Nechiporuk

state: OR

address: 3181 Sam Jackson Park Road

department: Vollum

institute: OHSU

description: control biological replicate 3

hyb_protocol: As per Affymetrix manufacture protocol

scan_protocol: As per Affymetrix manufacture protocol

data_processing: RMA normalization method, Rbioconductor

source_name: E12.5 mouse brain

label_protocol: As per Affymetrix manufacture protocol

growth_protocol: embryo to E12.5

extract_protocol: RNA was extracted using Trizol with subsequent Qiagen RNA purification column

treatment_protocol: tissue dissected fresh

value: brain

value: E12.5 embryo

tag: genotype/variation

value: Rest GTi/Gti


title: control biological replicate 2

description: control biological replicate 2


title: control biological replicate 1

description: control biological replicate 1


title: SkMC [miRNA]

source_name: Normal human skeletal muscle

value: SkMC

value: Normal human skeletal muscle


title: control biological replicate 4

description: control biological replicate 4


title: Control KTC Phase3 8d-1dp 4

value: in water control

tag: treatment duration


title: knockout biological replicate 3

description: knockout biological replicate 3

value: Nestin Cre+, Rest GTi/GTi


title: knockout biological replicate 2

description: knockout biological replicate 2


title: Control KTC Phase3 8d-16dp 3

value: 8 d exposure, 16 d depuration

tag: experiment


title: Control KTC Phase3 8d-16dp 4

tag: sampling date


title: Control KTC Phase3 8d-16dp 1

tag: scan date


title: knockout biological replicate 1

description: knockout biological replicate 1


title: Control KTC Phase3 8d-16dp 2


title: MCF7.ATRA.24hr rep3

city: Chicago

first: Yuwen

last: Liu

state: IL

address: 900 East 57th Street. KCDB building. Room 10250

department: Human Genetics

institute: University of Chicago

description: Gene expression after 24hr treatment or control

hyb_protocol: 1.65g labled cRNA was hybridized to Agilent Whole Genome Oligo Microarrays (G4112F).

scan_protocol: Hybridized microarrays were scanned using a GenePix 4000B scanner (Molecular Devices) at 5 μm resolution

data_processing:
Raw data was background-subtracted and quantile-normalized by LIMMA
Differentially expressed genes were identified with a Benjamini-Hochberg (BH) corrected FDR<0.05. All experiments were done in triplicates

source_name: MCF-7, 100nM ATRA  rep3

label_protocol: Cy3 labled cRNA was prepared from 1ug mRNA using the Agilent Low RNA Input Linear Amplification Kit PLUS (One-Color), labled cRNA was purified from Rneasy mini elute Kits.

growth_protocol: LNCaP cells were grown in RPMI medium with 10% FBS and antibiotics.

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen). The integrity of the RNA was monitored by Bioanalyzer 2100

treatment_protocol: LNCaP cells were starved in phenol-free RPMI medium supplemented with 10% charcoal-stripped FBS for 3 days followed by treatments.

tag: cell line

value: 100nM ATRA


title: MCF7.ATRA.24hr rep2

source_name: MCF-7, 100nM ATRA  rep2


title: knockout biological replicate 4

description: knockout biological replicate 4


title: MCF7.AM580.24hr rep2

source_name: MCF-7, 100nM AM580  rep1


title: NHOst [miRNA]

source_name: Normal human osteoblast

value: NHOst

value: Normal human osteoblast


title: NHDF [miRNA]

source_name: Normal human dermal fibroblast

value: NHDF

value: Normal human dermal fibroblast


title: hMSC [miRNA]

source_name: Normal human mesenchymal stem cell

value: hMSC

value: Normal human mesenchymal stem cell


title: NHAC-kn [miRNA]

source_name: Normal human chondrocyte

value: NHAC-kn

value: Normal human chondrocyte


title: Control KTC Phase3 8d 5

growth_protocol: Sexually mature adult fathead minnows (5-6 month old) were obtained from an on-site aquatic culture facility at the US EPA Mid-Continent Ecology Division, Duluth, MN, USA. Fish were held under a 16:8 light:dark photoperiod fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3), and dissolved oxygen (mean ± SD; 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups.

value: ovary

value: 8 d

tag: rna date

value: rnaL


title: MCF7.AM580.24hr rep1


title: MCF7.control.0hr rep2

source_name: MCF-7, control rep2

value: control


title: Control KTC Phase3 8d 4

tag: rna person


title: Control KTC Phase3 8d 3

tag: chip id


title: MCF7.AM580.24hr rep3


title: SK-ES-1 [miRNA]

value: human Ewing Sarcoma cell line


title: MCF7.control.0hr rep3

source_name: MCF-7, control rep3


title: MCF7.ATRA.24hr rep1

source_name: MCF-7, 100nM ATRA  rep1


title: VD3_sp_control.24hr rep3

source_name: Prostasphere, control for calcitriol, rep3

tag: sample type

value: Prostasphere

value: control for calcitriol


title: MCF7.control.0hr rep1

source_name: MCF-7, control rep1


title: VA-ES-BJ [miRNA]

source_name: Epitheloid

value: VA-ES-BJ

value: human Epitheloid cell line


title: MHM-25 [miRNA]

source_name: Sarcoma

value: human Sarcoma cell line


title: KHOS NP [miRNA]

source_name: Osteosarcoma

value: KHOS NP

value: human Osteosarcoma cell line


title: VD3_sp_control.24hr rep1

source_name: Prostasphere, control for calcitriol, rep1


title: Control KTC Phase3 4d-1dp 5

source_name: ovary tissue,fish in water control

value: in water control

value: 4 d exposure, 1 d depuration


title: VD3_sp.24hr rep2

source_name: Prostasphere, 100nM calcitriol, rep2

value: 100nM calcitriol


title: VD3_sp.24hr rep3

source_name: Prostasphere, 100nM calcitriol, rep3


title: Control KTC Phase3 4d-1dp 4


title: VD3_sp_control.24hr rep2

source_name: Prostasphere, control for calcitriol, rep2


title: VD3_sp.24hr rep1

source_name: Prostasphere, 100nM calcitriol, rep1


title: Control KTC Phase3 8d 1


title: 0.5h_3

value: HUVEC

tag: gender

value: 10 Pooled mixed gender

value: newborn


title: ATRA_sp.24hr rep3

source_name: Prostasphere, 100nM ATRA, rep3

value: 100nM ATRA


title: ES-4-rep [miRNA]

source_name: Ewing Sarcoma

tag: cell type


title: ATRA_sp_control.24hr rep1

source_name: Prostasphere, control for ATRA, rep1

value: control for ATRA


title: A-204-rep [miRNA]

source_name: Rhabdoid Tumor

value: human Rhabdoid Tumor cell line


title: ATRA_sp.24hr rep2

source_name: Prostasphere, 100nM ATRA, rep2


title: ATRA_sp_control.24hr rep3

source_name: Prostasphere, control for ATRA, rep3


title: ATRA_sp_control.24hr rep2

source_name: Prostasphere, control for ATRA, rep2


title: Control KTC Phase3 4d-1dp 3

value: ovary

value: rnaL


title: ATRA_sp.24hr rep1

source_name: Prostasphere, 100nM ATRA, rep1

value: Prostasphere


title: Control KTC Phase3 4d-1dp 2


title: LS141 [miRNA]

source_name: Dedifferentiated liposarcoma

value: human Dedifferentiated liposarcoma cell line


title: DDLS [miRNA]

value: DDLS


title: PPARG.24hr rep1

source_name: LNCaP,  100nM Troglitazone, rep1

value: LNCaP

value: 100nM Troglitazone


title: L_P.DMSO.24hr rep3

source_name: LNCaP,  control for T0901417, rep3

value: control for T0901417


title: PPARG.24hr rep2

source_name: LNCaP,  100nM Troglitazone, rep2


title: Control KTC Phase3 24h 5

source_name: ovary tissue,fish in water control

value: in water control


title: Control KTC Phase3 4d-1dp 1

value: 4 d exposure, 1 d depuration


title: SYO-1 [miRNA]

source_name: Synovial Sarcoma

value: human Synovial Sarcoma cell line


title: Control KTC Phase3 24h 4


title: LXR.24hr rep3


title: LXR.24hr rep1


title: PPARG.24hr rep3

source_name: LNCaP,  100nM Troglitazone, rep3


title: L_P.DMSO.24hr rep1

source_name: LNCaP,  control for T0901417, rep1


title: SK-UT-1B [miRNA]

source_name: Leiomyosarcoma

value: human Leiomyosarcoma cell line


title: L_P.DMSO.24hr rep2

source_name: LNCaP,  control for T0901417, rep2


title: Control KTC Phase3 24h 2


title: VD3.24hr rep2

source_name: LNCaP,  100nM calcitriol, rep2

value: 100nM calcitriol


title: HSSY-II [miRNA]

value: HSSY-II


title: Rh28 [miRNA]

source_name: Rhabdosarcoma

value: human Rhabdosarcoma cell line


title: ST8814 [miRNA]

source_name: Malignant peripheral nerve sheath

value: human Malignant peripheral nerve sheath cell line


title: Control KTC Phase3 1d-1dp 5

value: 1 d exposure, 1 d depuration


title: Control KTC Phase3 24h 3

value: ovary


title: Control KTC Phase3 24h 1

value: rnaL


title: VD3.EtOH.24hr rep1

source_name: LNCaP,  control for calcitriol, rep1

value: control for calcitriol


title: Control KTC Phase3 8d 2

value: 8 d


title: VD3.24hr rep1

source_name: LNCaP,  100nM calcitriol, rep1


title: VD3.24hr rep3

source_name: LNCaP,  100nM calcitriol, rep3


title: LXR.24hr rep2


title: VD3.EtOH.24hr rep2

source_name: LNCaP,  control for calcitriol, rep2


title: Control KTC Phase3 1d-1dp 3


title: Control KTC Phase3 1d-1dp 4


title: VD3.EtOH.24hr rep3

source_name: LNCaP,  control for calcitriol, rep3


title: DHT.24hr rep3

source_name: LNCaP, 10nM DHT, rep3

value: 10nM DHT


title: DHT.24hr rep1

source_name: LNCaP, 10nM DHT, rep1

value: LNCaP


title: DHT.24hr rep2

source_name: LNCaP, 10nM DHT, rep2


title: DHT.Control.24hr rep3

source_name: LNCaP, control for DHT, rep3

value: control for DHT


title: Control KTC Phase3 1d-1dp 2

source_name: ovary tissue,fish in water control


title: DHT.Control.24hr rep1

source_name: LNCaP, control for DHT, rep1


title: ATRA.24hr rep3

source_name: LNCaP, 100nM ATRA, rep3

value: 100nM ATRA


title: ATRA.24hr rep2

source_name: LNCaP, 100nM ATRA, rep2


title: MPNST [miRNA]

value: MPNST


title: Control KTC Phase3 1d-1dp 1

value: in water control


title: CHP-100 [miRNA]

source_name: Ewing Sarcoma

value: human Ewing Sarcoma cell line


title: SK-LMS-1 [miRNA]

source_name: Leiomyosarcoma

value: human Leiomyosarcoma cell line


title: SK-UT-1 [miRNA]


title: Rh18 [miRNA]

source_name: Rhabdosarcoma


title: U-2 OS [miRNA]

source_name: Osteosarcoma

value: U-2 OS

value: human Osteosarcoma cell line


title: TC-32 [miRNA]


title: TC-71 [miRNA]


title: Control KTC 0-12h 8h 2

value: 8 h


title: Control KTC 0-12h 8h 3


title: Control KTC 0-12h 8h 4


title: ATRA.Control.24hr rep2

source_name: LNCaP, control for ATRA, rep2

value: control for ATRA


title: Control KTC 0-12h 6h 4

value: 6 h


title: ATRA.Control.24hr rep3

source_name: LNCaP, control for ATRA, rep3


title: ATRA.Control.24hr rep1

source_name: LNCaP, control for ATRA, rep1


title: AM580.24hr rep3

source_name: LNCaP, 100nM AM580, rep3


title: Control KTC 0-12h 8h 1

value: ovary


title: AM580.24hr rep1

source_name: LNCaP, 100nM AM580, rep1


title: AM580.DMSO.24hr rep2

source_name: LNCaP, control for AM580, rep2

value: control for AM580


title: ATRA.24hr rep1

source_name: LNCaP, 100nM ATRA, rep1


title: Control KTC 0-12h 6h 3

value: rnaL


title: RA.24hr rep2

source_name: LNCaP, 100nM 9-cis-RA, rep2

value: 100nM 9-cis-RA


title: AM580.24hr rep2

source_name: LNCaP, 100nM AM580, rep2


title: SW 684 [miRNA]

source_name: Fibrosarcoma

value: human Fibrosarcoma cell line


title: SW 1353 [miRNA]

source_name: Chondrosarcoma

value: human Chondrosarcoma cell line


title: SW 982 [miRNA]

source_name: Synovial Sarcoma

value: human Synovial Sarcoma cell line


title: SK-N-MC [miRNA]

value: SK-N-MC


title: DHT.Control.24hr rep2

source_name: LNCaP, control for DHT, rep2

value: LNCaP

value: control for DHT


title: Control KTC 0-12h 6h 2

source_name: ovary tissue,fish in water control

value: in water control


title: SJSA-1 [miRNA]


title: RA.24hr rep1

source_name: LNCaP, 100nM 9-cis-RA, rep1


title: RA.EtOH.24hr rep3

source_name: LNCaP,control for 9-cis-RA, rep3

value: control for 9-cis-RA


title: AM580.DMSO.24hr rep1

source_name: LNCaP, control for AM580, rep1


title: SJCRH30(RMS 13) [miRNA]

source_name: Rhabdosarcoma

value: SJCRH30(RMS 13)

value: human Rhabdosarcoma cell line


title: Control KTC 0-12h 4h 4

value: 4 h


title: Control KTC 0-12h 6h 1


title: Donor 5 - 09FC49 - 80% confluence - mAdbID:107843

first: Jiaqiang

last: Ren

address: 9000 Rockville Pike

institute: National Institutes of Health

description: mAdb experiment ID: 107843

hyb_protocol: Agilent Hybridization Protocol Solution: 2x GEx Hybridization Buffer HI-RPM Blocking agent: 10x Blocking Agent Wash procedure: The hybridization gaskets were dissembled in GE Wash Buffer 1, washed in GE Wash Buffer 1 for 1 min at room temperature, and then washed in GE Wash Buffer 2 for 1 min at 37 C. Qty. of labeled target: 750 ng Time: 16 hours 825 ng of amplified cRNA were pooled, fragmented and then hybridized on 4x44K microarrays (Agilent) for 17 hours at 65 C.

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505B US45103062

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html ). Spots with signal intensity less than 20 in both channels were filtered out. If the signal intensity was less than 20 in one channel only, it was set to 20 in computing the log-ratio value. Global median normalization was performed on the filtered data by subtracting out the median log-ratio for each array.
FeatureExtractor_Version: 9.5.1.1
Protocol_Name: GE2-v5_95_Feb07 (Read Only)

source_name: Stratagene Universal Human Reference RNA

label_protocol:
Cy3 Labeling Protocol
Label amount: 500 ng
Human tissue RNA (Agilent, Santa Clara, CA) was amplified and labeled with Cy3-CTP using Agilent Quick Amp Labeling kit (Agilent, Santa Clara, CA).

extract_protocol: Agilent RNA Extraction

value: Composed of total RNA from nine human tissues or cell lines:placental tissue, adult liver tissue, adult brain tissue, adult heart tissue, adult breast tissue, adult colon tissue, adult testis tissue, fetal brain tissue, testis cell line.

source_name: Donor 5 - 09FC49

label_protocol:
Cy5 Labeling Protocol
Label amount: 500 ng
Total RNA (0.5 μg) was amplified and labeled with Cy5-CTP using Quick Amp Labeling kit (Agilent, Santa Clara, CA).

extract_protocol:
Qiagen miRNeasy Mini Kit Protocol
The total RNA was extracted using columns in Qiagen miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using Nano Drop 2000 (Thermo Scientific, Wilmington, DE) with A260/A280 ratios > 2.0 after dilution in DEPC water.

treatment_protocol: In-vitro treatment: Bone marrow collection and BMSC culture were performed. Passage 2 BMSCs from 7 consenting donors were thawed from a working cell bank and plated at a density of 3 x 103/cm2 in T-75 flasks (Corning Life Sciences, Corning, NY), the cells were cultured to passage 3 with complete culture medium [alpha MEM with 2 mM glutamine (Lonza, Walkersville, MD, USA), supplemented with 20% lot-selected FBS (Hyclone, Thermo Fischer Scientific, Waltham, MA) and 10 ug/ml Gentamicin]. Upon reaching 80% confluence, passage 3 BMSCs were lifted by TryPLE Express (Invitrogen, Life Technologies, Grand Island, NY) and sub-cultured at the same density. When the cells reached 50%, 80% and 100% confluence as determined by microscope observation, they were harvested.

value: Bone Marrow

value: Bone Marrow Stromal Cell (BMSC)

tag: individual


title: SAOS-2 [miRNA]

source_name: Osteosarcoma

value: human Osteosarcoma cell line


title: Rh41 [miRNA]


title: Donor 5 - 09FC49 - 100% confluence - mAdbID:107842

description: mAdb experiment ID: 107842


title: Control KTC 0-12h 4h 3

value: ovary

value: rnaL


title: Donor 4 - 09FC45 - 80% confluence - mAdbID:107838

description: mAdb experiment ID: 107838

source_name: Donor 4 - 09FC45


title: Control KTC 0-12h 4h 2


title: Donor 5 - 09FC49 - 50% confluence - mAdbID:107836

description: mAdb experiment ID: 107836


title: Control KTC 0-12h 4h 1


title: Donor 4 - 09FC45 - 50% confluence - mAdbID:107839

description: mAdb experiment ID: 107839


title: Donor 3 - 09FC44 - 80% confluence - mAdbID:107833

description: mAdb experiment ID: 107833

source_name: Donor 3 - 09FC44


title: RA.24hr rep3

source_name: LNCaP, 100nM 9-cis-RA, rep3

value: 100nM 9-cis-RA


title: Donor 3 - 09FC44 - 50% confluence - mAdbID:107834

description: mAdb experiment ID: 107834


title: Donor 2 - 09FC43 - 100% confluence - mAdbID:107835

description: mAdb experiment ID: 107835

source_name: Donor 2 - 09FC43


title: RA.EtOH.24hr rep1

source_name: LNCaP, control for 9-cis-RA, rep1


title: Control KTC 0-12h 2h 4

value: 2 h


title: AM580.DMSO.24hr rep3

source_name: LNCaP, control for AM580, rep3

value: control for AM580


title: Donor 1 - 09FC37 - 80% confluence - mAdbID:107831

description: mAdb experiment ID: 107831

source_name: Donor 1 - 09FC37


title: Donor 3 - 09FC44 - 100% confluence - mAdbID:107832

description: mAdb experiment ID: 107832


title: Donor 4- 09FC45 - 100% confluence - mAdbID:107837

description: mAdb experiment ID: 107837


title: Donor 1 - 09FC37 - 100% confluence - mAdbID:107830

description: mAdb experiment ID: 107830


title: Control KTC 0-12h 2h 3


title: RD-ES [miRNA]

source_name: Ewing Sarcoma

value: RD-ES

value: human Ewing Sarcoma cell line


title: Rh30 [miRNA]


title: RD [miRNA]

value: RD


title: Control KTC 0-12h 2h 1

value: in water control


title: RA.EtOH.24hr rep2

source_name: LNCaP, control for 9-cis-RA, rep2

value: LNCaP

value: control for 9-cis-RA


title: Rh36 [miRNA]

value: human Rhabdosarcoma cell line


title: Donor 2 - 09FC43 - 80% confluence - mAdbID:107828

description: mAdb experiment ID: 107828


title: Control KTC 0-12h 2h 2

source_name: ovary tissue,fish in water control


title: MHM-8 [miRNA]

source_name: Sarcoma

value: human Sarcoma cell line


title: Control KTC 0-12h 1h 3

value: 1 h


title: Control KTC 0-12h 1h 4


title: Donor 2 - 09FC43 - 50% confluence - mAdbID:107829

description: mAdb experiment ID: 107829

value: Composed of total RNA from nine human tissues or cell lines:placental tissue, adult liver tissue, adult brain tissue, adult heart tissue, adult breast tissue, adult colon tissue, adult testis tissue, fetal brain tissue, testis cell line.

value: Bone Marrow


title: MES-SA Dx5 [miRNA]

source_name: Uterine Sarcoma

value: MES-SA Dx5

value: human Uterine Sarcoma cell line


title: MES-SA [miRNA]

value: MES-SA


title: human PBMC patient canakinumab ind5

city: Nijmegen

first: Heleen

last: de Koning

state: Gelderland

address: Geert Grooteplein-Zuid 10

country: Netherlands

institute: Radboudumc

description: SAMPLE 11

hyb_protocol: 750 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT‐12 v4. Hybridization was done according to the Illumina protocol: ”Whole‐Genome Gene Expression Direct Hybridization Assay.

scan_protocol: The samples were scanned using the Illumina iScan array scanner. Scanning was done according to the Illumina protocol: ”Whole‐Genome Gene Expression Direct Hybridization Assay.

data_processing: Partek Genomics Suite Software (Version 6.4; Partek, Inc., St Louis, MO) was used to perform a quantile normalization, and a batch correction for the factor individual.

source_name: PBMC

label_protocol: The Illumina TotalPrep‐96 RNA Amplification Kit was used to generate Biotin labeled (biotin‐16‐UTP), amplified cRNA starting from 200ng total RNA.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were directly isolated and frozen upon blood sampling.

extract_protocol: RNA was extracted using the Rneasy kit (Qiagen).

treatment_protocol: Patients were in vivo either treated with anakinra 100mg daily, canakinumab 150mg monthly, or no treatment (nil/none).

tag: disease state

value: Schnitzler’s syndrome

tag: group

value: patient

value: canakinumab

value: PBMC


title: human PBMC patient canakinumab ind6

description: SAMPLE 12


title: OHS [miRNA]

value: OHS

value: human Osteosarcoma cell line


title: Control KTC 0-12h 1h 2

treatment_protocol:
To initiate a typical experiment, four males and four females were placed together in a glass test tank holding 10 L of Lake Superior water (4 µM filtered, UV sterilized) or test chemical dissolved in Lake Superior water, which was continuously renewed at a rate of about 45 mL/min. There were two such tanks for each treatment condition. The animals were held at 25 +/- 0.5 °C under a 16:8 L:D photoperiod, and were fed brine shrimp to satiation twice per day.
chemical abbreviations: BPA, bisphenol-A; EE2, 17a-ethynyl estradiol; FAD, fadrozole; FLU, flutamide; GEM, Gemfibrozil; KTC, ketoconazole; PRO,prochloraz; RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine; TB, 17 -trenbolone; TNT, 2,4,6-trinitrotoluene; TRI,trilostane; VIN, vinclozolin; WLSSD, effluent from Western Lake Superior Sanitary District

tag: tissue

value: ovary

tag: age (month)

value: in water control

value: rnaL


title: human PBMC patient anakinra ind6

description: SAMPLE 9

tag: treatment

value: anakinra


title: Donor 1 - 09FC37 - 50% confluence - mAdbID:107824

description: mAdb experiment ID: 107824

value: Bone Marrow Stromal Cell (BMSC)


title: human PBMC patient canakinumab ind4

description: SAMPLE 10


title: human PBMC patient anakinra ind4

description: SAMPLE 7


title: human PBMC patient anakinra ind5

description: SAMPLE 8


title: human PBMC patient none ind4

description: SAMPLE 4


title: Control KTC 0-12h 1h 1

tag: treatment duration

value: 1 h


title: Control KTC 0-12h 12h 4

tag: experiment


title: human PBMC control ind3

description: SAMPLE 3

value: control


title: Control KTC 0-12h 12h 3

tag: sampling date


title: human PBMC patient none ind6

description: SAMPLE 6


title: human PBMC patient none ind5

description: SAMPLE 5


title: human PBMC control ind2

description: SAMPLE 2


title: HT-1080 [miRNA]

source_name: Fibrosarcoma

value: human Fibrosarcoma cell line


title: human PBMC control ind1

description: SAMPLE 1


title: Hu09 [miRNA]


title: HOS [miRNA]

value: HOS


title: G-401 [miRNA]

source_name: Rhabdoid Tumor

value: human Rhabdoid Tumor cell line