title: 86C

description: MicroRNA expression profiles in colorectal tissue

hyb_protocol: Resuspend the dried sample in 18μl of nuclease-free water. Add 4.5μl 10x GE Blocking Agent and 22.5μl 2x Hi-RPM Hybridization Buffer to each sample for a total of 45μl. Mix well and incubate at 100°C for 5 minutes, then immediately transfer to an ice water bath for 5 minutes. Quickly spin in a centrifuge and hybridize to Agilent 8×16K Human miRNA Microarray V3 (G4470C) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent p/n 5188-5325) and 5 minute with 37°C GE Wash buffer 2 (Agilent p/n 5188-5326).

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for AgilentHD_miRNA (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 5%, dynamic range is extended).

data_processing: The scanned images were analyzed with the Agilent's Feature Extraction Software (v10.5)  using default parameters (protocol miRNA_105_Dec08 and Grid 021827_D_F_20100604) to obtain background subtracted and spatially detrended processed signal intensities. For miRNA raw data, quantile normalization was performed by R project.

label_protocol: 100ng total RNA, including miRNAs, were labeled using the miRNA Complete Labeling and Hyb Kit (Agilent, p/n 5190-0456) according to the manufacturer's instructions. After the 16°C labeling reaction,completely dry the samples using a vacuum concentrator.


title: 95C

status: Public on Oct 16 2015

type: RNA

city: Beijing

first: Xiaoyu

last: Shi

address: Chao Yang District Pan Jia Yuan Nan Li No.17

department: Cancer Institute (Hospital)

country: China

institute: Peking Union Medical College and Chinese Academy of Medical Sciences

molecule: total RNA

organism: Homo sapiens

source_name: Colorectal adenocarcinoma

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s specifications, and purified by the RNeasy mini Kit (Cat No.74106, Qiagen, Germany). RNA integrity was detected using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA concentration was determined using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: Colorectal epithelial neoplasms were obtained from patients undergoing polypectomy, and colorectal normal mucosae were obtained from patients with hemorrhoid undergoing surgical excision. Fresh tissue samples were frozen in liquid nitrogen after surgery and stored at -80℃ for subsequent molecular analysis.

tag: gender

value: Male

tag: age(years)

tag: pathologic grade

value: Adenocarcinoma

tag: ptnm


title: 56C

description: Gene expression in colorectal tissue

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3 per ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with 37°C GE Wash buffer 2 (Agilent p/n 5188-5326).

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100% and 10%, dynamic range is extended).

data_processing: The scanned images were analyzed with the Agilent's Feature Extraction Software (v10.5)  using default parameters (protocol GE1_105_Dec08 and Grid 014850_D_20070207) to obtain background subtracted and spatially detrended processed signal intensities. The raw data was normalized by the GenespringGX Software (Agilent, version 11.5).

label_protocol: 500ng purified total RNA was reverse transcribed into cDNA, transcribed into cRNA and labeled with Cyanine-3 (Cy3) using the Agilent’s Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

value: Female


title: 76C


title: 81C


title: 72C


title: 61C


title: Fibro-Control-10

city: Luebeck

first: Aloysius

last: Domingo

address: Maria Goeppert Str. 1

country: Germany

institute: Institute of Neurogenetics

hyb_protocol: The labeled cRNA samples were hybridized to SurePrint G3 Human GE v2 8x60K Microarray (Design ID: 039494). Fragmentation of labeled cRNA, hybridization and washing were done following the manufacturer's instructions. Briefly, 600ng of cy3 labeled samples were fragmented and hybridized in Agilent’s SureHyb Microarray Hybridization Chambers at 65º C for 17 hours.

scan_protocol: Fluorescence signals on microarrays were detected by the SureScan Microarray Scanner (Agilent) at a resolution of 3 micron generating 20 bit TIFF files.

data_processing: Quantile normalization and averaging of mutliple probes mapping to the same Entrez genes was performed using R and the EXPANDER software.

source_name: cultured fibroblasts

label_protocol: Samples were labeled using Low Input QuickAmp Labeling Kit  (Agilent) following the manufacturer's instructions. 100 ng of total RNA was used per sample.

growth_protocol: Fibroblasts were grown from skin biopsy samples, on modified Eagle medium with 10% FBS and 1% Pen/Strep, and passaged using Accutase treatment. Harvesting was done at passages 7-9.

extract_protocol: Total RNA was extracted using manufacturer's protocols. Blood: PAXGene tubes and kits. Fibroblasts: QIAGen RNeasy kits.

treatment_protocol: None.

tag: tissue

value: cultured fibroblasts

tag: Sex

value: male

tag: genotype

value: Control


title: 53C


title: 54C


title: Fibro-Control-9


title: 40C

description: Gene expression in colorectal tissue


title: 39C

description: Gene expression in colorectal tissue


title: 49C


title: 42C

description: Gene expression in colorectal tissue


title: Fibro-Control-7


title: 44C


title: 42C


title: Fibro-Control-8


title: 37C

description: Gene expression in colorectal tissue


title: 56C


title: Fibro-Control-6


title: 41C


title: 47C


title: Fibro-Control-5


title: Fibro-Control-4


title: 36C

description: Gene expression in colorectal tissue


title: 33C

description: Gene expression in colorectal tissue


title: 35C

description: Gene expression in colorectal tissue


title: 45C


title: 38C

description: Gene expression in colorectal tissue


title: 39C


title: 40C


title: 38C


title: 37C


title: 33C


title: 35C


title: 31C


title: Fibro-Control-1


title: 28C


title: Fibro-Control-2


title: 26C


title: 36C


title: 28C

description: Gene expression in colorectal tissue


title: Fibro-XDP-14

value: XDP


title: 25C


title: 23C


title: GBMJ1 cells treated with 2Gy, collected at 1h, polysome-bound RNA, biological replicate 1

city: Bethesda

first: Philip

middle: J

last: Tofilon

state: Maryland

address: 10 Center Drive-MSC 1002

department: Radiation Oncology

country: USA

institute: NCI

description:
GBMJ1 Polysome 2Gy1h 1.
GSCs isolated from glioblastoma multiforme (GBM) surgical specimens.

hyb_protocol: cDNA was hybridized to GeneChip Human Genome U133A 2.0 Array chips (Affymetrix) per manufacturer's protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 300 7G.

data_processing: The data were analyzed with Expression Console using MAS5 normalization.

label: Biotin

source_name: GBMJ1 GSCs, 2Gy, 1h, polysome-bound RNA

label_protocol: The isolated RNA was amplified with GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: GSCs were grown at 37°C, 5%CO2/5%O2.

extract_protocol: For polysome-bound RNA, cells incubated in 100 μg of cycloheximide/mL for 15 minutes before collection. Cytoplasmic RNA was obtained by lysing cells in 1 mL of polysome buffer [15 mmol/L Tris-HCl (pH 7.5), 300 mmol/L NaCl, 15 mmol/L MgCl2, 1% Triton X100, 100 μg/mL cycloheximide, 1 mg/mL heparin, and 500 units/mL RNasin (Promega)]. After 15 minutes on ice, lysates were centrifuged (12,000 x g for 15 minutes), and the resulting cytosolic supernatant was layered onto a 10% to 50% sucrose gradient. Gradients were then centrifuged at 35,000 x g for 3 hours at 4°C and polysome-bound fractions were collected using an ISCO Density Gradient Fractionation System (ISCO, Lincoln, NE) with continuous monitoring based on A254. The RNA in each fraction was extracted using TRIzol LS (Invitrogen). Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were grown to ~80% confluence in 150-mm2 tissue culture dishes and irradiated with 2Gy and collected either 1h or 6h after irradiation. Radiation was delivered using a 320 kV X-ray machine (Precision XRay Inc.) at a dose rate of 2.3 Gy/min.

tag: cell line

tag: cell type

value: glioblastoma stem-like cells (GSCs)

tag: treatment

value: 2Gy radiation

tag: time point

tag: rna type

value: polysome-bound


title: 31C

description: Gene expression in colorectal tissue


title: Fibro-XDP-13


title: 29C

description: Gene expression in colorectal tissue


title: Fibro-XDP-15


title: 25C

description: Gene expression in colorectal tissue


title: 53C

description: Gene expression in colorectal tissue


title: 45C

description: Gene expression in colorectal tissue


title: 19C


title: 22C


title: 23C

description: Gene expression in colorectal tissue


title: Fibro-XDP-12


title: Fibro-XDP-11


title: Fibro-Control-3


title: 13C


title: 127C


title: 22C

description: Gene expression in colorectal tissue


title: 123C


title: 88A

source_name: Colorectal adenoma

value: Low-grade dysplasia


title: 119C


title: f10A

description: Gene expression in colorectal tissue

value: High-grade dysplasia


title: 85A


title: Fibro-XDP-10


title: 84A


title: 83A


title: 81A


title: 78A


title: 79A


title: f11A

description: Gene expression in colorectal tissue


title: 76A


title: Fibro-XDP-9


title: Fibro-XDP-6


title: 75A


title: 87A


title: f07A

description: Gene expression in colorectal tissue


title: Fibro-XDP-5


title: Fibro-XDP-7


title: f06A

description: Gene expression in colorectal tissue


title: f08A

description: Gene expression in colorectal tissue


title: 74A


title: Healthy control 1

city: Newcastle

first: QIAN

last: LI

address: University drive

country: Australia

institute: University of Newcastle

description: baseline

hyb_protocol: 750 ng cRNA was hybridised to Illumina Sentrix HumanRef-8 V3 Expression BeadChips (Illumina, San Diego, CA, USA) using standard protocols

scan_protocol: Each BeadChip measured the expression of 24,354 genes and was scanned using the Illumina Bead Station and captured using BeadScan 3.5.11 (Illumina)

data_processing: Sample and gene profiling results were included in the analysis if the sample was of suitable purity (OD 260/280 ratio between 1.7-2.1) and was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (correlation coefficients and priciple component analysis plots)

label: biotin

source_name: induced sputum

label_protocol: A total of 500 ng of sputum RNA was amplified and labelled with biotin-uridine triphosphate using the Total Prep RNA amplification kit as per manufacturer’s instructions (Life Technologies)

extract_protocol: RNA was extracted from induced sputum using the RNeasy Mini Kit (Qiagen, Hilden, Germany);RNA quatitation was performed using the Quanti-iT RiboGreen RNA

tag: disease state

value: healthy

tag: age

tag: bmi

tag: smoking pack-years

tag: ID


title: f05A

description: Gene expression in colorectal tissue

tag: gender


title: Fibro-XDP-8


title: Fibro-XDP-4


title: f04A

description: Gene expression in colorectal tissue

tag: age(years)


title: 80A

tag: pathologic grade


title: Fibro-XDP-3


title: f03A

description: Gene expression in colorectal tissue


title: 73A


title: 71A


title: 69A


title: Fibro-XDP-1


title: Fibro-XDP-2


title: f02A

description: Gene expression in colorectal tissue


title: 68A


title: 67A


title: 65A


title: 66A


title: 59A


title: 60A


title: 56A


title: 51A


title: 55A


title: 54A


title: 13C

description: Gene expression in colorectal tissue

tag: ptnm


title: 95A

description: Gene expression in colorectal tissue


title: 50A


title: Blood-Control-12

source_name: whole blood

tag: tissue

value: whole blood


title: Blood-Control-11

tag: Sex


title: Blood-Control-10

tag: genotype


title: Blood-Control-13


title: f01A

description: Gene expression in colorectal tissue


title: 91A

description: Gene expression in colorectal tissue


title: 88A

description: Gene expression in colorectal tissue


title: 64A


title: 87A

description: Gene expression in colorectal tissue


title: Blood-Control-8


title: 86A

description: Gene expression in colorectal tissue


title: Blood-Control-9


title: 49A


title: 48A


title: 46A


title: 45A


title: 44A


title: 41A


title: 43A


title: 81A

description: Gene expression in colorectal tissue


title: 36A


title: 35A


title: 40A


title: Blood-Control-6


title: Blood-Control-7


title: 84A

description: Gene expression in colorectal tissue


title: 26A


title: 28A


title: 83A

description: Gene expression in colorectal tissue


title: Blood-Control-5


title: Blood-Control-4


title: 25A


title: 79A

description: Gene expression in colorectal tissue


title: 76A

description: Gene expression in colorectal tissue


title: Blood-Control-3


title: 22A


title: 31A


title: 20A


title: Blood-Control-1


title: 68A

description: Gene expression in colorectal tissue


title: 69A

description: Gene expression in colorectal tissue


title: 70A

description: Gene expression in colorectal tissue


title: Blood-Control-2


title: 67A

description: Gene expression in colorectal tissue


title: Blood-XDP-9


title: Blood-XDP-8


title: 18A


title: 19A


title: 23A


title: 16A


title: 21A


title: 14A


title: 17A


title: 127A


title: 126A


title: 122A


title: 65A

description: Gene expression in colorectal tissue


title: 120A


title: 121A


title: Blood-XDP-6


title: Blood-XDP-4


title: 116A


title: 115C


title: 119A


title: Blood-XDP-5


title: 60A

description: Gene expression in colorectal tissue


title: Blood-XDP-7


title: N34

source_name: Colorectal normal mucosa

value: Normal epithelium


title: Blood-XDP-3


title: N32


title: 49C

description: Gene expression in colorectal tissue


title: 117C


title: Blood-XDP-1


title: 55A

description: Gene expression in colorectal tissue


title: N36


title: 56A

description: Gene expression in colorectal tissue


title: N31


title: Blood-XDP-2


title: N29


title: N28


title: 66A

description: Gene expression in colorectal tissue


title: N23


title: N27


title: N24


title: N22


title: VvMYBAsi_white_Berry_Shiraz_rep4

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (white phenotype), replicate 4

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Transgenic Chardonnay/Shiraz and non-transformed WT controls were all grown in the same glasshouse in CSIRO Plant Industry, Adelaide (Australia) in ambient light with a night break. Day and night temperatures were approximately 27oC and 22oC respectively.

extract_protocol: Whole berries were sampled from three independent transgenic Chardonnay and four from transgenic Shiraz lines, resulting in three and four biological replicates respectively. the samples were immediately frozen in liquid nitrogen. For skin samples, the skins were first removed from fresh berries then frozen in liquid nitrogen. All samples were stored at -80oC. Total RNA was extracted using a modified perchlorate method previously described in Boss et al. (2001).

treatment_protocol: Stable transformation of grapevines: A pART7 vector containing the VvMYBA1 cDNA sequence between a Cauliflower Mosaic Virus 35S promoter and an octopine synthase gene (OCE) transcriptional terminator (Gleave, 1992), had been previously constructed (Walker et al., 2007). This expression cassette was excised from pART7 using a NotI restriction enzyme and ligated to the plant expression vector pART27 (Gleave, 1992) to create the 35S:VvMYBA1 construct[kos036 1] . Primers A13pfxho and A13prasp (containing XhoI and Asp178 restriction sites respectively, Table S6) were used to amplify a 400 bp sense fragment from the 3’ end of the VvMYBA1 gene, and primers A13pfxba and A13prcla (containing XbaI and ClaI restriction sites respectively, Table S6) amplified the same fragment in the anti-sense direction by PCR (RED TAQ®, Invitrogen, USA). PCR cycling conditions were as follows: 94oC for 3 min followed by 35 cycles of 94oC for 30 s, 58oC for 30 s and 72oC for 2 min, then final extension at 72oC for 10 min. Fragments were ligated to pDrive (Qiagen, Netherlands), from which the sense and anti-sense fragments were excised using XhoI/Asp178 and XbaI/ClaI restriction enzymes respectively. These fragments were then sequentially ligated into the pN6 vector. The silencing cassette was excised from pN6 using a NotI restriction enzyme and this fragment was ligated into the pART27 vector to create the VvMYBA silencing (VvMYBAsi) construct. pART27 VvMYBA expression or silencing constructs were inserted into the Agrobacterium tumefaciens strain EHA105 which was used to transform embryogenic callus using the method of (Iocco et al., 2001). Callus was initiated from anthers of immature flowers of Shiraz (BVRC12) and Chardonnay (I10V1) growing in the Coombe Vineyard, Adelaide University, Urrbrae, South Australia. Shiraz was initiated onto PIV medium and Chardonnay onto HT medium. Embryogenic callus from both cultivars was maintained on C1 and in culture for 12-20 months prior to transformation. Transformed callus was selected using 100 µg/mL kanamycin. Germinated embryos were cut to remove the roots and the tips, comprising the cotyledons supported on approximately 5 mm of hypocotyl, were transferred to shooting medium containing 10 µM benzylaminopurine (BAP) for shoot development. Rooted plantlets, whose leaves tested positive by PCR to the transgene were deflasked into potting mix and hardened off over 3 weeks in the glasshouse under shade and with a gradual reduction in humidity.

tag: cultivar

value: Shiraz

tag: genotype/variation

value: VvMYBA silencing

value: Whole berries


title: N17

value: Male


title: 57A

description: Gene expression in colorectal tissue


title: 51A

description: Gene expression in colorectal tissue

value: Female


title: 54A

description: Gene expression in colorectal tissue


title: N18


title: VvMYBAsi_white_Berry_Shiraz_rep3

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (white phenotype), replicate 3


title: 50A

description: Gene expression in colorectal tissue


title: 49A

description: Gene expression in colorectal tissue


title: VvMYBAsi_white_Berry_Shiraz_rep2

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (white phenotype), replicate 2


title: N12


title: N11


title: N15


title: 35A

description: Gene expression in colorectal tissue


title: 36A

description: Gene expression in colorectal tissue


title: VvMYBAsi_rose_Berry_Shiraz_rep4

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (rose phenotype), replicate 4


title: 25A

description: Gene expression in colorectal tissue


title: VvMYBAsi_rose_Berry_Shiraz_rep2

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (rose phenotype), replicate 2


title: WT_Berry_Shiraz_rep4

description: Whole berries of wild type Vitis vinifera cv Shiraz (control), replicate 4

value: wild type


title: VvMYBAsi_rose_Berry_Shiraz_rep3

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (rose phenotype), replicate 3


title: VvMYBAsi_rose_Berry_Shiraz_rep1

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (rose phenotype), replicate 1


title: 28A

description: Gene expression in colorectal tissue


title: VvMYBAsi_white_Berry_Shiraz_rep1

description: Whole berries of VvMYBA silenced Vitis vinifera cv Shiraz (white phenotype), replicate 1


title: WT_Berry_Shiraz_rep3

description: Whole berries of wild type Vitis vinifera cv Shiraz (control), replicate 3


title: 21A

description: Gene expression in colorectal tissue


title: 26A

description: Gene expression in colorectal tissue


title: 23A

description: Gene expression in colorectal tissue


title: 22A

description: Gene expression in colorectal tissue


title: 43A

description: Gene expression in colorectal tissue


title: 19A

description: Gene expression in colorectal tissue


title: WT_Berry_Shiraz_rep2

description: Whole berries of wild type Vitis vinifera cv Shiraz (control), replicate 2


title: Staphylococcus aureus USA300 derived from Human Skin Pus Agilent_252282510021_S01_GE2_107_Sep09_1_3

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description: Staphylococcus aureus USA300 derived from Human Skin Pus - InVivo

hyb_protocol: Cy3 labeled S. aureus USA300 reference and Cy5 labeled sample-derived cRNA (825 ng each) were fragmented following instructions in the Agilent’s In situ Hybridizatyion kit-plus. Hybridization and washing were performed using Tecan HS4800 Pro hybridization station (Tecan, Research Triangle Park, NC).

scan_protocol: Arrays were scanned in the Agilent Surescan Microarray Scanner.

data_processing: Array images were extracted using the Agilent Feature Extraction software version 10.7. Data from infected tissues were first normalized by calculating ratios of fluorescence signal of test RNA versus Reference, and then expressed as linear fold change relative to values from USA300 from 4 hours’ subculture in TSB (n = 3), also normalized to Reference. For studies in infected mouse kidneys, USA300 from 4 hours’ subculture in TSB served as infection inoculum, representing the start of infection. Microarray data were analyzed using the Bioconductor package. The fold change was derived from the fitted coefficient on the treatment term, and significance was assessed via Limma’s moderated F statistic.

organism: Staphylococcus aureus subsp. aureus USA300

label_protocol: Bacterial cRNA was prepared as follows. About 100 ng of bacterial total RNA was polyadenylated and reverse transcribed  using MessageAmpTM II-Bacteria kit (Life Technologies, Grand Island, NY). After cDNA synthesis, cRNA labeled with Cy3 or Cy5 was synthesized using T7 RNA polymerase (Agilent). The labeled cRNA was purified on an affinity resin column (Qiagen). Cy-dye incorporation and yield of labeled cRNA were measured with the ND-1000 spectrophotometer.

growth_protocol: Cutaneous abscess samples were collected from patients undergoing incision and drainage procedure as part of clinical care at the San Francisco General Hospital, and were frozen in RNA-later (Qiagen, Valencia, CA) until RNA isolation. For RNA isolation from infected mouse kidneys, C57Bl/6 mice (Charles River, Wilmington, MA) were injected intravenously with 100 μL phosphate-buffered saline (PBS) containing 1 × 108 colony forming units (CFUs) USA300 from 4 hours’ cultures in TSB. Three days later, kidneys were frozen in RNA-later until RNA isolation. To start the liquid Staphylococcus aureus USA300 control cultures, single colonies from tryptic soy agar (TSA) plates supplemented with 5% sheep blood were inoculated into tryptic soy broth (TSB) and incubated at 37°C while shaking at 200 rpm for the indicated times. The liquid cultures were grown to mid log phase [4 hours].

extract_protocol: Frozen tissues in RNAlater were homogenized using a gentleMACS cell dissociator (Miltenyi), followed by 10 minutes’ incubation at room temperature (RT) in nuclease-free PBS (Ambion, Grand Island, NY) containing 0.05% Triton-X100 (Thermo), 10 U/mL RNAse inhibitor RNAseIn (Promega, Madison, WI) and 20 mg/mL DNAseI grade II (Roche). The suspensions were passed through a 40-μm filter (BD Biosciences, San Jose, CA), washed twice with PBS containing 10 U/mL RNAse inhibitor RNAseIn, incubated for 5 minutes at RT in RNA Protect Bacteria Reagent (Qiagen), pelleted, and frozen. Bacteria were lysed by incubation for 30 minutes at 37°C in 30 mM Tris ( pH 8.0) containing 1 mM EDTA, lysostaphin (Sigma, St. Louis, MO) at 5 mg/mL, and protease K (Qiagen). RNA was isolated using RNAEasy RNA purification kit (Qiagen). Bacterial RNA was further enriched using the MicrobEnrich purification kit (Ambion).

tag: animal

value: Human

value: Skin

tag: condition

value: Pus

tag: group

value: C

tag: subgroup

value: E

source_name: Staphylococcus aureus USA300 In Vitro reference pool

growth_protocol: To start liquid cultures, single colonies from tryptic soy agar (TSA) plates supplemented with 5% sheep blood were inoculated into tryptic soy broth (TSB) and incubated at 37°C while shaking at 200 rpm for the indicated times.

tag: reference


title: 20A

description: Gene expression in colorectal tissue


title: Staphylococcus aureus USA300 derived from Human Skin Pus Agilent_252282510024_S01_GE2_107_Sep09_1_3

source_name: Staphylococcus aureus USA300 derived from Human Skin Pus - InVivo

value: Staphylococcus aureus USA300 In Vitro reference pool


title: WT_Berry_Shiraz_rep1

description: Whole berries of wild type Vitis vinifera cv Shiraz (control), replicate 1


title: Staphylococcus aureus USA300 4 hour Log Control Agilent_252282510023_S01_GE2_107_Sep09_1_4

description: Staphylococcus aureus USA300 4 hour Log Control - Culture

value: A


title: Staphylococcus aureus USA300 derived from Human Skin Pus Agilent_252282510020_S01_GE2_107_Sep09_1_3


title: 35S::VvMYBA1_Berry_Chardonnay_rep2

description: Whole berries of 35S::VvMYBA1 Vitis vinifera cv Chardonnay, replicate 2

value: Chardonnay


title: Staphylococcus aureus USA300 4 hour Log Control Agilent_252282510022_S01_GE2_107_Sep09_1_4

source_name: Staphylococcus aureus USA300 4 hour Log Control - Culture


title: 17A

description: Gene expression in colorectal tissue

value: High-grade dysplasia


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510015_S01_GE2_107_Sep09_1_3

description: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess - InVivo

value: Mouse

value: Kidney

value: Abscess

value: F


title: 35S::VvMYBA1_Berry_Chardonnay_rep3

description: Whole berries of 35S::VvMYBA1 Vitis vinifera cv Chardonnay, replicate 3

value: Whole berries


title: 35S::VvMYBA1_Berry_Chardonnay_rep1

description: Whole berries of 35S::VvMYBA1 Vitis vinifera cv Chardonnay, replicate 1


title: 124A

description: Gene expression in colorectal tissue

value: Male


title: WT_Berry_Chardonnay_rep3

description: Whole berries of wild type Vitis vinifera cv Chardonnay (control), replicate 3


title: Staphylococcus aureus USA300 4 hour Log Control Agilent_252282510021_S01_GE2_107_Sep09_1_4


title: 14A

description: Gene expression in colorectal tissue


title: WT_Berry_Chardonnay_rep2

description: Whole berries of wild type Vitis vinifera cv Chardonnay (control), replicate 2


title: WT_Berry_Chardonnay_rep1

description: Whole berries of wild type Vitis vinifera cv Chardonnay (control), replicate 1


title: 16A

description: Gene expression in colorectal tissue

value: Female


title: N32

description: Gene expression in colorectal tissue

value: Normal epithelium


title: 117A

description: Gene expression in colorectal tissue

value: Low-grade dysplasia


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510015_S01_GE2_107_Sep09_1_2

source_name: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess - InVivo


title: 35S::VvMYBA1_Skin_Chardonnay_rep3

description: Skin of 35S::VvMYBA1 Vitis vinifera cv Chardonnay, replicate 3

value: Skin


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510014_S01_GE2_107_Sep09_1_4


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510015_S01_GE2_107_Sep09_1_1


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510014_S01_GE2_107_Sep09_1_3


title: Differentiated WT ESC (RA for 4d) 3

city: San Francisco

first: Andrei

last: Goga

state: CA

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

description:
Test
esra d4

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization we used GAPDH
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
The fold_change.txt reports test/control (i.e., differentiated ESC/undifferentiated ESC) ratios based on average of replicates, as calculated by the software package.

label: SYBR Green

organism: Mus musculus

label_protocol: PCR assays were performed using the p53 Signaling Pathway PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 400 ng of total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed on a Roche LightCycler 480II: 95°C, 10 min; 45 cycles at 94°C, 15 seconds and 60°C, 60 seconds.

extract_protocol: Total RNA was isolated from cells using mirVana (Ambion) and treated with DNaseI (Ambion).

value: wild type

tag: cell type

value: Embryonic stem cell

tag: treated with

value: retinoic acid for 4 days

tag: cell status

value: differentiated


title: 35S::VvMYBA1_Skin_Chardonnay_rep2

description: Skin of 35S::VvMYBA1 Vitis vinifera cv Chardonnay, replicate 2


title: 114A

description: Gene expression in colorectal tissue

tag: gender


title: Differentiated WT ESC (RA for 4d) 2

description:
Test
esra d3


title: WT_Skin_Chardonnay_rep3

description: Skin of wild type Vitis vinifera cv Chardonnay (control), replicate 3


title: WT_Skin_Chardonnay_rep2

description: Skin of wild type Vitis vinifera cv Chardonnay (control), replicate 2


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510014_S01_GE2_107_Sep09_1_1

value: C

value: Staphylococcus aureus USA300 In Vitro reference pool


title: N27

description: Gene expression in colorectal tissue

tag: age(years)


title: N28

description: Gene expression in colorectal tissue

tag: pathologic grade


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510013_S01_GE2_107_Sep09_1_4


title: N24

description: Gene expression in colorectal tissue


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510013_S01_GE2_107_Sep09_1_3


title: N29

description: Gene expression in colorectal tissue


title: N22

description: Gene expression in colorectal tissue


title: Differentiated WT ESC (RA for 4d) 1

description:
Test
esra d2


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510014_S01_GE2_107_Sep09_1_2


title: Para-carcinoma tissue_replicate 3

city: Shanghai

first: Jiwen

last: Wang

state: State...

address: Fenglin Road 180

institute: Fudan University

description: Gene expression of surgical specimens

hyb_protocol: According to the Agilent lncRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Para-carcinoma gallbladder tissue, replicate 3

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent lncRNA microarray, according to manufacturer's protocol.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Paired tissues of gallbladder carcinoma and peri-carcinomatous tissues from every patient were quick-frozen by liquid nitrogen as soon as possible and then were moved to -80℃ condition for long-term storage

value: gallbladder

tag: age


title: Undifferentiated WT ESC 3

description:
Control
mES d4

value: none (control)

value: undifferentiated


title: Para-carcinoma tissue_replicate 2

description: Gene expression of surgical specimens

source_name: Para-carcinoma gallbladder tissue, replicate 2

tag: tissue


title: 35S::VvMYBA1_Skin_Chardonnay_rep1

description: Skin of 35S::VvMYBA1 Vitis vinifera cv Chardonnay, replicate 1

value: Chardonnay


title: N23

description: Gene expression in colorectal tissue


title: WT_Skin_Chardonnay_rep1

description: Skin of wild type Vitis vinifera cv Chardonnay (control), replicate 1


title: Undifferentiated WT ESC 2

description:
Control
mES d3


title: Ovary of BHPF treated mice

first: Zhaobin

last: Zhang

address: Yiheyuan Road 5#

institute: Peking Univ

description: Gene expression in ovary of BHPF treated mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 mouse gene expression microarrays 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 Technologies Scanner G2505C US10313827 using one color scan setting.

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: Ovary of BHPF treated mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA from each pool of tissue samples (a mixture from three animals) using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by  RNA purification using RNA Clean-up Kit (MN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the livers, ovaries, and uteri of 24-day-old female CD-1 mice that had been treated with 50 mg/kg body weight of BHPF or peanut oil via daily intragastric administration for a period of 3 days using TRIzol reagent (Invitrogen).

treatment_protocol: Immature (24-day-old) female CD-1 mice were treated with 50 mg/kg body weight of BHPF or peanut oil via daily intragastric administration for a period of 3 days.

value: Ovary

tag: strain

value: female


title: Undifferentiated WT ESC 1

description:
Control
mES d2


title: Staphylococcus aureus USA300 derived from Mouse Kidney Abscess Agilent_252282510013_S01_GE2_107_Sep09_1_2

value: Mouse

value: Kidney

value: Abscess

value: F


title: N12

description: Gene expression in colorectal tissue

value: Male

value: Normal epithelium


title: Uterus of BHPF treated mice

description: Gene expression in uterus of BHPF treated mice

source_name: Uterus of BHPF treated mice

value: Uterus


title: Gallbladder_carcinoma_rep3

description: Gene expression of surgical specimens

source_name: Gallbladder carcinoma, replicate 3


title: Ovary of control mice

description: Gene expression in ovary of control mice

source_name: Ovary of control mice


title: Uterus of control mice

description: Gene expression in uterus of control mice

source_name: Uterus of control mice


title: Liver of BHPF treated mice

description: Gene expression in liver of BHPF treated mice

source_name: Liver of BHPF treated mice

value: Liver


title: N11

description: Gene expression in colorectal tissue


title: Young mouse replicate 1

status: Public on Oct 15 2015

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

description: Gene expression data of young mouse replicate 1

hyb_protocol: Fragmented and biotin-labeled targets were hybridized to Mouse Gene ST 1.0 (Affymetrix) gene chips for analysis of over 6,553,000 probe sets.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 - 7G.

data_processing:
The data were analyzed with R-Bioconductor (RMA) using Affymetrix default analysis settings and global scaling as normalization method.
Pathway analysis is done by GSEA with KEGG pathway

source_name: Young mouse replicate 1

label_protocol: Starting with an input of 100 ng RNA, cDNA was prepared using the WT-Ovation Pico RNA Amplification System (NuGen; Cat No. 3300-12), ST cDNA was generated using the WT-ovation Exon Module (Nugen; Cat. No. 2000-12), and the samples were fragmented and biotinylated using the FL-Ovation cDNA Biotion Module V2 (Nugene; Cat. No. 4200-12)

growth_protocol: Sorted pro- and pre- B-cell progenitors were isolated from young (2 month) and old (24 month) BALB/c mice

extract_protocol: RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturers instructions.

treatment_protocol: The cells were unmanipulated prior to performing the microarray analysis

value: pro- and pre- B-cell progenitors

value: BALB/c

value: 2 month


title: Old mouse replicate 3

description: Gene expression data of old mouse replicate 3

source_name: Old mouse replicate 3

value: 24 month


title: Old mouse replicate 2

description: Gene expression data of old mouse replicate 2

source_name: Old mouse replicate 2


title: N10

description: Gene expression in colorectal tissue


title: N15

description: Gene expression in colorectal tissue


title: Gallbladder_carcinoma_rep2

description: Gene expression of surgical specimens

source_name: Gallbladder carcinoma, replicate 2

value: gallbladder


title: Para-carcinoma tissue_replicate 1

description: Gene expression of surgical specimens

source_name: Para-carcinoma gallbladder tissue, replicate 1

value: Female


title: Young mouse replicate 2

description: Gene expression data of young mouse replicate 2

source_name: Young mouse replicate 2


title: Gallbladder_carcinoma_rep1

description: Gene expression of surgical specimens

source_name: Gallbladder carcinoma, replicate 1


title: Liver of control mice

description: Gene expression in liver of control mice

source_name: Liver of control mice


title: Old mouse replicate 1

description: Gene expression data of old mouse replicate 1

source_name: Old mouse replicate 1


title: Cd-high rep1

city: West Lafayette

first: SHUAI

last: CHEN

state: IN

address: 195 Marsteller Street

department: Forestry and Natural Resources

institute: PURDUE UNIVERSITY

description:
Gene expression data from Cd-high
small RNAs

hyb_protocol: The labeled samples were hybridized to the arrays for 17 hours and were stained and washed using the standard miRNA protocol.

scan_protocol: Affymetrix GeneChip Command Console Software was used to scan the arrays and generate CEL files.

data_processing: Arrays were visually scanned for abnormalities or defects. CEL files were imported into Genespring 12.0 (Agilent, Santa Clara, CA, USA) to generate RMA (robust multi-array average) expression levels (Lrizarry et al., 2003) using the RMA normalization option.

organism: Daphnia pulex

source_name: Daphnia pulex neonates <96hours

label_protocol: In brief, 300ng of small RNA from each sample was labeled using the Affymetrix FlashTag Bioton HSR kit.

growth_protocol: D. pulex were cultured in moderatly reconstituted hard water

extract_protocol: Small RNAs including miRNAs were extracted by PureLink miRNA extraction kit by invitrogen.

treatment_protocol: Fifty D. pulex were randomly selected from each replicate for small RNA extraction

tag: developmental stage

value: neonate

tag: stress

value: Cd

tag: dose

value: 40 ppb

value: whole organsim


title: Young mouse replicate 3

description: Gene expression data of young mouse replicate 3

source_name: Young mouse replicate 3


title: Cd-high rep2


title: Cd-low rep1

description:
Gene expression data from Cd-low
small RNAs

value: 20 ppb


title: H3K27me3 of CpG island in colonic epithelial cells of 23-week-old mice treated with DSS (n=3, pooled)

type: genomic

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

description: DSS-treated

hyb_protocol: Labelled DNA was hybridized to microarray for 40 hours at 67℃ and 20 rpm rotation. Microarrays was washed according to Agilent protocol.

scan_protocol: The microarray was scanned with an Agilent G2565BA microarray scanner (Agilent Technologies).

data_processing: Scanned data was analyzed with Feature Extraction Ver.9.1 and normalized (Background subtraction) using Agilent G4477AA ChIP Analytics 1.3 software.  Obtained signal ratio [Cy5 signal /Cy3 signal] was further analyzed as described previously (DNA Res, 16, 275-286, 2009), and normalized by the median of signal ratios of all the probes.

molecule: genomic DNA

source_name: sonicated_WCE_chromatin_colonic epithelial cells 23-weeks_DSS

label_protocol: Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K27me3 (07-449, Millipore) at 4ºC overnight. Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl. After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 33 μl of 1 x TE. 500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).

growth_protocol: To induce colitis, 7-week-old mice were treated with DSS at a concentration of 2% for one week.

extract_protocol: Colonic epithelial cells were isolated by the crypt isolation technique, and were cross-linked with 1 % formaldehyde, lysed, and sonicated with a Bioruptor UCD-250 (Cosmo Bio, Tokyo, Japan).

value: colon

tag: cell fraction

value: WCE

value: Balb/c

value: male

source_name: Sonicated chromatin (IP)_colonic epithelial cells_23weeks_DSS

value: IP

tag: antibody


title: Cd-low rep2


title: H3K27me3 of CpG island in colonic epithelial cells of 23-week-old mice (n=3, pooled)

description: Untreated

source_name: sonicated_WCE_chromatin_colonic epithelial cells 23-weeks

source_name: Sonicated chromatin (IP)_colonic epithelial cells_23weeks


title: Cd-low rep3


title: Control rep3

description:
Gene expression data from Control
small RNAs

value: Control

value: 0 ppb (control)


title: Control rep2


title: LYMPHOMA3 74

city: Columbus

first: Alessandra

last: Drusco

address: 460 W 12th Ave

institute: The Ohio State University

description: MIRNA EXPRESSION FROM CSF

hyb_protocol: The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Hybridization reactions were performed with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h. Hybridized probes were purified using the nCounter Prep Station (NanoString Technologies) following the manufacturer’s instructions

scan_protocol: For each assay, a high density scan (600 fields of view) was performed.

data_processing: Nanostring data were normalized by using the Top-100 expressed miRNA normalization as implemented by the Nanostring nSolver software. P-values were calculated using the LIMMA package (Linear Models for Microarray Data) from the Bioconductor R project. The heatmap was generated by the Hierarchical Clustering module of GenePattern software based on normalized miRNA expression data.

source_name: CSF

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies). Preparation of small RNA samples involves the ligation of a specific DNA tag onto the 3’ end of each mature miRNA. These tags are designed to normalize the Tm’s of the miRNAs as well as to provide a unique identification for each miRNA species in the sample. Following the ligation reaction, excess tags and bridges were removed,

extract_protocol: Trizol extraction was performed following the manufacturer's instructionsm. RNA was purified and concentrated by Norgen RNA clean up and concentration kit.

tag: sample type

value: CSF

tag: disease state

value: LYMPHOMA


title: CCA1-ox, 12am, small polysomal, replicate 3

city: Knoxville

first: Albrecht

middle: G

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

institute: The University of Tennessee

hyb_protocol: cRNA was hybridized for 16 hr at 45C on the GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained with streptavidin-phycoerythrin (Invitrogen-Molecular Probes, Carlsbad, CA, USA), followed by a wash with biotinylated antibody goat IgG and another staining with streptavidin-phycoerythrin.

scan_protocol: GeneChips were scanned using the GeneChip 7G high-resolution scanner.

data_processing: The data were analyzed using R version 3.1.  Normalization was performed using the gcrma function from the gcrma package from Bioconductor (version 2.36), and absolute calls (columns labeled ABS_CALL)  were generated using the mas5calls function from the affy package (version 1.42.3), all with default settings.  AGI annotations (column labeled AGI) were matched with Affymetrix probe IDs using the ath1121501.db package from Bioconductor (version 2.14).    Translation state (TL) was calculated as (2*small polysomal + 7*large polysomal)/(non-polysomal + small polysomal + large polysomal) after back-transforming the log2 values.

organism: Arabidopsis thaliana

source_name: CCA1-ox_12am_small polysomal

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from total and polysome-fractionated RNA (Expression Analysis Technical Manual, 2001, Affymetrix) after priming cDNA synthesis with oligo(dT).

growth_protocol: Plants were grown on agar plates with full strength Murashige and Skoog salts, pH 5.7, 1% sucrose, in a 16-hour light/8-hour dark cycle (lights on at 6am) for 10 days.

extract_protocol: RNA extraction, polysome fractionation, and microarray hybridization were performed as described previously (Genome Biol. 2007;8(4):R60)

tag: ecotype background

value: Columbia

tag: genotype/variation

value: 10 days

value: aerial part

tag: harvested at

tag: molecule subtype

value: Small polysomal RNA


title: CCA1-ox, 12am, large polysomal, replicate 3

source_name: CCA1-ox_12am_large polysomal

value: Large polysomal RNA


title: CCA1-ox, 12pm, large polysomal, replicate 3

source_name: CCA1-ox_12pm_large polysomal


title: H3K27me3 of CpG island in colonic epithelial cells of 7-week-old mice (n=3, pooled)

description: Untreated

source_name: sonicated_WCE_chromatin_colonic epithelial cells 7-weeks

tag: gender

source_name: Sonicated chromatin (IP)_colonic epithelial cells_7weeks


title: CCA1-ox, 12am, non-polysomal, replicate 3

value: Non-polysomal RNA


title: CCA1-ox, 12pm, small polysomal, replicate 3

source_name: CCA1-ox_12pm_small polysomal


title: CCA1-ox, 6pm, small polysomal, replicate 3

source_name: CCA1-ox_6pm_small polysomal


title: Control rep1

value: neonate

value: whole organsim


title: CCA1-ox, 6am, large polysomal, replicate 3

source_name: CCA1-ox_6am_large polysomal


title: CCA1-ox, 6pm, large polysomal, replicate 3

source_name: CCA1-ox_6pm_large polysomal


title: CCA1-ox, 6pm, non-polysomal, replicate 3


title: CCA1-ox, 6am, small polysomal, replicate 3

source_name: CCA1-ox_6am_small polysomal


title: LYMPHOMA2 73

description: MIRNA EXPRESSION FROM CSF


title: Liver_vehicle treated_8w_rep2

first: Jun

last: Li

state: Shanghai

address: 800 Dongchuan Road

department: Shanghai Cancer Institute

institute: State Key Laboratory for Oncogenes and Related Genes

description: gene expression after 8w in vehicle treated mouse liver

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: liver, vehicle treated, 8w

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: C57BL6/J mice were intraperitoneally injected with CCl4 or vehicle twice every week, livers were obtained after 8 weeks.

value: liver


title: Liver_CCl4 treated_8w_rep2

description: gene expression after 8w in CCl4 treated mouse liver

source_name: liver, CCl4 treated, 8w


title: Liver_vehicle treated_8w_rep1


title: Liver_vehicle treated_8w_rep3


title: Liver_CCl4 treated_8w_rep1


title: LYMPHOMA1 72

description: MIRNA EXPRESSION FROM CSF


title: BREAST MET5 70

description: MIRNA EXPRESSION FROM CSF

value: BREAST MET


title: BREAST MET4 69

description: MIRNA EXPRESSION FROM CSF


title: BREAST MET4 67

description: MIRNA EXPRESSION FROM CSF


title: BREAST MET4 68

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 12pm, non-polysomal, replicate 3


title: CCA1-ox, 6am, non-polysomal, replicate 3


title: BREAST MET4 66

description: MIRNA EXPRESSION FROM CSF


title: BREAST MET3 65

description: MIRNA EXPRESSION FROM CSF


title: BREAST MET3 64

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 12am, non-polysomal, replicate 2


title: CCA1-ox, 12am, large polysomal, replicate 2


title: hLXRa L439A/E441A iBMDM_GW/veh

city: Los Angeles

first: Ayaka

last: Ito

address: 675 Charles E Young Dr. South

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

description: Gene expression after O/N GW3965 treatment and vehicle 4hr treatment in iBMDM expressing human LXRa L439A/E441A

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software 11.5.1.11 version

source_name: immortalized bone marrow macrophages expressing human LXRa L439A/E441A, GW/veh

label_protocol: Agilent standard protocol

growth_protocol: Human LXRa wildtype, K328R/K434R or K439A/E441A mutant were retrovirally overexpressed in immortalized bone marrow macrophages (iBMDM) from LXRa/b knockour mice. Cells were maintained in DMEM containing 10% FBS, 10% CMG-conditioned medium, 1% penicillin/streptomycin, 1% HEPES.

extract_protocol: RNA was isolated from liver tissue RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: 5x105 cells/well were plated in 12 well-plate. Cells were placed in DMEM containing 0.5% FBS, 5 μM simvastatin, 100 μM mevalonic acid and 1μM GW3965 or DMSO overnight.  Cells were then stimulated with 10ng/ml LPS or vehicle for 4 hours

tag: cell

value: immortalized bone marrow macrophages

tag: expressing gene

value: human LXRa L439A/E441A

tag: treatment

value: O/N GW3965 and vehicle 4hr


title: CCA1-ox, 12am, small polysomal, replicate 2

tag: age

tag: tissue


title: hLXRa L439A/E441A iBMDM_GW/LPS

description: Gene expression after O/N GW3965 treatment and LPS 4hr treatment in iBMDM expressing human LXRa L439A/E441A

source_name: immortalized bone marrow macrophages expressing human LXRa L439A/E441A, GW/LPS 4h

value: O/N GW3965 and LPS 4hr


title: hLXRa L439A/E441A iBMDM_veh/veh

description: Gene expression after O/N DMSO treatment and vehicle 4hr treatment in iBMDM expressing human LXRa L439A/E441A

source_name: immortalized bone marrow macrophages expressing human LXRa L439A/E441A, veh/veh

value: O/N DMSO and vehicle 4hr


title: CCA1-ox, 6pm, small polysomal, replicate 2


title: hLXRa K328/L434R iBMDM_GW/LPS

description: Gene expression after O/N GW3965 treatment and LPS 4hr treatment in iBMDM expressing human LXRa  K328R/K434R

source_name: immortalized bone marrow macrophages expressing human LXRa K328R/K434R, GW/LPS 4h

value: human LXRa K328R/K434R


title: hLXRa L439A/E441A iBMDM_veh/LPS

description: Gene expression after O/N DMSO treatment and LPS 4hr treatment in iBMDM expressing human LXRa L439A/E441A

source_name: immortalized bone marrow macrophages expressing human LXRa L439A/E441A, veh/LPS 4h

value: O/N DMSO and LPS 4hr


title: BREAST MET3 63

description: MIRNA EXPRESSION FROM CSF

source_name: CSF

value: CSF


title: hLXRa K328/L434R iBMDM_GW/veh

description: Gene expression after O/N GW3965 treatment and vehicle 4hr treatment in iBMDM expressing human LXRa  K328R/K434R

source_name: immortalized bone marrow macrophages expressing human LXRa K328R/K434R, GW/veh


title: N17

description: Gene expression in colorectal tissue

source_name: Colorectal normal mucosa

value: Male

tag: age(years)

tag: pathologic grade

value: Normal epithelium


title: CCA1-ox, 12pm, large polysomal, replicate 2

source_name: CCA1-ox_12pm_large polysomal

value: Columbia

value: 10 days

value: aerial part


title: CCA1-ox, 6pm, large polysomal, replicate 2

value: Large polysomal RNA


title: CCA1-ox, 12pm, small polysomal, replicate 2

value: Small polysomal RNA


title: CCA1-ox, 12pm, non-polysomal, replicate 2

value: Non-polysomal RNA


title: CCA1-ox, 6pm, non-polysomal, replicate 2


title: hLXRa K328/L434R iBMDM_veh/LPS

description: Gene expression after O/N DMSO treatment and LPS 4hr treatment in iBMDM expressing human LXRa K328R/K434R

source_name: immortalized bone marrow macrophages expressing human LXRa K328R/K434R, veh/LPS 4h


title: hLXRa K328/L434R iBMDM_veh/veh

description: Gene expression after O/N DMSO treatment and vehicle 4hr treatment in iBMDM expressing human LXRa K328R/K434R

source_name: immortalized bone marrow macrophages expressing human LXRa K328R/K434R, veh/veh


title: hLXRa WT iBMDM_GW/LPS

description: Gene expression after O/N GW3965 treatment and LPS 4hr treatment in iBMDM expressing human LXRa wildtype

source_name: immortalized bone marrow macrophages expressing human LXRa wildtype, GW/LPS 4h

value: human LXRa wildtype


title: CCA1-ox, 6am, large polysomal, replicate 2

source_name: CCA1-ox_6am_large polysomal


title: BREAST MET3 61

description: MIRNA EXPRESSION FROM CSF

value: BREAST MET


title: CCA1-ox, 6am, small polysomal, replicate 2


title: BREAST MET3 60

description: MIRNA EXPRESSION FROM CSF


title: BREAST MET3 62

description: MIRNA EXPRESSION FROM CSF


title: BREAST MET1 58

description: MIRNA EXPRESSION FROM CSF


title: LUNG MET4 57

description: MIRNA EXPRESSION FROM CSF

value: LUNG MET


title: LUNG MET3 56

description: MIRNA EXPRESSION FROM CSF


title: LUNG MET3 55

description: MIRNA EXPRESSION FROM CSF


title: Cd-high rep3

source_name: Daphnia pulex neonates <96hours

tag: developmental stage

value: neonate

tag: stress

value: Cd

tag: dose

value: 40 ppb

value: whole organsim


title: LUNG MET3 54

description: MIRNA EXPRESSION FROM CSF

tag: sample type


title: LUNG MET2 53

description: MIRNA EXPRESSION FROM CSF

tag: disease state


title: ABCA1fl/fl LysM Cre BMDM_GW/veh

description: Gene expression after O/N GW3965 treatment and vehicle 4hr treatment in BMDM from ABCA1fl/fl LysM Cre mice

source_name: bone marrow macrophages from ABCA1fl/fl LysM Cre mice, GW/veh

growth_protocol: Bone marrow cells were harvested from ABCA1fl/fl and ABCA1fl/fl LysM Cre mice. Cells were differentiated into macrophages in DMEM containing 20% FBS, 30% L929-conditioned medium, 1% penicillin/streptomycin for 7 days.

treatment_protocol: On day7, cells were placed in DMEM containing 0.5% FBS, 5 μM simvastatin, 100 μM mevalonic acid and 1μM GW3965 or DMSO overnight.  Cells were then stimulated with 10ng/ml LPS or vehicle for 4 hours

value: primary bone marrow macrophages

tag: genotype

value: ABCA1fl/fl LysM Cre

value: O/N GW3965 and vehicle 4hr


title: hLXRa WT iBMDM_veh/veh

description: Gene expression after O/N DMSO treatment and vehicle 4hr treatment in iBMDM expressing human LXRa wildtype

source_name: immortalized bone marrow macrophages expressing human LXRa wildtype, veh/veh

value: immortalized bone marrow macrophages

value: O/N DMSO and vehicle 4hr


title: BREAST MET2 59

description: MIRNA EXPRESSION FROM CSF

value: CSF


title: ABCA1fl/fl LysM Cre BMDM_GW/LPS

description: Gene expression after O/N GW3965 treatment and LPS 4hr treatment in BMDM from ABCA1fl/fl LysM Cre mice

source_name: bone marrow macrophages from ABCA1fl/fl LysM Cre mice, GW/LPS

value: O/N GW3965 and LPS 4hr


title: CCA1-ox, 12am, small polysomal, replicate 1

source_name: CCA1-ox_12am_small polysomal

tag: ecotype background

value: Columbia

tag: genotype/variation

value: 10 days

value: aerial part


title: hLXRa WT iBMDM_GW/veh

description: Gene expression after O/N GW3965 treatment and vehicle 4hr treatment in iBMDM expressing human LXRa wildtype

source_name: immortalized bone marrow macrophages expressing human LXRa wildtype, GW/veh

value: human LXRa wildtype


title: hLXRa WT iBMDM_veh/LPS

description: Gene expression after O/N DMSO treatment and LPS 4hr treatment in iBMDM expressing human LXRa wildtype

source_name: immortalized bone marrow macrophages expressing human LXRa wildtype, veh/LPS 4h

value: O/N DMSO and LPS 4hr


title: ABCA1fl/fl LysM Cre BMDM_veh/LPS

description: Gene expression after O/N DMSO treatment and LPS 4hr treatment in BMDM from ABCA1fl/fl LysM Cre mice

source_name: bone marrow macrophages from ABCA1fl/fl LysM Cre mice, veh/LPS


title: ABCA1fl/fl BMDM_GW/LPS

description: Gene expression after O/N GW3965 treatment and LPS 4hr treatment in BMDM from ABCA1fl/fl mice

source_name: bone marrow macrophages from ABCA1fl/fl mice, GW/LPS


title: CCA1-ox, 12am, large polysomal, replicate 1

source_name: CCA1-ox_12am_large polysomal

tag: harvested at

tag: molecule subtype

value: Large polysomal RNA


title: CCA1-ox, 6pm, non-polysomal, replicate 1

value: Non-polysomal RNA


title: CCA1-ox, 12am, non-polysomal, replicate 1


title: CCA1-ox, 6am, non-polysomal, replicate 2


title: CCA1-ox, 6pm, large polysomal, replicate 1

source_name: CCA1-ox_6pm_large polysomal


title: ABCA1fl/fl BMDM_veh/LPS

description: Gene expression after O/N DMSO treatment and LPS 4hr treatment in BMDM from ABCA1fl/fl mice

source_name: bone marrow macrophages from ABCA1fl/fl mice, veh/LPS

tag: cell


title: LUNG MET1 52

description: MIRNA EXPRESSION FROM CSF

source_name: CSF

value: LUNG MET


title: MEDULLOBLASTOMA4 51

description: MIRNA EXPRESSION FROM CSF

value: MEDULLOBLASTOMA


title: CCA1-ox, 6pm, small polysomal, replicate 1

source_name: CCA1-ox_6pm_small polysomal

value: Small polysomal RNA


title: ABCA1fl/fl BMDM_GW/veh

description: Gene expression after O/N GW3965 treatment and vehicle 4hr treatment in BMDM from ABCA1fl/fl mice

source_name: bone marrow macrophages from ABCA1fl/fl mice, GW/veh

value: primary bone marrow macrophages


title: 1.5 mM Gallic acid 10 min replicate 3

city: Madrid

first: Felix

last: Lopez de Felipe

address: Jose Antonio Novais

country: Spain

institute: ICTAN-CSIC

description:
Biological replicate 3 of 3
Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GPL5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).

hyb_protocol: Preparation of probes and hybridization was performed as described on the Two-Color Microarray Based Gene Expression Analysis Manual (Quick Amp Labeling) with Tecan HS Pro Hybridization (Ver. 5.7/Agilent Technologies): for each hybridization 300 ng of Cy3 and HyPer5 probes were added to 5 uL of 10x Blocking Agent, 1.2 uL of 25x Fragmentation Buffer and nuclease-free water to bring volume to 25 uL reaction and incubated at 60 ºC for 30 min. Then, 25 uL the 2x GEx Hybridization Buffer HI-RPM were added and loaded onto the arrays. The arrays were hybridized for 17 hours at 65ºC, and washed in GE Wash Buffer 1 and then in GE Wash Buffer 2. Finally, these were drained by centrifugation and scanned.

scan_protocol: Images were captured with a Agilent Technologies Scanner G2505C / GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using the methods normexp and loess in LIMMA. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg. The expected False Discovery Rate (FDR) was controlled to be less than 5%. Genes were considered differentially expressed when nominal p-values were <0.05 and had a fold change (FC) equal or higher than ±1.5. FC was calculated as the average of the fold change between significantly regulated probes.

organism: Lactiplantibacillus plantarum

source_name: Untreated cells: Control

label_protocol: Fluorescently labelled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen): 20 ug of total RNA was transformed to cDNA with SuperscriptTM III Reverse Transcriptase using anchored oligo(dT)20 primers, and including aminoallyl-modified nucleotides. After cDNA purification, the Cy3 and HyPer5 fluorescent dyes (Amersham Biosciences) were coupled to the aminoallyl-modified first-strand cDNA. Purification of Cy3- and HyPer5-labeled cDNA probes was carried out with the CyScribe GFX Purification Kit.

growth_protocol: Paired independent L. plantarum batch cultures (50 mL each) were grown in MRS lacking GA to an OD600 ≈ 0.8-0.9, then one pair of the culture were exposed  to GA to bring their final concentration to 1.5 mM. Cell cultures were centrifuged after 10 minutes of exposure toGA and RNA was extracted and purified.

extract_protocol: For RNA extraction the celular pellet was mixed with 2 mL of quenching buffer (60% methanol, 66.7 mM HEPES, pH 6.5, -40 ºC) . Following quenching, the cells were pelleted by centrifugation at 9,000 x g for 10 min at -10 ºC, transferred to a screw cap tube containing an extraction mixture (500 uL 1:4 chloroform-acid phenol, 30uL of 10% SDS, 30uL Na-acetate 3M pH 5.2, 400uL Tris-EDTA buffer [10 mM Tris(hydroxymethyl)amino methane, 1 mM EDTA] pH 7.4, 15 mg of polyvinylpoly-pyrrolidone, and 500 mg of 75-150um glass beads). The cells were broken under frozen conditions in  the FastPrepTM Fp120 (SAVANT) using three treatments of 5000 rpm for 40 seconds cycles (and chilled on dry ice for 60 seconds between cycles). The suspension was then centrifuged at 4 ºC at 10,000 x g for 2 min. Two extractions with 500 uL of chloroform were performed, and the supernatant containing the RNA was separated by centrifugation.  The sample was immediately frozen in liquid nitrogen, and stored at -80 ºC. NanoDrop ND-1000 instrument was used for quantification of RNA. Continued with the QUIAGEN RNA isolation kit. Two treatments with DNase I (Ambion) were applied and the absence of genomic DNA was confirmed by PCR.

treatment_protocol: Cell cultures were centrifuged after 10 minutes of exposure to GA and RNA was extracted and purified.

tag: strain

tag: agent

value: none, without gallic acid

source_name: Treated cells: Experimental

value: gallic acid 1.5 mM


title: CCA1-ox, 12pm, large polysomal, replicate 1

source_name: CCA1-ox_12pm_large polysomal

tag: age


title: MEDULLOBLASTOMA3 50

description: MIRNA EXPRESSION FROM CSF


title: ABCA1fl/fl BMDM_veh/veh

description: Gene expression after O/N DMSO treatment and vehicle 4hr treatment in BMDM from ABCA1fl/fl mice

source_name: bone marrow macrophages from ABCA1fl/fl mice, veh/veh

tag: treatment


title: MEDULLOBLASTOMA3 49

description: MIRNA EXPRESSION FROM CSF


title: MEDULLOBLASTOMA3 48

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 12pm, small polysomal, replicate 1

source_name: CCA1-ox_12pm_small polysomal

tag: tissue


title: ABCA1fl/fl LysM Cre BMDM_veh/veh

description: Gene expression after O/N DMSO treatment and vehicle 4hr treatment in BMDM from ABCA1fl/fl LysM Cre mice

source_name: bone marrow macrophages from ABCA1fl/fl LysM Cre mice, veh/veh

value: ABCA1fl/fl LysM Cre


title: MEDULLOBLASTOMA3 46

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 6am, large polysomal, replicate 1

source_name: CCA1-ox_6am_large polysomal


title: MEDULLOBLASTOMA3 47

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 12pm, non-polysomal, replicate 1


title: 1.5 mM Gallic acid 10 min replicate 1

description:
Biological replicate 1 of 3
Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GPL5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).


title: Gallic acid 10 min replicate 3

description: Biological replicate 3 of 3

hyb_protocol: Preparation of probes and hybridization was performed as described on the Two-Color Microarray Based Gene Expression Analysis Manual (Quick Amp Labeling) with Tecan HS Pro Hybridization (Ver. 5.7/Agilent Technologies): for each hybridization 300 ng of Cy3 and HyPer5 probes were added to 5 uL of 10x Blocking Agent, 1.2 uL of 25x Fragmentation Buffer and nuclease-free water to bring volume to 25 uL reaction and incubated at 60C for 30 min. Then, 25 uL the 2x GEx Hybridization Buffer HI-RPM were added and loaded onto the arrays. The arrays were hybridized for 17 hours at 65C, and washed in GE Wash Buffer 1 and then in GE Wash Buffer 2. Finally, these were drained by centrifugation and scanned. Slide L. plantarum WCFS1 8x15K microarray GE Agilent-026636 G2509F Oligo Microarrays was custom designed and contains 60-mer probes. The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).

scan_protocol: Images were captured with a Agilent Technologies Scanner G2505C/GenePix 4000B (Axon) and spots quantified using GenPix software (Axon).

data_processing: Background correction and normalization of expression data were performed using the methods normexp and loess in LIMMA. Linear model methods were used for determining differentially expressed genes. Each probe was tested for changes in expression over replicates by using an empirical Bayes moderated t-statistic. To control the false discovery rate p-values were corrected by using the method of Benjamani and Hochberg. The expected False Discovery Rate (FDR) was controlled to be less than 5%. Genes were considered differentially expressed when nominal p-values were <0.05 and had a fold change (FC) equal or higher than ±1.5. FC was calculated as the average of the fold change between significantly regulated probes (complete_data.txt).

growth_protocol: Paired independent L. plantarum batch cultures (50 mL each) were grown in MRS lacking GA to an OD600 ≈ 0.8-0.9, then one pair of the culture were exposed  to GA to bring their final concentration to 15 mM. Cell cultures were centrifuged after 10 minutes of exposure toGA and RNA was extracted and purified.

tag: exposed to

value: gallic acid (final conc. 15 mM)

tag: compound

value: none (control)


title: MEDULLOBLASTOMA3 45

description: MIRNA EXPRESSION FROM CSF

value: CSF


title: 1.5 mM Gallic acid 10 min replicate 2

description:
Biological replicate 2 of 3
Slide L. plantarum WCFS1 8x15K microarray GE Agilent G2509F Oligo Microarrays No. 026636 was custom designed and contains 60-mer probes that were taken at the gene expression omnibus database (GEO accession number GPL5874). The oligo-microarray contained an average of three probes per transcript. Each slide contains 8 arrays, these are numbered as follows: 1_1 (1st column upper row), 1_2 (2nd column upper row), 1_3 (3rd column upper row), 1_4 (4th column upper row),  2_1 (1st column lower row),2_2 (2nd column lower row), 2_3 (3rd column lower row), 2_4 (4th column lower row).


title: Gallic acid 10 min replicate 2

description: Biological replicate 2 of 3


title: CCA1-ox, 6am, small polysomal, replicate 1

source_name: CCA1-ox_6am_small polysomal

value: Columbia


title: Gallic acid 10 min replicate 1

description: Biological replicate 1 of 3


title: MEDULLOBLASTOMA3 44

description: MIRNA EXPRESSION FROM CSF


title: wild type, 12am, large polysomal, replicate 3

source_name: wild type_12am_large polysomal

value: wild type

value: 10 days


title: CCA1-ox, 6am, non-polysomal, replicate 1

value: aerial part


title: MEDULLOBLASTOMA2 43

description: MIRNA EXPRESSION FROM CSF


title: wild type, 12am, non-polysomal, replicate 3

source_name: wild type_12am_non-polysomal


title: wild type, 6pm, large polysomal, replicate 3

source_name: wild type_6pm_large polysomal


title: MEDULLOBLASTOMA2 42

description: MIRNA EXPRESSION FROM CSF


title: wild type, 12am, small polysomal, replicate 3

source_name: wild type_12am_small polysomal


title: miRNA_E95K mutant IhhN induced cells_rep2

first: Lu

last: Shen

address: RM 218 Little White House 1954 Huashan RD

department: Bio-X Institutes

institute: Shanghai Jiao Tong University

description: miRNA expression after 48hr in C3H10T1/2 cells in the presence of 750nM E95K mutant IhhN

hyb_protocol: Cy3-labelled miRNA sample was hybridized following the manufacturers instructions. Hybridized to Agilent 8x15K miRNA Microarrays for 20 hours at 55°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 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: E95K mutant IhhN induced cells, 750nM for 2 days, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA according to the manufacturer's instructions. (http://www.agilent.com/cs/library/usermanuals/Public/G4170-90011_miRNA_Protocol_3.1.pdf)

extract_protocol: RNA was prepared from cells using Trizol reagent (Invitrogen) according to manufacturer's instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C3H10T1/2 cells, diluted 1:1 with MEM/EBSS medium supplemented with 10% heat-inactivated fetal bovine serum in the presence of 750nM IhhN protein, were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: induction

value: E95K mutant IhhN


title: miRNA_E95K mutant IhhN induced cells_rep1

source_name: E95K mutant IhhN induced cells, 750nM for 2 days, replicate 1


title: miRNA_non-protein induced normal cells_rep1

description: miRNA expression after 48hr incubation in C3H10T1/2 cells

source_name: non-protein induced normal cells, 750nM for 2 days, replicate 1


title: miRNA_wild type IhhN induced cells_rep2t2

description: miRNA expression after 48hr in C3H10T1/2 cells in the presence of 750nM wild type IhhN

source_name: wild type IhhN induced cells, 750nM for 2 days, replicate 2

value: wild type IhhN


title: miRNA_non-protein induced normal cells_rep2

source_name: non-protein induced normal cells, 750nM for 2 days, replicate 2


title: MEDULLOBLASTOMA2 38

description: MIRNA EXPRESSION FROM CSF

source_name: CSF

tag: sample type


title: miRNA_wild type IhhN induced cells_rep2t1


title: wild type, 6pm, small polysomal, replicate 3

source_name: wild type_6pm_small polysomal


title: wild type, 12pm, small polysomal, replicate 3

source_name: wild type_12pm_small polysomal


title: wild type, 6pm, non-polysomal, replicate 3

source_name: wild type_6pm_non-polysomal

value: Non-polysomal RNA


title: wild type, 12pm, large polysomal, replicate 3

source_name: wild type_12pm_large polysomal

value: Large polysomal RNA


title: wild type, 6am, large polysomal, replicate 3

source_name: wild type_6am_large polysomal


title: MEDULLOBLASTOMA2 40

description: MIRNA EXPRESSION FROM CSF

tag: disease state

value: MEDULLOBLASTOMA


title: wild type, 6am, non-polysomal, replicate 3

source_name: wild type_6am_non-polysomal


title: MEDULLOBLASTOMA2 39

description: MIRNA EXPRESSION FROM CSF


title: wild type, 12pm, non-polysomal, replicate 3

source_name: wild type_12pm_non-polysomal


title: MEDULLOBLASTOMA2 41

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA3 34

description: MIRNA EXPRESSION FROM CSF

value: GLIOBLASTOMA


title: GLIOBLASTOMA3 32

description: MIRNA EXPRESSION FROM CSF


title: wild type, 12am, large polysomal, replicate 2

source_name: wild type_12am_large polysomal


title: GLIOBLASTOMA3 35

description: MIRNA EXPRESSION FROM CSF


title: MEDULLOBLASTOMA 1 37

description: MIRNA EXPRESSION FROM CSF


title: miRNA_wild type IhhN induced cells_rep1t1

source_name: wild type IhhN induced cells, 750nM for 2 days, replicate 1


title: miRNA_wild type IhhN induced cells_rep1t2


title: wild type, 6am, small polysomal, replicate 3

source_name: wild type_6am_small polysomal

value: Small polysomal RNA


title: wild type, 12am, small polysomal, replicate 2

source_name: wild type_12am_small polysomal


title: wild type, 6pm, non-polysomal, replicate 2


title: GLIOBLASTOMA2 28

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA3 33

description: MIRNA EXPRESSION FROM CSF


title: wild type, 6am, large polysomal, replicate 2


title: wild type, 6pm, large polysomal, replicate 2

source_name: wild type_6pm_large polysomal


title: wild type, 12am, non-polysomal, replicate 2

source_name: wild type_12am_non-polysomal


title: GLIOBLASTOMA1 23

description: MIRNA EXPRESSION FROM CSF


title: wild type, 6pm, small polysomal, replicate 2


title: GLIOBLASTOMA3 31

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA2 27

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA2 25

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA1 24

description: MIRNA EXPRESSION FROM CSF


title: wild type, 12pm, small polysomal, replicate 2


title: wild type, 12pm, non-polysomal, replicate 2


title: wild type, 12pm, large polysomal, replicate 2


title: GLIOBLASTOMA1 22

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA3 29

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA1 19

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA1 20

description: MIRNA EXPRESSION FROM CSF


title: GLIOMA7 18

description: MIRNA EXPRESSION FROM CSF

value: GLIOMA


title: wild type, 6am, non-polysomal, replicate 2


title: wild type, 6am, small polysomal, replicate 2


title: wild type, 12am, non-polysomal, replicate 1


title: wild type, 12am, large polysomal, replicate 1


title: wild type, 12am, small polysomal, replicate 1


title: GLIOMA6 17

description: MIRNA EXPRESSION FROM CSF


title: GLIOBLASTOMA1 21

description: MIRNA EXPRESSION FROM CSF


title: GLIOMA5 16

description: MIRNA EXPRESSION FROM CSF


title: GLIOMA3 13

description: MIRNA EXPRESSION FROM CSF


title: GLIOMA4 15

description: MIRNA EXPRESSION FROM CSF


title: MENINGIOMA4 12

description: MIRNA EXPRESSION FROM CSF

value: MENINGIOMA


title: MENINGIOMA1 8

description: MIRNA EXPRESSION FROM CSF


title: MENINGIOMA3 11

description: MIRNA EXPRESSION FROM CSF


title: wild type, 6pm, large polysomal, replicate 1


title: wild type, 6pm, small polysomal, replicate 1


title: wild type, 12pm, large polysomal, replicate 1


title: MENINGIOMA2 9

description: MIRNA EXPRESSION FROM CSF


title: wild type, 12pm, small polysomal, replicate 1


title: wild type, 6am, non-polysomal, replicate 1


title: EPENDIMOMA2 6

description: MIRNA EXPRESSION FROM CSF

value: EPENDIMOMA


title: wild type, 6pm, non-polysomal, replicate 1


title: Modafinil treatment PFC 8

city: Braine L'Alleud

first: Andre

last: Nogueira da Costa

address: Chemin du Foriest 1

country: Belgium

institute: UCB Biopharma SPRL

description: Treatment 8 Brain region PFC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 – 18 hr at 45°C on GeneChip Mouse 430_2 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were washed, stained and scanned using a GeneArray scanner and scans were processed with Affymetrix GeneChip® Command Console (AGCC).

data_processing:
The data was processed with Affymetrix GeneChip® Command console. Array studio software (Omicsoft Corporation, USA) was used to analyse the microarray CEL files, applying the RMA algorithm for normalisaion.
affymetrix-algorithm-name = Rma
affymetrix-algorithm-param-quantification-scale = log2
program-company = Omicsoft
program-name = oplatformlib
program-version = 1.0.0.0

source_name: PFC dissected out from control mice injected with modafinil 65 mg/kg during conditioning

label_protocol: The 3’IVT protocol (Affymetrix, UK) was used for total RNA samples. The aRNA synthesized using the 3’IVT protocol was purified and fragmented before hybridization onto Affymetrix GeneChip® arrays (Mouse 430_2).

extract_protocol: Total RNA was extracted using a combined Trizol/RNeasy® method (Life Technologies and Qiagen Respectively. RNA quality was determined by UV spectrophotometry using a NanoDrop (Thermo Fischer Scientific, USA), and RNA quality assessed by calculating a RNA integrity number (RIN) using a Bioanalyzer 2100 (Agilent Technologies, France). RIN values of between 7 and 10 were considered of good quality to be used in microarray analysis.

treatment_protocol:
Immediately following the post-conditioning test on day eleven, thus 24h after the last administration of podafinil or saline, mice were sacrificed by cervical dislocation and the brain rapidly dissected out.
Brains were dissected out and immersed in RNAlater® solution (Life Technologies, Belgium), and stored for a maximum of 48 hours at 4˚c before storage at -80˚c for later analysis. The brain regions of interest (VTA, NAC, PFC) were cut in 100 μm thick slices using a Leica VT 1000S Vibratome. The VTA, NAC and PFC were dissected out, according to stereotaxic cooordinates of Franklin and Pxinos, using a biopsy ounch with a plunger system of 1 mm in diameter.

tag: gender

value: male

tag: weight

tag: injected with

value: modafinil 65 mg/kg during conditioning

value: brain

tag: tissue subtype

value: prefrontal cortex (PFC)


title: Modafinil treatment PFC 4

description: Treatment 4 Brain region PFC


title: wild type, 6am, small polysomal, replicate 1

tag: ecotype background

value: Columbia

tag: genotype/variation

value: wild type

tag: harvested at

tag: molecule subtype


title: CCA1-ox, 12am, total RNA, replicate 3

tag: age

value: 10 days

value: aerial part


title: wild type, 12pm, non-polysomal, replicate 1


title: wild type, 6am, large polysomal, replicate 1


title: Modafinil treatment PFC 6

description: Treatment 6 Brian region PFC

tag: strain


title: Modafinil treatment PFC 3

description: Treatment 3 Brain region PFC

tag: tissue


title: CCA1-ox, 6pm, total RNA, replicate 3


title: Modafinil treatment PFC 2

description: Treatment 2 Brain region PFC


title: Modafinil treatment PFC 7

description: Treatment 7 Brain region PFC


title: Modafinil treatment PFC 1

description: Treatment 1 Brain region PFC


title: Modafinil treatment PFC 5

description: Treatment 5 Brain region PFC


title: EPENDIMOMA1 4

description: MIRNA EXPRESSION FROM CSF

value: CSF


title: Vehicle PFC 8

description: Vehicle 8 Brain region PFC

source_name: PFC dissected out from control mice injected with saline during conditioning

value: saline during conditioning


title: GLIOMA2 3

description: MIRNA EXPRESSION FROM CSF


title: Vehicle PFC 6

description: Vehicle 6 Brain region PFC


title: Vehicle PFC 7

description: Vehicle 7 Brain region PFC


title: GLIOMA1 1

description: MIRNA EXPRESSION FROM CSF


title: NORMAL/NON DISEASED 14 N14

description: MIRNA EXPRESSION FROM CSF

value: NORMAL/NON DISEASED


title: NORMAL/NON DISEASED 13 N13

description: MIRNA EXPRESSION FROM CSF


title: NORMAL/NON DISEASED 12 N12

description: MIRNA EXPRESSION FROM CSF


title: NORMAL/NON DISEASED 11 N11

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 12am, total RNA, replicate 2


title: CCA1-ox, 12pm, total RNA, replicate 3


title: NORMAL/NON DISEASED 10 N10

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 6pm, total RNA, replicate 2


title: Vehicle PFC 3

description: Vehicle 3 Brain region PFC


title: NORMAL/NON DISEASED 9 N9

description: MIRNA EXPRESSION FROM CSF


title: NORMAL/NON DISEASED 15 N15

description: MIRNA EXPRESSION FROM CSF


title: NORMAL/NON DISEASED 8 N8

description: MIRNA EXPRESSION FROM CSF


title: CCA1-ox, 6am, total RNA, replicate 3


title: Vehicle PFC 5

description: Vehicle 5 Brain region PFC


title: Vehicle PFC 4

description: Vehicle 4 Brain region PFC


title: CCA1-ox, 12pm, total RNA, replicate 2


title: Vehicle PFC 1

description: Vehicle 1 Brain region PFC


title: CCA1-ox, 6am, total RNA, replicate 2


title: Modafinil Tratment NAC 5

description: Treatment 5 Brain region NAC

source_name: NAC dissected out from control mice injected with modafinil 65 mg/kg during conditioning

extract_protocol: Total RNA was extracted using a combined Trizol/RNeasy® method (Life Technologies and Qiagen Respectively. RNA quality was determined by UV spectrophotometry using a NanoDrop (Thermo Fischer Scientific, USA), and RNA quality assessed by calculating a RNA integrity number (RIN) using a Bioanalyzer 2100 (Agilent Technologies, France). RNA concentrations of the two pieces of 50 mouse brain samples ranged from 5.8 to 46.9ng/μL. RNA (50ng) with a RIN score >7 were pooled and labelled. Five samples with RIN <7 were not pooled with their respective second sample.

value: nucleaus accumbens (NAC)


title: Vehicle PFC 2

description: Vehicle 2 Brain region PFC


title: Modafinil Tratment NAC 4

description: Treatment 4 Brain region NAC


title: CCA1-ox, 12am, total RNA, replicate 1


title: CCA1-ox, 12pm, total RNA, replicate 1


title: CCA1-ox, 6am, total RNA, replicate 1


title: Modafinil Tratment NAC 3

description: Treatment 3 Brain region NAC


title: wild type, 12am, total RNA, replicate 3

source_name: wild type_12am


title: CCA1-ox, 6pm, total RNA, replicate 1


title: Modafinil Tratment NAC 1

description: Treatment 1 Brain region NAC


title: NORMAL/NON DISEASED 7 N7

description: MIRNA EXPRESSION FROM CSF

source_name: CSF


title: NORMAL/NON DISEASED 6 N6

description: MIRNA EXPRESSION FROM CSF


title: NORMAL/NON DISEASED 5 N5

description: MIRNA EXPRESSION FROM CSF


title: NORMAL/NON DISEASED 4 N4

description: MIRNA EXPRESSION FROM CSF


title: wild type, 6am, total RNA, replicate 3

source_name: wild type_6am


title: wild type, 12pm, total RNA, replicate 3

source_name: wild type_12pm


title: NORMAL/NON DISEASED 2 N2

description: MIRNA EXPRESSION FROM CSF


title: wild type, 6pm, total RNA, replicate 3

source_name: wild type_6pm


title: Vehicle NAC 5

description: Vehicle 5 Brain region NAC

source_name: NAC dissected out from control mice injected with saline during conditioning


title: NORMAL/NON DISEASED 3 N3

description: MIRNA EXPRESSION FROM CSF


title: Vehicle NAC 3

description: Vehicle 3 Brain region NAC


title: wild type, 6pm, total RNA, replicate 2


title: Modafinil Tratment NAC 2

description: Treatment 2 Brain region NAC


title: wild type, 12am, total RNA, replicate 2


title: wild type, 6am, total RNA, replicate 2


title: wild type, 12pm, total RNA, replicate 2


title: wild type, 12am, total RNA, replicate 1


title: wild type, 12pm, total RNA, replicate 1


title: Vehicle NAC 4

description: Vehicle 4 Brain region NAC


title: Vehicle NAC 2

description: Vehicle 2 Brain region NAC


title: wild type, 6pm, total RNA, replicate 1


title: Vehicle VTA 5

description: Vehicle 5 Brain region VTA

source_name: VTA dissected out from control mice injected with saline during conditioning

value: ventral tegmental area (VTA)


title: Modafinil Tratment VTA 3

description: Treatment 3 Brain region VTA

source_name: VTA dissected out from mice injected with modafinil 65mg/kg during conditioning


title: Modafinil Tratment VTA 1

description: Treatment 1 Brain region VTA


title: wild type, 6am, total RNA, replicate 1


title: Vehicle NAC 1

description: Vehicle 1 Brain region NAC


title: Modafinil Tratment VTA 4

description: Treatment 4 Brain region VTA


title: ProliferativeVsQuiescent Replicate 4

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

country: Canada

institute: University of Saskatchewan

hyb_protocol: Labelled cDNA hybridised the to arrays for 16 hours using Slidebooster (Advalytix). Arrays then washed in 2x SSC (+0.2 % SDS), 2x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min. Hybridization of the Cy3/Cy5-containing dendrimers were then performed followed by repetition of the washing steps prior to drying and scanning.

scan_protocol: Arrays were scanned using InnoScan700. Arrays images were imported into BlueFuse 3.2 software for analysis.

data_processing: Raw data was imported into the BioArray Software Environment (BASE), subjected to cross-channel correction, and normalized using the LOWESS algorithm. Intensity values were log transformed and comparison between dye-swapped Cy3/Cy5 samples performed. Four biological replicates were analyzed. Fold-change values were calculated.

source_name: Quiescent human normal diploid fibroblast

label_protocol: cDNAs were labeled using the 3DNA array 900 labeling kit (Genisphere) as per manufacturer's instructions

growth_protocol: Proliferative fibroblasts were grown in 10% FBS/DMEM high glucose in 5% CO2.

extract_protocol: Trizol/MP24 fast RNA extraction kit (green) were used for extractions.

treatment_protocol: Quiescence was induced by the addition of 0.5% FBS containing DMEM for 5 days in 5% CO2.

tag: cell type

value: normal diploid fibroblast

tag: cell state

value: quiescent

source_name: Proliferative human normal diploid fibroblast

value: proliferative


title: Modafinil Tratment VTA 5

description: Treatment 5 Brain region VTA


title: Modafinil Tratment VTA 2

description: Treatment 2 Brain region VTA


title: GLIOBLASTOMA3 30

description: MIRNA EXPRESSION FROM CSF

value: GLIOBLASTOMA


title: ProliferativeVsQuiescent Replicate 3


title: Vehicle VTA 4

description: Vehicle 4 Brian region VTA

value: male


title: Extravillous trophoblast - sample 6

city: Maplewood

first: Nick

last: Illsley

state: NJ

address: Richmond Ave

institute: Placental Research Group LLC

description:
Test
EVT6

data_processing:
The data from the PCR Array was analyzed using DDCT methodology to obtain the fold-change in relative gene expression between CTB and EVT
The B2M, GAPDH, RPLP0 and HPRT1 housekeeping genes were used to normalize our samples
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Statistical significance was calculated using a two-tailed Mann-Whitney U test using the  2^-deltaCt values
the fold_change.txt reports test/control (i.e., EVT/CTB) ratios.

source_name: Placenta 6

label_protocol: For each sample cDNA was transcribed from 10 ng of RNA using an RT2 PreAmp cDNA Synthesis Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, using the RT2 PreAmp Pathway Primer Mix specific for the Epithelial-Mesenchymal Transition (EMT) RT2 Profiler PCR Array (Cat. #PBH-090Z, Qiagen). The RT2 Profiler PCR Array (Cat# PAHS-090Z) was analyzed using an ABI 7900 HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA) under cycling conditions recommended by the manufacturer.

extract_protocol: RNA was extracted using the Invitrogen PureLink RNA Mini Kit (Life Technologies) according to the manufacturer's instructions.

treatment_protocol: EVT and CTB were sorted into 2 mL RNAse-free tubes containing 0.5 mL RNAlater (Life Technologies)

value: placenta

tag: gestational age

value: Extravillous trophoblast


title: Extravillous trophoblast - sample 4

description:
Test
EVT4

source_name: Placenta 4


title: Extravillous trophoblast - sample 5

description:
Test
EVT5

source_name: Placenta 5

value: 10 wk


title: Vehicle VTA 2

description: Vehicle 2 Brain region VTA

value: brain


title: ProliferativeVsQuiescent Replicate 1


title: ProliferativeVsQuiescent Replicate 2


title: Vehicle VTA 1

description: Vehicle 1 Brain region VTA


title: Extravillous trophoblast - sample 1

description:
Test
EVT1

source_name: Placenta 1


title: Extravillous trophoblast - sample 2

description:
Test
EVT2

source_name: Placenta 2

value: 6 wk


title: Extravillous trophoblast - sample 3

description:
Test
EVT3

source_name: Placenta 3


title: Cytotrophoblast - sample 6

description:
Control
CTB6

value: Cytotrophoblast


title: mRNA_non-protein induced normal cells_rep1

description: Gene expression after 48hr incubation in C3H10T1/2 cells

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

source_name: non-protein induced normal cells, 750nM for 2 days, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared from cells using Trizol reagent (Invitrogen) according to manufacturer's instruction.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: induction


title: Control, biological rep1

city: London

first: David

middle: E

last: Carter

state: ON

address: 1151 Richmond Street North

department: London Regional Genomics Centre

institute: Robarts Research Institute

description: Gene expression from control rep1

hyb_protocol: 12.5 ug of amplified RNA was hybridized for 16 hr at 45C onto Affymetrix Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek, and differentially expressed genes were identified by a combination of statistical analysis (p<0.05) and comparison analysis (displayed >1.5-fold increase or decrease from the control to BMP treatment).

source_name: Cells not treated

label_protocol: Biotin end labeled single strand cRNA was prepared according to the Affymetrix GeneChip 3' IVT Express Kit User Manual (P/N 702646 Rev. 1)

growth_protocol: Cells were grown under standard culture conditions

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to the manufacturer's instructions

treatment_protocol: Cells were treated with and without 100 ng/ml recombinant human BMP3 for 6 hours

value: C3H10T1/2 cells

value: mesenchymal stem cells


title: Control, biological rep2

description: Gene expression from control rep2


title: BMP3l, biological rep1

description: Gene expression from BMP3 treated rep1

source_name: Cells treated with BMP3


title: mRNA_E95K mutant IhhN induced cells_rep1

description: Gene expression after 48hr in C3H10T1/2 cells in the presence of 750nM E95K mutant IhhN

source_name: E95K mutant IhhN induced cells, 750nM for 2 days, replicate 1

value: E95K mutant IhhN


title: Cytotrophoblast - sample 5

description:
Control
CTB5


title: Vehicle VTA 3

description: Vehicle 3 Brain region VTA

value: saline during conditioning


title: Cytotrophoblast - sample 4

description:
Control
CTB4


title: Cytotrophoblast - sample 3

description:
Control
CTB3


title: Cytotrophoblast - sample 2

description:
Control
CTB2


title: Cytotrophoblast - sample 1

description:
Control
CTB1


title: mRNA_wild type IhhN induced cells_rep1

description: Gene expression after 48hr in C3H10T1/2 cells in the presence of 750nM wild type IhhN

source_name: wild type IhhN induced cells, 750nM for 2 days, replicate 1

value: wild type IhhN