title: HEK/RPF-1 Tet13- vs HEK/RPF1 Tet9+

city: Milano

first: gabriele

last: bucci

address: via olgettina 58

department: CTGB

institute: IRCCS Ospedale San Raffaele

description: ChIP-chip HEK/RPF-1 Tet-/Tet+; IP by HA

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, resuspended in H2O, and hybridized in 18 μl of hybrization buffer according to the manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Two-color arrays were scanned with a GenePix 4000B scanner according to the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: HA ChIP DNA from Tet13- cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 and Cy5-labeled nonamers following the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: HEK/RPF-1 cells were cultured 48 h Tet-depleted medium (Tet-)

extract_protocol: 6x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.1 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 0.5 ml of lysis buffer (0.25% SDS, 8 mM EDTA, 50 mM HEPES pH7.5 plus 0.2 mM DTT, 0.5 MM PMSF, 0.2mM Na3VO4) for 15 min on ice before crosslinked chromatin was sheared to an average size of 500-bp by ten 10-second pulses at 60% output using a Branson Digital Sonifier 450 (Branson Ultrasonics). The lysates were then centrifuged to remove cell debris and diluted with 4-vol of ChIPbuffer (1% Triton X-100, 50 mM HEPES pH 7.5, 180 mM KCl plus protease inhibitors) and pre-cleared with 20 µl protein A/G sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 1 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4°C. After incubation with protein A/G sepharose beads (40 µl) for 2h at 4°C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4°C; washing buffer (145 mM KCl, 50 mM HEPES pH 7.5, 0.05% SDS), high-salt buffer (washing plus 0.3M KCl), LiCl buffer (250 mM LiCl, 50 mM HEPES pH 7.5, 0.2% Na deoxycholate, 1% NP40), and 2x TE (20 mM Tris pH8, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 400 µl elution buffer (1% SDS, 10mM Tris pH 8) at 50°C for 1 h followed by O/N incubation at 65°C and ProteinaseK digestion at 45 °C. Genomic DNA was isolated from the precipitated material by phenol/chloroform extraction, ethanol precipitation, RNAse digestion, and purification by QIAquick minicolumns (Quiagen). Purified genomic DNA was amplified by WGA reamplification kit (Sigma).

treatment_protocol: Cells were treated with 1% formaldehyde before harvesting

value: HEK293/RPF-1 Tet- (test)

tag: chip ab

value: anti-HA

source_name: HA ChIP DNA from Tet9+ cells

growth_protocol: HEK/RPF-1 cells were cultured 48 h in presence of (Tet+)

value: HEK293/RPF-1 Tet+ (control)


title: HEK/RPF-1 Tet- vs HEK/RPF1 Tet+

status: Public on Sep 06 2016

type: genomic

state: MI

country: Italy

description: ChIP-chip HEK/RPF-1 Tet-/Tet+; IP by HA

molecule: genomic DNA

organism: Homo sapiens

source_name: HA ChIP DNA from Tet- cells

tag: cell type

tag: cell line

source_name: HA ChIP DNA from Tet+ cells


title: CNTRL 3

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalization with BeadStudio software

label: biotin

molecule: total RNA

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

growth_protocol: HEK293 cells were cultured 3 d in complete medium

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cultured in

value: complete medium for 3d (uninduced control)


title: tRA/cAMP 1

growth_protocol: HEK293 cells were cultured 3 d in tRA/cAMP-supplemented medium

value: tRA/cAMP-supplemented medium for 3d


title: CNTRL 2


title: HEK/RPF-1 Tet4- vs HEK/RPF1 Tet3+

description: ChIP-chip HEK/RPF-1 Tet-/Tet+; IP by HA

source_name: HA ChIP DNA from Tet4- cells

source_name: HA ChIP DNA from Tet3+ cells


title: tRA/cAMP 3


title: HEK/RPF-1 Tet10- vs HEK/RPF1 Tet7+

description: ChIP-chip HEK/RPF-1 Tet-/Tet+; IP by HA

source_name: HA ChIP DNA from Tet10- cells

source_name: HA ChIP DNA from Tet7+ cells


title: GEK70

type: SRA

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: smallRNA

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Jatropha curcas

source_name: mature seed

growth_protocol: Jatropha curcas plants were grown in an open environment (15°16'16.68"S 39°05'34.50"W). Flowers were tagged upon opening and fruits from different plants were collected in the middle of a light cycle at 40 to 60 days after flower opening (DAF) (mature seeds). The seeds were dissected from the fruits and immediately frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing and sequencing by Illumina HiSeq2000. Three libraries were generated from immature, intermediate and mature seeds. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.

tag: sample

value: pool

tag: daf

tag: tissue

value: seeds


title: CNTRL 1


title: FSH 3

city: Chicago

first: Carlos

middle: Oscar

last: Stocco

state: IL

address: 835 S Wolcot Ave

department: Physiology and Biophysics

country: USA

institute: Univ Of Illinois at Chicago

hyb_protocol: RNA samples were labeled and hybridized according to standard 3’ IVT target labeling protocol recommended by Affymetrix.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
Data was processed using Genomics Suite 6.6 statistical package (Partek, Inc).  The following parameters were applied for hybridization signal processing: Algorithm: RMA, Background Correction: RMA Background Correction. Normalization: Quantile Normalization ;Log Probes using Base: 2 Probeset Summarization: Median Polish
Log Probes using Base: 2

source_name: Human cumulus cells, FSH treated

label_protocol: 3’ IVT target labeling protocol

growth_protocol: 37C in cell culture incubator

extract_protocol: Direct-zol™ RNA MiniPrep (Zymo Research)

treatment_protocol: Control, FSH, AEW, FSH+AEW

value: primary cumulus cells

tag: treatment

value: FSH


title: FSH+AEW 3

source_name: Human cumulus cells, Combined treatment

value: FSH+AEW


title: Control 2

source_name: Human cumulus cells, Untreated

value: control


title: FSH+AEW 1


title: Control 1


title: Control 3


title: FSH 2


title: FSH+AEW 2


title: FSH 1


title: week_14_DISEASED_8

city: Cambridge

first: Agnes

last: Gardet

state: MA

address: 115 broadway

department: Immunology

institute: Biogen

hyb_protocol: HT MG-430 PM plates were hybridized, washed, and stained using the Affymetrix automated protocol (HYB_0001 and WS_0001) according to the GeneChip Expression Analysis Technical manual for HT Plate Arrays Using the GeneChip Array Station (P/N 702063, Affymetrix Inc.)

scan_protocol: Labeled cDNA was hybridized to plate arrays and were scanned using a GeneChip HT Array plate scanner v1.0 (Affymetrix Inc.) to acquire raw image files

data_processing: Probe intensity values were normalized using Robust Multi-array Average (RMA) normalization, using Partek® Genomics Suite® software (version 6.6 Copyright ©; 2014).

organism: Mus musculus

source_name: kidney

label_protocol: Sample labeling and hybridization were carried out using the NuGEN Ovation Biotin systems (NuGEN Technologies, Inc.) as described in the NuGEN Ovation Biotin system for 96 well plates (version 5).

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

value: Pristane

tag: time point

value: week 14

tag: mouse strain


title: AEW 1

source_name: Human cumulus cells, AEW treated

value: AEW


title: week_14_DISEASED_6


title: week_14_NORMAL_3


title: week_14_DISEASED_4


title: week_14_DISEASED_7


title: week_14_DISEASED_5


title: week_14_DISEASED_2


title: week_14_NORMAL_2


title: week_14_NORMAL_5


title: week_14_DISEASED_3


title: week_14_NORMAL_1


title: week_14_DISEASED_9


title: week_14_DISEASED_1


title: Liver_DW_4hr_no4

city: Kawasaki

first: Fumika

last: SHINOZAKI

address: 3-25-13 Tonomachi, Kawasaki-ku

country: Japan

institute: Kanagawa Institute of Industrial Science and Technology

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

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

data_processing: CEL files were quantified with the Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

source_name: Liver of mouse administrated water

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA ( GeneChip 3'IVT Express Kit User Manual, P/N702646 Rev.8, Affymetrix).

tag: strain

value: ddY

tag: Sex

value: Male

value: Liver


title: tRA/cAMP 2


title: week_14_NORMAL_4


title: AEW 2


title: week_12_DISEASED_5

value: week 12


title: week_12_DISEASED_6


title: week_12_DISEASED_2


title: week_12_DISEASED_8


title: week_12_DISEASED_4


title: week_12_NORMAL_9


title: week_12_NORMAL_8


title: week_12_NORMAL_7


title: week_12_NORMAL_10


title: week_12_DISEASED_1


title: week_12_NORMAL_4


title: week_12_NORMAL_5


title: week_12_NORMAL_6


title: AEW 3


title: week_8_DISEASED_6

value: week 8


title: week_12_NORMAL_2


title: week_12_NORMAL_1


title: week_8_DISEASED_3


title: week_8_DISEASED_4


title: week_8_DISEASED_8


title: week_8_DISEASED_5


title: week_12_NORMAL_3


title: week_8_DISEASED_7


title: week_8_DISEASED_2


title: week_8_NORMAL_10


title: week_8_NORMAL_9


title: week_8_NORMAL_6


title: week_8_NORMAL_5


title: week_4_DISEASED_10

value: week 4


title: week_8_NORMAL_8


title: week_8_NORMAL_1


title: week_8_NORMAL_2


title: week_4_DISEASED_9


title: week_8_NORMAL_7


title: week_4_DISEASED_6


title: week_4_NORMAL_6


title: week_4_DISEASED_8


title: week_4_DISEASED_3


title: week_4_DISEASED_7


title: week_4_DISEASED_2


title: week_12_DISEASED_3


title: week_4_DISEASED_1


title: week_4_NORMAL_8


title: week_4_NORMAL_9


title: week_4_NORMAL_3


title: week_4_NORMAL_4


title: week_12_DISEASED_7


title: week_8_NORMAL_4


title: week_4_DISEASED_5


title: week_4_NORMAL_5


title: week_8_NORMAL_3


title: week_4_NORMAL_7


title: week_4_DISEASED_4


title: week_2_DISEASED_9

value: week 2


title: week_2_DISEASED_5


title: week_2_NORMAL_10


title: week_2_DISEASED_7


title: week_2_DISEASED_3


title: week_2_DISEASED_1


title: week_2_NORMAL_6


title: week_2_DISEASED_2


title: week_2_NORMAL_3


title: week_2_NORMAL_5


title: week_0_NORMAL_4

value: week 0


title: week_0_NORMAL_5


title: week_0_NORMAL_2


title: week_2_NORMAL_9


title: week_0_NORMAL_7


title: week_2_NORMAL_8


title: week_4_NORMAL_2


title: week_2_NORMAL_7


title: week_2_DISEASED_4


title: week_0_NORMAL_3


title: week_0_NORMAL_6


title: week_2_DISEASED_6


title: week_2_NORMAL_4


title: week_0_NORMAL_1


title: week_2_NORMAL_2


title: week_2_NORMAL_1


title: week_8_DISEASED_1


title: untreated_Week_2_8

source_name: whole blood

value: whole blood

value: Week 2


title: untreated_Week_2_5


title: untreated_Week_2_2


title: untreated_Week_2_4


title: untreated_Week_2_1


title: untreated_Week_2_6


title: Pristane_treated_Week_2_2


title: untreated_Week_2_3


title: Pristane_treated_Week_2_8


title: Pristane_treated_Week_2_1


title: Pristane_treated_Week_2_7


title: untreated_Week_2_7


title: Pristane_treated_Week_2_5


title: Pristane_treated_Week_2_6


title: untreated_Week_4_7

value: Week 4


title: Pristane_treated_Week_2_4


title: untreated_Week_4_4


title: Pristane_treated_Week_4_5


title: untreated_Week_4_6


title: untreated_Week_4_3


title: untreated_Week_4_8


title: Pristane_treated_Week_2_3


title: Pristane_treated_Week_4_8


title: Pristane_treated_Week_4_4


title: untreated_Week_4_2


title: untreated_Week_4_5


title: Pristane_treated_Week_4_7


title: untreated_Week_4_1


title: Pristane_treated_Week_4_6


title: Pristane_treated_Week_4_1


title: Pristane_treated_Week_4_2


title: untreated_Week_8_6

value: Week 8


title: untreated_Week_8_7


title: untreated_Week_8_3


title: Pristane_treated_Week_4_3


title: untreated_Week_8_4


title: untreated_Week_8_1


title: untreated_Week_8_8


title: untreated_Week_8_5


title: Pristane_treated_Week_8_8


title: untreated_Week_8_2


title: Pristane_treated_Week_8_7


title: Pristane_treated_Week_8_4


title: Pristane_treated_Week_8_3


title: Pristane_treated_Week_8_6


title: Pristane_treated_Week_8_5


title: Pristane_treated_Week_8_2


title: Pristane_treated_Week_8_1


title: untreated_week_12_6

value: Week 12


title: untreated_week_12_3


title: Pristane_treated_week_12_8


title: untreated_week_12_7


title: untreated_week_12_8


title: untreated_week_12_5


title: Pristane_treated_week_12_7


title: week_4_NORMAL_1


title: untreated_week_12_1


title: week_2_DISEASED_8


title: untreated_week_12_2


title: Pristane_treated_week_12_5


title: Pristane_treated_week_12_4


title: untreated_week_14_4

value: Week 14


title: Pristane_treated_week_12_2

value: Pristane


title: untreated_week_14_6


title: untreated_week_12_4


title: Pristane_treated_week_12_6


title: untreated_week_14_1


title: untreated_week_14_3


title: Pristane_treated_week_14_8


title: untreated_week_14_7


title: Pristane_treated_week_12_1


title: Pristane_treated_week_14_6


title: Pristane_treated_week_12_3


title: untreated_week_14_2


title: Pristane_treated_week_14_7


title: HepG2_siRNA_48hrs-rep3

city: Yuzhong distict

first: Li

last: Chuanwei

state: Chongqing

address: Changjiang road 10th

department: Department of cardiology

country: China

institute: The third military university

hyb_protocol: The fragmented and biotin labeled cDNA target were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0 ST array. Then the Gene Chips were washed with Affymetrix wash buffer and ddH2O and stained with by Affymetrix stain cocktail.

scan_protocol: After hybridization and washing, processed slides were scanned with the Affymetrix Gene Chip Scanner 3000 7G (Affymetrix, U.S.).

data_processing:
The Affymetrix Expression Console (version 1.2.1) implementation of robust microarray analysis (RMA) was used for quantile normalization and background correction. All gene level files were imported into Affymetrix Expression Console (version 1.2.1) and normalized by the RMA algorithm. A random variance model (RVM) t-test was applied to discriminate differentially expressed mRNAs between siRNA group and controls because the RVM t-test can raise degrees of freedom effectively in the case of small samples.
After false-discovery rate (FDR) analysis, we selected differentially expressed genes only if p value < 0.05 and the change in expression was >1.2-fold or <0.8 (provided in the 'Differential expressed genes.xlsx').

label_protocol: Total RNA was used to synthesize double-stranded complementary DNA (cDNA) utilizing a random priming method, and then double-stranded cDNA was fragmented, labelled with biotin according to the standard Affymetrix protocol.

growth_protocol: The cells were cultured in Dulbecco's Modified Eagle Medium (DMEM,Gibco, U.S. ), supplemented with 10% fetal bovine serum (FBS, Gibco, U.S.) as well as 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen , U.S.) and maintained at 37°C with 5% CO2.

extract_protocol: Cells were homogenized using RNAiso plus (Takara, Japan), total RNA was extracted by RNeasy kit (Qiagen, Germany), and RNA was quantified by spectrophotometry (Nanodrop 2000, U.S.).

treatment_protocol: For transient transfections, cells were plated at 1 × 10^5 cells ml−1 for 24 hours  before transfection  with antibiotic free medium. Transfections (50 nM) were conducted with siRNA (targeting pool) against AP000770.1-1 (GenePharma, China) or nontargeting controls (GenePharma, China) according to the manufacturer’s protocol for 48 hours.

value: Human hepatocellular carcinoma cell line

tag: genotype/variation

value: AP000770.1-1 knockdown


title: HepG2_control_48hrs-rep2

value: control


title: HepG2_siRNA_48hrs-rep2


title: HepG2_control_48hrs-rep3


title: untreated_week_14_8


title: Pristane_treated_week_14_4


title: HepG2_control_48hrs-rep1


title: Pristane_treated_week_14_3


title: Pristane_treated_week_14_1


title: untreated_Week_36_6

value: spontaneous disease

value: Week 36


title: Comparison of healthy donors versus Rheumatoid arthritis patients

city: Montpellier

first: Florence

last: Apparailly

address: CHU Saint Eloi, 80 rue Augustin Fliche

country: France

institute: INSERM

description: Additional eligibility criteria: methotrexate (MTX) treatment; DAS28 ≥ 3.2; and resistance to at least 2 DMARDs (MTX and anti-TNF included). For one month or more before the start of this study, every patient was given stable doses of oral corticosteroids and did not receive any intra-articular steroid injections.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C. After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

source_name: Blood of healthy donors

label_protocol: The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

extract_protocol: Blood samples were collected using EDTA-coated tubes (BD VacutainerTM 5 ml; BD Diagnostics, France) according to standard procedure. Aliquots of 0.5 ml of blood samples were immediately transferred to 1.2 ml of RNAlater medium (Applied Biosystems) and stored at -20°C. Total RNA was extracted using a modified protocol from the Ribopure-Blood RNA isolation kit (Applied Biosystems). Briefly, 10µl glacial acid (Sigma, France) was added to blood cell lysate (800µl, step 1 and 2 according to the manufacturer’s instruction). The samples were extracted with acid phenol/Chloroform, 1 ml of GuSCN Lysis solution (4 M Guanidinium Thiocyanate, 25 mM Sodium Citrate, 0.5%(w/v) Sodium N-lauroyl Sarcosinate and 0.1 M beta-mercaptoethanol and 1.25 volumes of ethanol were added to the aqueous phase. The samples were passed through a Filter cartridge and washed first with wash solution 1 (70% EtOH/30%GuSCN lysis solution) and second with wash solution 2 (80% EtOH/ 50 mM NaCl). The RNA was eluted in 100µl Elution solution preheated to 80°C and stored at -20°C. The concentration and integrity of RNA were determined by NanoDrop ND-1000 spectrophotometry (NanoDrop Tech, Rockland, Del) and by a Bioanalyzer Agilent 1. For pool samples, measures were taken to guarantee that RNA from each subject was of equal amount.

value: fresh peripheral blood

tag: disease status

value: healthy donor with no history of autoimmune disease

source_name: Blood of Rheumatoid arthritis patients

value: Rheumatoid arthritis patients fulfilling the 1987 revised classification criteria of the american college of rheumatology.

tag: therapy

value: oral corticosteroids for at least one month


title: untreated_Week_36_7


title: untreated_Week_36_5


title: HepG2_siRNA_48hrs-rep1


title: Pristane_treated_week_14_2


title: untreated_Week_36_4


title: untreated_Week_36_1


title: T6

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

hyb_protocol: On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs were chosen for further data analysis,Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. The threshold set for up- and down-regulate genes was a fold change≥2.0 and a P-value≤0.05. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples

source_name: adjacent normal tissue6

label_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.

growth_protocol: HEK-293T cells and pancreatic cancer cells PANC-1 and AsPC-1 were obtained from the Ametican Type Culture Collection(Rockville, MD, USA) and HPDE6-C7, Patu 8988, BxPC-3 and SW 1990 cells were purchased from the Institute of Biochemistry and Cell Biology of the Chinese Academy of Sciences(Shanghai, China). All cells were tested and authenticated by DNA typing at the Shanghai Jiao Tong University Analysis Core. The cells were maintained in DMEM or RPMI 1640(Gibco) supplemented with 10% FBS, 2 mmol/L L-glutamine, and penicillin，(5U/mL)/streptomycin (50 mg/mL) at 37℃ under 5% CO2 in a humidified chamber.

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen) according to the manufacturer’s instructions. Total RNA (2 μg) was reverse transcribed in a final volume of 10 μl using random primers under standard conditions for the PrimeScript RT Reagent Kit (Invitrogen)

value: adjacent normal tissue


title: T2

source_name: adjacent normal tissue2


title: untreated_Week_36_2

value: whole blood


title: untreated_Week_36_3


title: untreated_Week_36_8


title: ADV_IFNa_week9_04

value: kidney

value: week 9

value: NZB X NZW F1 (BWF1)


title: T4

source_name: adjacent normal tissue4


title: N3

source_name: Pancreatic cancer 3

value: Pancreatic cancer


title: T5

source_name: adjacent normal tissue5


title: N2

source_name: Pancreatic cancer 2


title: ADV_IFNa_week9_03


title: T1

source_name: adjacent normal tissue1


title: N6

source_name: Pancreatic cancer 6


title: ADV_IFNa_week9_02


title: T3

source_name: adjacent normal tissue3


title: ADV_IFNa_week9_01


title: N5

source_name: Pancreatic cancer 5


title: ADV_IFNa_week7_05

value: week 7


title: N1

source_name: Pancreatic cancer 1


title: ADV_IFNa_week9_05

source_name: kidney


title: N4

source_name: Pancreatic cancer 4


title: ADV_IFNa_week7_03


title: ADV_IFNa_week7_04


title: ADV_IFNa_week5_04

value: week 5


title: ADV_IFNa_week7_01


title: ADV_IFNa_week5_05


title: ADV_IFNa_week7_02


title: ADV_IFNa_week5_02


title: ADV_IFNa_week3_04

value: week 3


title: ADV_IFNa_week3_02


title: ADV_IFNa_week3_03


title: ADV_IFNa_week2_03

value: week 2


title: ADV_IFNa_week2_04


title: ADV_IFNa_week5_03


title: ADV_IFNa_week3_05


title: ADV_IFNa_week2_01


title: ADV_IFNa_week5_01


title: ADV_IFNa_week2_05


title: SET/I2PP2A targeting shRNA expressing MKN45

city: Yamaguchi

first: Takashi

last: Ohama

address: 1677-1 Yoshida

institute: Yamaguchi University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing:
Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1
The comparative analysis between test sample and control sample was carried out using fold change.

source_name: MKN45 shSET

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: RPMI1640 medium with 10% fetal calf serum

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

tag: gender

value: Female

value: Stomach (adenocarcinoma)

value: SET knockdown


title: ADV_IFNa_week3_01


title: Untreated_02

value: Untreated


title: ADV_IFNa_week1_02

value: week 1


title: ADV_IFNa_week1_04


title: ADV_IFNa_week1_03


title: Untreated_03


title: ADV_IFNa_week1_01


title: ADV_IFNa_week1_05


title: Untreated_01


title: ADV_IFNa_week2_02


title: Zika virus

city: Ribeirao Preto

first: Victor

middle: Hugo

last: Aquino

state: Sao Paulo

address: Avenida do Cafe, s/n

department: Fculty of Pharmaceutical Sciences

institute: University of Sao Paulo

hyb_protocol: The fragmented cRNA of each samplte was resuspended with 2X hybridization buffer and directly pipetted onto each sub-array of the RoboArboChip v2 microarray. The arrays were hybridized at 65 ºC with a rotation of 10 rpm, for 17 h using the Agilent Hybridization oven (Agilent Technology, USA). The RoboArboChip  slides were washed with the Gene Expression Wash Buffer 1 for 1min and then with the Gene Expression Wash Buffer 2 for 1min. The slides were added to a rack containing the Stabilization and Draying Solution for 30seconds.

scan_protocol: The RoboArboChip slides were scanned with the Axon GenePix 4000B scanner (Molecular Devices, USA) at a 532 nm wavelength with a pixel size of 10 μm.

data_processing: The median fluorescence intensity of each spot with local background subtraction were calculated from the scanned images with the GenePix Pro 7 software (Molecular Devices, USA). For data analysis, we have developed the RoboArboChip Analysis Form (RAF) using the Microsoft Excel software. The RAF contains an algorithm similar to that used by the DetectiV software (Watson et al., 2007). All the raw data were normalized against the negative control probes, distributed randomly in 78 spots of each sub-array; thus, the fluorescence intensity of each probe was divided by the mean fluorescence intensity of the negative control probes. After normalization, all the values £1 were transformed to 1. Normalized data were log2 transformed to reduce variability. The mean signal intensity of all the spots containing the probes of each virus species were calculated. The hypothesis that the mean signal intensity of the group of probes of each virus species is equal to the mean signal intensity of the negative control probes was tested by Welch’s t-test that is useful when two samples have unequal variances and unequal sample sizes, which is the case of the data obtained with the RoboArboChip platform. A virus was considered present in the analyzed sample when the mean signal intensity of the group of probes was significantly (p≤0.05) higher than the mean signal intensity of the negative control probes and showed a normalized mean intensity of 1 or higher than 1, i.e. at least two times higher than the mean signal intensity of the negative control probes.

organism: Zika virus

source_name: Baby mouse brain

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, one color (Agilent Technology, USA), according to the manufacturer’s instructions. Briefly, total RNA was mixed with the WT primer mix, a 1:5000 dilution of the positive RNA control (Agilent, USA) and incubated at 65 ºC for 10min. cDNA master mix (5X first strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was added to the reaction mixer. The samples were incubated at 40 ºC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 ºC for 15min. The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours. The transcirption reaction product was purified using the MEGAclear Kit (Amion, USA), according to the manufacturer’s instructions. Cyanine 3-labeled cRNA was fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 ºC for 30min.

growth_protocol: Laboratory viruses were propagated in C6/36 or Vero cells using Leibovitz's L-15 medium containing 10% fetal bovine serum (FBS) (Cultilab, Brazil). The Zika virus was obtained from Baby mice cerebrum.

extract_protocol: Total RNA was purified from 140 µL of the supernatant of infected and uninfected cell cultures with the AxyPrep viral RNA/DNA Miniprep Kit (Axigen, USA), following the manufacturer’s recommendation. The RNA was stored at -80ºC until use.

tag: virus strain

tag: virus family

value: Flaviviridae

tag: virus genus

value: Alphavirus


title: Negative control

organism: Aedes albopictus

source_name: Uninfected C6/36 cells


title: Control Non-Targeting shRNA expressing MKN45

source_name: MKN45 shNT

tag: cell line

value: control


title: Pool of three viruses: Zika virus, Dengue virus-1, Chikungunya virus

organism:
dengue virus type 1
Chikungunya virus
Zika virus

source_name: Baby mice brain (ZIKV), supernatant of C6/36 cells

tag: mammalian host

value: mouse brain

value: N/A, Mochizuki, ATCCVR 64

value: Flaviviridae, Togaviridae

value: Flavivirus, Alphavirus


title: v2 Dengue virus type 4

organism: dengue virus type 4

source_name: Supernatant of C6/36 cells

value: Flavivirus


title: v2 Dengue virus type 1

organism: dengue virus type 1

value: Mochizuki


title: v2 Dengue virus type 2

organism: dengue virus type 2

value: New Guinea C


title: HRG_PI3K_NFkB_(11h) N

status: Public on Sep 05 2016

city: Shirokanedai Minato-ku

first: Kana

last: Tominaga

state: Tokyo

department: Molecular therapy

institute: Insutitute of Medical Science, University of Tokyo

description: SAMPLE 95

hyb_protocol: Hybridization was carried out using the Gene Expression Hybridization Kit (Agilent Technologies) as follows: 1.65 mg of cRNA samples were fragmented (30 min at 60 ℃) and were then hybridized to a 4x180K Agilent Whole Human genome Oligo DNA Custom Microarray (G4862A, Agilent Technologies).

scan_protocol: Microarrays were scanned using a dynamic autofocus microarray scanner (Agilent DNA Microarray Scanner, Agilent Technologies) under default parameters (Green PMT was set to 100%, and the scan resolution was set to 5 μm).

data_processing: Feature Extraction Software v9.1 (Agilent Technologies) was used to obtain a raw signal value and a quality flag (Present [P], Marginal [M], or Absent [A]).

label_protocol: Total RNA samples (100 ng) were labeled with Cyanine 3-CTP using the Low Input Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was subsequently isolated using the Trizol reagent (Life technologies).

value: female


title: Pristane_treated_week_14_5

source_name: whole blood

value: whole blood

value: Pristane

value: Week 14


title: HRG_PI3K_NFkB_(13h) N

description: SAMPLE 97


title: HRG_PI3K_NFkB_(5h) N

description: SAMPLE 89


title: HRG_PI3K_NFkB_(14h) N

description: SAMPLE 98


title: HRG_PI3K_NFkB_(3h) N

description: SAMPLE 87


title: HRG_PI3K_NFkB_(4h) N

description: SAMPLE 88


title: HRG_PI3K_NFkB_(16h) N

description: SAMPLE 100


title: HRG_PI3K_NFkB_(16h) LY

description: SAMPLE 82


title: HRG_PI3K_NFkB_(12h) N

description: SAMPLE 96


title: HRG_PI3K_NFkB_(6h) N

description: SAMPLE 90


title: HRG_PI3K_NFkB_(0h) N

description: SAMPLE 84


title: HRG_PI3K_NFkB_(10h) N

description: SAMPLE 94


title: HRG_PI3K_NFkB_(15h) N

description: SAMPLE 99


title: HRG_PI3K_NFkB_(7h) N

description: SAMPLE 91


title: HRG_PI3K_NFkB_(1h) N

description: SAMPLE 85


title: HRG_PI3K_NFkB_(2h) N

description: SAMPLE 86


title: HRG_PI3K_NFkB_(15h) LY

description: SAMPLE 81


title: HRG_PI3K_NFkB_(13h) LY

description: SAMPLE 79


title: HRG_PI3K_NFkB_(-2h) N

description: SAMPLE 83


title: HRG_PI3K_NFkB_(9h) N

description: SAMPLE 93


title: HRG_PI3K_NFkB_(12h) LY

description: SAMPLE 78


title: HRG_PI3K_NFkB_(8h) N

description: SAMPLE 92


title: HRG_PI3K_NFkB_(11h) LY

description: SAMPLE 77


title: HRG_PI3K_NFkB_(9h) LY

description: SAMPLE 75


title: HRG_PI3K_NFkB_(10h) LY

description: SAMPLE 76


title: HRG_PI3K_NFkB_(14h) LY

description: SAMPLE 80


title: HRG_PI3K_NFkB_(8h) LY

description: SAMPLE 74


title: HRG_PI3K_NFkB_(2h) LY

description: SAMPLE 68


title: HRG_PI3K_NFkB_(4h) LY

description: SAMPLE 70


title: HRG_PI3K_NFkB_(5h) LY

description: SAMPLE 71


title: HRG_PI3K_NFkB_(14h) HLY

description: SAMPLE 63


title: HRG_PI3K_NFkB_(7h) LY

description: SAMPLE 73


title: HRG_PI3K_NFkB_(15h) HLY

description: SAMPLE 64


title: HRG_PI3K_NFkB_(6h) LY

description: SAMPLE 72


title: HRG_PI3K_NFkB_(13h) HLY

description: SAMPLE 62


title: HRG_PI3K_NFkB_(16h) HLY

description: SAMPLE 65


title: HRG_PI3K_NFkB_(11h) HLY

description: SAMPLE 60


title: HRG_PI3K_NFkB_(0h) LY

description: SAMPLE 66


title: HRG_PI3K_NFkB_(1h) LY

description: SAMPLE 67


title: HRG_PI3K_NFkB_(12h) HLY

description: SAMPLE 61


title: HRG_PI3K_NFkB_(6h) HLY

description: SAMPLE 55


title: HRG_PI3K_NFkB_(3h) LY

description: SAMPLE 69


title: HRG_PI3K_NFkB_(7h) HLY

description: SAMPLE 56


title: HRG_PI3K_NFkB_(9h) HLY

description: SAMPLE 58


title: HRG_PI3K_NFkB_(8h) HLY

description: SAMPLE 57


title: HRG_PI3K_NFkB_(1h) HLY

description: SAMPLE 50


title: HRG_PI3K_NFkB_(10h) HLY

description: SAMPLE 59


title: HRG_PI3K_NFkB_(5h) HLY

description: SAMPLE 54


title: HRG_PI3K_NFkB_(13h) HD

description: SAMPLE 46


title: HRG_PI3K_NFkB_(4h) HLY

description: SAMPLE 53


title: HRG_PI3K_NFkB_(14h) HD

description: SAMPLE 47


title: HRG_PI3K_NFkB_(3h) HLY

description: SAMPLE 52


title: HRG_PI3K_NFkB_(15h) HD

description: SAMPLE 48


title: HRG_PI3K_NFkB_(16h) HD

description: SAMPLE 49


title: C2_control 'normal' small bowel

city: London

first: Andrea

last: Frilling

address: Du Cane Road

department: Department of Surgery and Cancer, Hammersmith Campus

country: United Kingdom

institute: Imperial College London

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Each dataset was normalised and analysed using DESeq2

label: nanostring probe

source_name: control 'normal' small bowel

label_protocol: Samples were processed according to the manufacturer's instructions, NanoString nCounter Human miRNA Expression Assay v2 (NanoString Technologies)

extract_protocol: Total RNA extracted using miRNeasy FFPE kit (QIAGEN)

tag: patient number

value: control 'normal' small bowel


title: HRG_PI3K_NFkB_(2h) HLY

description: SAMPLE 51


title: C1_control 'normal' small bowel


title: HRG_PI3K_NFkB_(12h) HD

description: SAMPLE 45


title: HRG_PI3K_NFkB_(7h) HD

description: SAMPLE 40


title: PatientB125_liver metastasis

source_name: liver metastasis

value: liver metastasis


title: HRG_PI3K_NFkB_(5h) HD

description: SAMPLE 38


title: HRG_PI3K_NFkB_(9h) HD

description: SAMPLE 42


title: HRG_PI3K_NFkB_(8h) HD

description: SAMPLE 41


title: HRG_PI3K_NFkB_(4h) HD

description: SAMPLE 37


title: HRG_PI3K_NFkB_(6h) HD

description: SAMPLE 39


title: HRG_PI3K_NFkB_(3h) HD

description: SAMPLE 36


title: PatientB124_liver metastasis


title: PatientB57_liver metastasis


title: PatientB66_liver metastasis_10.7


title: PatientB66_liver metastasis_10.8


title: HRG_PI3K_NFkB_(2h) HD

description: SAMPLE 35


title: HRG_PI3K_NFkB_(11h) HD

description: SAMPLE 44


title: PatientB133_liver metastasis_9.8


title: HRG_PI3K_NFkB_(16h) H

description: SAMPLE 33


title: HRG_PI3K_NFkB_(10h) HD

description: SAMPLE 43


title: v2 Dengue virus type 3

organism: dengue virus type 3


title: HRG_PI3K_NFkB_(14h) H

description: SAMPLE 31


title: HRG_PI3K_NFkB_(13h) H

description: SAMPLE 30


title: PatientB121_liver metastasis


title: PatientB118_liver metastasis


title: HRG_PI3K_NFkB_(11h) H

description: SAMPLE 28


title: HRG_PI3K_NFkB_(15h) H

description: SAMPLE 32


title: PatientB84_liver metastasis_9.1


title: PatientB133_liver metastasis_9.7


title: PatientB77_liver metastasis


title: PatientB84_liver metastasis_7.7


title: HRG_PI3K_NFkB_(1h) HD

description: SAMPLE 34


title: HRG_PI3K_NFkB_(12h) H

description: SAMPLE 29


title: PatientB103_lymph node metastasis

source_name: lymph node metastasis

value: lymph node metastasis


title: PatientB117_lymph node metastasis


title: PatientB124_lymph node metastasis


title: PatientB77_lymph node metastasis


title: PatientB9_liver metastasis


title: HRG_PI3K_NFkB_(7h) H

description: SAMPLE 24


title: PatientB74_lymph node metastasis


title: HRG_PI3K_NFkB_(6h) H

description: SAMPLE 23


title: HRG_PI3K_NFkB_(1h) H

description: SAMPLE 18


title: HRG_PI3K_NFkB_(5h) H

description: SAMPLE 22


title: HRG_PI3K_NFkB_(10h) H

description: SAMPLE 27


title: HRG_PI3K_NFkB_(9h) H

description: SAMPLE 26


title: HRG_PI3K_NFkB_(4h) H

description: SAMPLE 21


title: PatientB133_lymph node metastasis


title: HRG_PI3K_NFkB_(2h) H

description: SAMPLE 19


title: HRG_PI3K_NFkB_(8h) H

description: SAMPLE 25


title: HRG_PI3K_NFkB_(16h) D

description: SAMPLE 17


title: HRG_PI3K_NFkB_(15h) D

description: SAMPLE 16


title: HRG_PI3K_NFkB_(14h) D

description: SAMPLE 15


title: HRG_PI3K_NFkB_(13h) D

description: SAMPLE 14


title: PatientB89_lymph node metastasis


title: PatientB121.1_lymph node metastasis


title: PatientB60_lymph node metastasis


title: PatientB86_lymph node metastasis


title: PatientB76_lymph node metastasis_8.6


title: PatientB76_lymph node metastasis_8.7


title: PatientB84_lymph node metastasis


title: PatientB140_lymph node metastasis


title: PatientB125_SBNET

source_name: SBNET

value: SBNET


title: PatientB121.1_SBNET


title: HRG_PI3K_NFkB_(8h) D

description: SAMPLE 9


title: PatientB119_SBNET


title: PatientB117_SBNET


title: HRG_PI3K_NFkB_(12h) D

description: SAMPLE 13


title: HRG_PI3K_NFkB_(3h) H

description: SAMPLE 20


title: PatientB103_SBNET


title: HRG_PI3K_NFkB_(7h) D

description: SAMPLE 8


title: HRG_PI3K_NFkB_(11h) D

description: SAMPLE 12


title: HRG_PI3K_NFkB_(4h) D

description: SAMPLE 5


title: HRG_PI3K_NFkB_(10h) D

description: SAMPLE 11


title: HRG_PI3K_NFkB_(2h) D

description: SAMPLE 3


title: HRG_PI3K_NFkB_(5h) D

description: SAMPLE 6


title: HRG_PI3K_NFkB_(0h) D

description: SAMPLE 1


title: HRG_PI3K_NFkB_(6h) D

description: SAMPLE 7


title: PatientB124_SBNET


title: PatientB89_SBNET


title: PatientB77_SBNET


title: PatientB86_SBNET


title: HRG_PI3K_NFkB_(3h) D

description: SAMPLE 4


title: HRG_PI3K_NFkB_(1h) D

description: SAMPLE 2


title: PatientB65_SBNET


title: PatientB53_SBNET


title: PatientB74_SBNET


title: Patient15_SBNET


title: Patient14_SBNET


title: Patient13_SBNET


title: Patient13_normal lymph node

source_name: normal lymph node

value: normal lymph node


title: Patient13_lymph node metastasis


title: Patient13_adjacent normal small bowel

source_name: adjacent normal small bowel

value: adjacent normal small bowel


title: HRG_PI3K_NFkB_(9h) D

description: SAMPLE 10


title: PatientB66_SBNET


title: Patient12_SBNET


title: Patient11_SBNET


title: Iguape virus

hyb_protocol: Pre-hyb protocol: The cDNA of the purified RNA was synthesized using random primers with eight nucleotides linked to an artificial specific sequence (5’- GTT TCC CAG TAG GTC TCN NNN NNN N-3') (Palacios, 2007; Wang et al., 2002). The reaction mixture for synthesis of cDNA  contained: 12 μl of RNA, 1.2 mM of the random primers (Invitrogen, USA), 2 µL of a 1:5000 dilution of the positive RNA control (Agilent, USA), 0.4 mM dNTPs (Invitrogen, USA), 40 U RNAse inhibitor (RNAseOUT, Invitrogen, U.S.), 4 mM DTT, 200 U of M-MLV reverse transcriptase (Invitrogen,USA) and 5 μl of 5X buffer (250mM Tris-HCl [pH 8.3], 375mM KCl, 15mM MgCl 2) in a total volume of  25μl. The mixture was incubated at 25°C for 10 minutes, followed by incubation at 37°C for 2 hours and, finally, at 85°C for 5 minutes. The cDNA was amplified by PCR using a 1:9 mixture of the random primers and a primer targeting the specific primer sequence on the random primer (5’-CGC CGT TTC CCA GTA GGT CTC-3') (Palacios et al., 2007; Wang et al., 2002). In addition to the primers, the PCR reaction mixture contained 4 μl of cDNA, 2 mM MgCl2, 0.2 mM dNTP, 5U enzyme Platinum Taq DNA Polymerase (Invitrogen, USA), 5μl  of 10X buffer [SO4 600mm Tris (pH 8.9), NH4 SO4 180mM] in a total volume of 50μl. Amplification was performed using the Thermal Cycler MyCycler (BIO-RAD, USA). The reaction mixture was subjected to 8 cycles of 94°C for 30 seconds, 25oC for 1 min and 72°C for 1 minute, followed by 35 cycles at 94°C for 30 seconds, 55°C for 1 minute, and 72°C for 1 minute. PCR products were purified using Wizard SV Gel and PCR Clean-Up System (Progmega, USA), following the manufacturer's recommendations. The PCR products were tagged with a capture sequence for 3DNA dendrimers, which contain Cy3 dye as fluorescent reported molecule (Genisphere, Hatfield, PA, USA), following manufacturer’s recommendations. The tagged PCR products were added to the hybridization buffers (Genisphere, USA), heated at 80°C for 10 minutes, and then added to each sub-array of the RoboArboChip for hybridization at 65ºC overnight in the Agilent Hybridization oven (Agilent Technology, USA) with a rotation of 15 rpm. After hybridization, slides were washed (2X SSC, 0.2% SDS) three times to remove non-hybridized PCR products. The 3DNA dendrimers were mixed with the hybridization buffer (Genisphere, USA) and then added to the RoboArboChip for hybridization at 65ºc for 4 hours with a rotation of 15 rpm, following by a washing step as mention above.

organism: Iguape virus

label_protocol: The PCR products were tagged with a capture sequence for 3DNA dendrimers, which contains fluorescent reported molecules (Agilent Kit, USA), following manufacturer’s recommendations.

growth_protocol: Reference viruses were propagated in C6/36 or Vero cells using Leibovitz's L_15 medium containing 10% fetal bovine serum (FBS) (Cultlab, Brazil).

extract_protocol: Total RNA was purified from 140 µL of the supernatant of infected and uninfected cell cultures, clarified total blood samples, serum samples, and clarified mosquito homogenate samples with the AxyPrep viral RNA/DNA Miniprep Kit (Axigen, USA), following the manufacturer’s recommendation. The RNA was stored at -80ºC until use.

tag: viral strain

tag: age (years)

tag: viral family

value: Flaviviridae

tag: viral genus


title: Patient14_adjacent normal small bowel

tag: tissue


title: Patient10_adjacent normal small bowel


title: Guaroa virus

organism: Guaroa virus

value: BeAn 277

value: Bunyaviridae

value: Orthobunyavirus


title: Dengue virus type 4

value: Flavivirus


title: Dengue virus type 3


title: Dengue virus type 2


title: Patient9_adjacent normal liver

source_name: adjacent normal liver

value: adjacent normal liver


title: Patient9_liver metastasis


title: Patient10_SBNET


title: Dengue virus type 1

value: Mochizuki


title: Patient9_normal lymph node


title: Cacipacore virus

organism: Cacipacore virus

value: Phlebovirus


title: Mosquitoes pool sample spiked with DENV_2

organism:
Aedes aegypti
dengue virus type 2

source_name: Pool of mosquitoes

value: Adults

value: Culicidae/Flaviviridae

tag: sex (male/female)

value: Female

value: Aedes/Flavivirus


title: Patient10_lymph node metastasis


title: Patient9_lymph node metastasis


title: Bussuquara virus

organism: Bussuquara virus

value: BeAn 4073


title: Mosquitoes pool sample_2

organism: Aedes aegypti

value: Culicidae

value: Aedes


title: Mosquitoes pool sample_3


title: Patient9_adjacent normal small bowel


title: Patient8_adjacent normal small bowel


title: Patient9_SBNET

value: SBNET


title: Mosquitoes pool sample_1


title: Mosquitoes pool sample_4


title: Patient7_normal lymph node

value: normal lymph node


title: Patient8_lymph node metastasis

value: lymph node metastasis


title: Malaria suspected patient 9_wb spiked with DENV_2

source_name: Whole blood sample


title: Patient8_SBNET


title: Patient7_lymph node metastasis


title: Malaria suspected patient 9_wb


title: Patient7_SBNET


title: Patient7_adjacent normal small bowel

value: adjacent normal small bowel


title: Patient6_SBNET


title: Malaria suspected patient 6_wb


title: Malaria suspected patient 8_wb


title: Malaria suspected patient 4_wb

value: Male


title: Patient8_normal lymph node


title: Malaria suspected patient 5_wb

value: Unknown


title: Patient5_lymph node metastasis


title: Malaria suspected patient 3_wb


title: Patient5_SBNET


title: Patient5_adjacent normal small bowel


title: Malaria suspected patient 7_wb


title: Patient4_lymph node metastasis


title: Malaria suspected patient 1_wb


title: Patient4_normal lymph node


title: Patient4_adjacent normal small bowel


title: Patient3_adjacent normal small bowel


title: Patient4_SBNET


title: Patient3_SBNET


title: Patient2_normal lymph node


title: Malaria suspected patient 4

source_name: Serum


title: Malaria suspected patient 5


title: Patient2_liver metastasis

value: liver metastasis


title: Malaria suspected patient 6


title: Patient2_adjacent normal liver

value: adjacent normal liver


title: Malaria suspected patient 2


title: Dengue suspected patient 26


title: Malaria suspected patient 2_wb


title: Malaria suspected patient 3


title: Patient2_lymph node metastasis


title: Malaria suspected patient 1


title: Dengue suspected patient 28


title: Dengue suspected patient 27


title: Dengue suspected patient 24


title: Patient2_adjacent normal small bowel


title: Patient2_SBNET


title: Dengue suspected patient 23


title: Patient1_normal lymph node


title: Dengue suspected patient 22


title: Dengue suspected patient 25


title: Patient1_lymph node metastasis


title: Dengue suspected patient 19


title: Patient1_SBNET


title: Dengue suspected patient 21


title: Dengue suspected patient 20


title: Dengue suspected patient 13


title: Dengue suspected patient 14


title: Dengue suspected patient 6


title: Dengue suspected patient 17


title: Patient1_adjacent normal small bowel


title: Chikungunya virus

organism: Chikungunya virus

value: ATCCVR 64

value: Togaviridae

value: Alphavirus


title: Dengue suspected patient 16

organism: Homo sapiens


title: Dengue suspected patient 8


title: Dengue suspected patient 9


title: Dengue suspected patient 7


title: Dengue suspected patient 11


title: Dengue suspected patient 10


title: Dengue suspected patient 5


title: Dengue suspected patient 3


title: Dengue suspected patient 4


title: Dengue suspected patient 15


title: Dengue suspected patient 12


title: Dengue suspected patient 1


title: Dengue suspected patient 18


title: Dengue virus type 4 infected patient_RP_3

value: Flaviviridae

value: Flavivirus


title: Dengue virus type 4 infected patient_RP_2

value: Female


title: Dengue virus type 3 infected patient


title: Dengue virus type 1 infected patient_RP_52


title: Dengue virus type 1 infected patient_RP_45


title: Dengue virus type 2 infected patient


title: Pool of four DENV serotypes

organism: Dengue virus

value: Mochizuki, New Guinea C, H87 and H 241


title: Dengue suspected patient 2


title: Vero E6 cells

organism: Chlorocebus sabaeus

source_name: Uninfected Vero E6 cells

value: uninfected


title: Pool of three viruses from the Flavivirus genus

organism: Flavivirus

value: New Guinea C, SPH 34675 and BeH 356964


title: Dengue virus type 1 LLOD

value: Mochizuki


title: C6/36 cells

organism: Aedes albopictus


title: Yellow Fever virus

organism: Yellow fever virus

value: 17D (vaccine)


title: Pool of four viruses from three families (Rhabdoviridae, Togaviridae, Flaviviridae)

organism:
Togaviridae
Flaviviridae
Rhabdoviridae

value: Rhabdoviridae, Togaviridae and Flaviviridae

value: Vesiculovirus, Alphavirus and Flavivirus


title: West Nile virus

organism: West Nile virus

value: NY 99


title: Piry virus

organism: Piry virus

value: Rhabdoviridae

value: Vesiculovirus


title: Mayaro virus

organism: Mayaro virus


title: Ilheus virus

organism: Ilheus virus


title: Rocio virus

organism: Rocio virus


title: Rio Mamore virus

organism: Rio Mamore hantavirus

source_name: Supernatant of VERO E6

value: Bunyaviridae

value: Hantavirus


title: Mucambu virus

organism: Mucambo virus

value: ATCCRV 580

value: Togaviridae


title: Patient15_adjacent normal small bowel

value: adjacent normal small bowel


title: St. Louis encephalitis virus

organism: St. Louis encephalitis virus

value: Flaviviridae

value: Flavivirus


title: Oropouche virus

organism: Oropouche virus

value: Orthobunyavirus


title: BGC-823, parent

city: Nanjing

first: Yajie

last: Zhang

address: 140 Hanzhong Road

department: Cell biology

institute: Nanjing Medical University

description: RPMI 1640,10%FBS,100U/ml penicillin, and 100μg/mL streptomycin

hyb_protocol: All the samples were hybrided, washed, stained by Eukaryotic Hybridization Control Kit (Affymetrix,900454) and Hybridization, Wash and Stain Kit(Affymetrix,900720). 21.5 ul of biotin-labeled RNA was hybridized for 16 hr at 48oC on Affymetrix miRNA 2.0 Arrays. The miRNA 2.0 Arrays were washed and stained in the Affymetrix Fluidics Station 450 using fludics script FS450_0003.

scan_protocol: Scanner 3000 7G (Affymetrix),AGCC 2.0

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

source_name: gastric cells

label_protocol: All the samples were labeled by FlashTag™ Biotin RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays(Genisphere, FT30AFYB).Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA .

growth_protocol: SGC-7901 and BGC-823  were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin, and 100μg/mL streptomycin (Life Technologies, Gibco, MD, USA). Cells were grown at 37°C, in a humidified incubator with 5% CO2. Cisplatin resistant gastric cancer cells lines SGC-7901/DDP and BGC-823/DDP were produced from parental SGC-7901 and BGC-823 cells by persistence gradient exposure to cisplatin for about 12 months, which were subjected to increasing concentrations from 0.05μg/mL until the cells acquired resistance to 1μg/mL of cisplatin (Sigma-Aldrich, St. Louis, MO, USA). Prior to experiment, SGC-7901/DDP and BGC-823/DDP cells were cultured in original RPMI 1640 medium for 2 weeks.

extract_protocol: Totol miRNAs was extracted by TRIzol Reagent (Invitrogen Life Technologies) and MirVana® miRNA isolation Kit(Ambion, AM1560) according to the manufacturer's instructions.

treatment_protocol: All cells were grown in a 10 cm dish when cells were 70–80% confluent.Cells were harvested by trypsinization, centrifugation from the PBS washed.

tag: cell type

value: gastric cells

tag: description

value: parental cells


title: BGC-823/DDP,resistance

description: BGC-823/DDP were produced from parental BGC-823 by persistence gradient exposure to cisplatin for about 12 months, which were subjected to increasing concentrations from 0.05μg/mL until the cells acquired resistance to 1μg/mL of cisplatin (Sigma-Aldrich, St. Louis, MO, USA). Prior to experiment, BGC-823/DDP cells were cultured in original RPMI 1640 medium for 2 weeks.

value: resistant cells


title: SGC-7901/DDP,resistance

description: SGC-7901/DDP produced from parental SGC-7901 by persistence gradient exposure to cisplatin for about 12 months, which were subjected to increasing concentrations from 0.05μg/mL until the cells acquired resistance to 1μg/mL of cisplatin (Sigma-Aldrich, St. Louis, MO, USA). Prior to experiment, SGC-7901/DDP cells were cultured in original RPMI 1640 medium for 2 weeks.


title: SGC-7901,parent


title: animal_65_time_T0

status: Public on Sep 04 2016

city: jouy en josas

first: Nuria

last: Mach

address: Domaine de Vilvert

institute: INRA

description: validation

hyb_protocol: 55 µl of 2x Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the array following the recommended protocol. After hybridization, microarrays were washed 1 minute at room temperature with the GE Wash Buffer 1 (Agilent Technologies, USA) and 1 minute at 37°C using the GE Wash Buffer 2 (Agilent Technologies, USA).

scan_protocol: The slides were then scanned using a G2565CA Scanner System (Agilent Technologies, USA), using a scan protocol with a resolution of 3 µm and a dynamic range of 20 bit. The resulting TIFF images were analysed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the GE1_107_Sep09 protocol.

data_processing: All the steps of transcriptome pre-processing, normalization and statistical analysis were carried out using several Bioconductor packages in R programming language (version 3.02). To begin with, a first quality control on the data was performed using arrayQualityMetrics package58. Subsequently, all of the probes showing any of the following Agilent flags gIsFeatPopnOL = 1, gIsBGNonUnifOL= 1, gIsFeatNonUnifOL = 1 were removed from further analysis steps. The raw intensity values were then background corrected using the “normexp” function and the expression data were quantile normalized (Limma package59; version 3.14.4). Probe summarization was performed based on the median expression value between replicated probes. A total of 24,415 genes were retained in this study. As many of the original annotations for the equine custom Agilent microarray (AMAMID 021322, enriched with 384 equine transcripts) have been found to be incomplete, the annotation available June 2014 at (http://www.genomics.agilent.com/en/Custom-Design-Tools/eArray/?cid=AG-PT-122&tabId=AG-PR-1047) was used to re-annotate the probes to new probe sets.

organism: Equus caballus

label_protocol: Transcriptome profiling was performed using an equine custom 4x44K microarray (ID: 044466, Agilent Technologies, USA). Cyanine-3 (Cy3) labelled cRNAs were prepared from 100 ng of total RNA and using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies, USA). Specific activities and cRNA yields were measured using the NanoDrop ND-1000 (Thermo Scientific, USA). For each sample 1.65 µg of Cy3-labeled cRNA (specific activity > 9.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes in a volume of 55 µl containing 25x of Agilent Fragmentation Buffer and 10x of Agilent Blocking Agent.

extract_protocol: Blood for transcriptome and miRNome profiling was sampled at the same time using PAXgene Blood RNA tubes (Qiagen, Germany), in order to have a direct correspondence between mRNA and miRNA expression for each animal. Total RNA from circulating leukocytes, including B cells, T cells, neutrophils, monocytes and other less abundant cell types was isolated using PAXgene Blood RNA Kit (Qiagen,) according to the manufacturer’s instructions. The RNA purity and concentration were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was assessed using the Bioanalyzer 2100 (Agilent Technologies, USA). Each of the total 61 RNA samples was then divided into two aliquots that were used either for the miRNA microarray or the gene expression microarray

value: female

tag: breed

value: AR

tag: time


title: BCL11B-KO MEFs

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description: KO

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

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

data_processing: CEL files were quantified with the robust multi-array average (RMA) method, using the statistical language R (R-3.0.3) and Bioconductor 2.13.

organism: Mus musculus

source_name: Primary MEFs from embryos at embryonic day (E) 12.5 of BCL11B-KO mouse

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Primary MEFs were cultured in DMEM with 10% fetal bovine serum (FBS), 100 units/mL penicillin and 100 μg/mL streptomycin, and passage was discontinued before they became confluent. Differentiation experiments were carried out using the cells at passage 2.

extract_protocol: Total RNA was isolated using ISOGEN (Nippon Gene Co., Toyama, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: MEFs were differentiated using the adipocyte differentiation medium (DMEM containing 0.5 mM methylisobutylxanthine (MIX), 1 μM dexamethasone (DEX), 10 μg/ml insulin, 10 μM pioglitazone, and 10% FBS) for 12h.

tag: strain

value: mouse embryonic fibroblasts

tag: genotype/variation


title: animal_63_time_T1

description: validation

tag: gender

value: gelding


title: untreated_week_14_5

value: whole blood

tag: treatment

tag: time point

value: Week 14

tag: mouse strain


title: animal_64_time_T1

description: training


title: PatientB66_lymph node metastasis

organism: Homo sapiens

tag: patient number

value: lymph node metastasis


title: animal_64_time_T0

description: training


title: animal_58_time_T1

description: training


title: WT MEFs

description: WT

source_name: Primary MEFs from embryos at embryonic day (E) 12.5 of wild type mouse

value: wild type (BCL11B +/+)


title: animal_50_time_T0

description: validation


title: animal_51_time_T0

description: training


title: animal_52_time_T0

description: validation


title: animal_61_time_T1

description: validation


title: animal_49_time_T0

description: training


title: animal_55_time_T1

description: validation

value: Autre


title: animal_54_time_T1

description: validation


title: animal_60_time_T1

description: validation


title: animal_58_time_T0

description: training


title: animal_53_time_T1

description: validation


title: animal_62_time_T1

description: validation


title: animal_51_time_T1

description: training


title: animal_59_time_T1

description: training


title: animal_56_time_T1

description: validation


title: animal_48_time_T1

description: validation


title: animal_46_time_T1

description: validation


title: animal_45_time_T1

description: validation


title: animal_49_time_T1

description: training


title: animal_57_time_T0

description: validation


title: animal_47_time_T0

description: validation


title: animal_43_time_T1

description: validation


title: animal_38_time_T1

description: validation


title: animal_40_time_T0

description: validation


title: animal_41_time_T1

description: training


title: animal_26_time_T1

description: validation


title: animal_37_time_T0

description: training


title: animal_41_time_T0

description: training


title: animal_37_time_T1

description: training


title: animal_44_time_T1

description: validation


title: animal_30_time_T0

description: validation


title: animal_32_time_T0

description: training


title: animal_35_time_T0

description: training


title: animal_33_time_T1

description: training


title: animal_27_time_T0

description: training


title: animal_35_time_T1

description: training


title: animal_34_time_T1

description: validation


title: animal_31_time_T1

description: validation


title: animal_28_time_T0

description: validation


title: animal_22_time_T1

description: validation


title: animal_23_time_T1

description: validation


title: animal_29_time_T0

description: validation


title: animal_36_time_T1

description: validation


title: animal_25_time_T1

description: validation


title: animal_33_time_T0

description: training


title: animal_32_time_T1

description: training


title: animal_27_time_T1

description: training


title: animal_24_time_T1

description: validation


title: animal_59_time_T0

description: training


title: animal_21_time_T1

description: validation


title: animal_20_time_T1

description: training


title: animal_17_time_T1

description: validation


title: animal_18_time_T0

description: validation


title: animal_20_time_T0

description: training


title: animal_16_time_T0

description: validation


title: animal_19_time_T1

description: validation


title: animal_12_time_T1

description: validation


title: animal_63_timeT1

description: validation

hyb_protocol: MicroRNAs were hybridized to the arrays using the miRNA Complete Labeling and Hybridization Kit (Agilent Technologies, USA) according to the manufacturer’s instructions

scan_protocol: Hybridized microarray slides were then washed and eventually scanned using a G2565CA Scanner System (Agilent Technologies, USA) using a scan protocol with a resolution of 3 µm and a dynamic range of 20 bits. The resulting TIFF images were analysed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using the miRNA_107_Sep09 protocol.

data_processing: The raw data was pre-processed using a variant of the robust multi-array average (RMA) algorithm that was specifically implemented for Agilent miRNA microarrays by Lopez-Romero et al 62. The RMA implementation from the AgiMicroRna package was used without the initial background correction step, as recommended 62. A miRNA transcript was considered detectable only if it met the following two conditions: 1) miRNA expressed in at least 33% of the experimental samples; 2) signal intensity higher than the mean of the negative control expression + 1.5 x sd. Identification of DEmiRNAs between groups was performed with the Limma package. In this case, the Benjamini-Hochberg adjustment, which represents a compromise between the unadjusted analysis of the multiple test and the Bonferroni procedures, was used for multiple test correction (FDR < 0.05). Multivariate analysis was performed as explained above. Additionally, we used the analysis of similarities (ANOSIM) to test for intragroup dispersion. As specified by 63, ANOSIM is a permutation-based test of the null hypothesis that within-group distances are not significantly smaller than between-group distances. The test statistic (R) can range from 1 to 0, with a value of 1 indicating that all samples within groups are more similar to each other than to any other samples from different groups. R is ≈0 when the null hypothesis is true, that distances within and between groups are the same on average.

label_protocol: For the miRNome profiling, an Agilent custom equine miRNA 8x60K microarray was used (ID: 060464). For each sample (n=61), a total amount of 100 ng of total RNA was dephosphorylated, 3' end-labelled with Cy3-pCp, purified on Micro Bio-Spin 6 columns (Bio-Rad, USA), dried, and hybridized to the arrays using the miRNA Complete Labeling and Hybridization Kit (Agilent Technologies, USA) according to the manufacturer’s instructions.


title: animal_64_timeT1

description: training


title: animal_64_timeT0

description: training


title: animal_5_time_T1

description: validation


title: animal_8_time_T1

description: validation


title: animal_9_timeT0

description: training


title: animal_9_timeT1

description: training


title: animal_13_time_T0

description: validation


title: animal_7_timeT1

description: validation

value: DSA


title: animal_6_time_T0

description: validation


title: animal_14_time_T0

description: validation


title: animal_7_time_T1

description: validation


title: animal_10_time_T0

description: validation


title: animal_60_timeT1

description: validation


title: animal_2_time_T1

description: training


title: animal_61_timeT1

description: validation


title: animal_62_timeT1

description: validation

value: AA


title: animal_1_time_T1

description: validation


title: animal_9_time_T0

description: training


title: animal_6_timeT0

description: validation


title: animal_4_time_T1

description: validation


title: animal_9_time_T1

description: training


title: animal_15_time_T0

description: validation


title: animal_2_time_T0

description: training


title: animal_65_timeT0

description: validation


title: animal_8_timeT1

description: validation


title: animal_59_timeT1

description: training


title: animal_59_timeT0

description: training


title: animal_54_timeT1

description: validation


title: animal_57_timeT0

description: validation


title: animal_58_timeT1

description: training


title: animal_53_timeT1

description: validation


title: animal_52_timeT0

description: validation


title: animal_58_timeT0

description: training


title: animal_49_timeT1

description: training


title: animal_47_timeT0

description: validation

value: SF


title: animal_49_timeT0

description: training


title: animal_48_timeT1

description: validation


title: animal_51_timeT1

description: training


title: animal_46_timeT1

description: validation


title: animal_44_timeT1

description: validation


title: animal_43_timeT1

description: validation

value: male


title: animal_51_timeT0

description: training


title: animal_50_timeT0

description: validation


title: animal_41_timeT1

description: training

value: OI


title: animal_41_timeT0

description: training


title: animal_40_timeT0

description: validation


title: animal_5_timeT1

description: validation


title: animal_4_timeT1

description: validation

value: PFS


title: animal_56_timeT1

description: validation


title: animal_38_timeT1

description: validation


title: animal_36_timeT1

description: validation


title: animal_37_timeT1

description: training

value: SHA


title: animal_35_timeT1

description: training


title: animal_37_timeT0

description: training


title: animal_45_timeT1

description: validation


title: animal_33_timeT0

description: training


title: animal_32_timeT0

description: training


title: animal_32_timeT1

description: training


title: animal_34_timeT1

description: validation


title: animal_27_timeT0

description: training


title: animal_30_timeT0

description: validation


title: animal_33_timeT1

description: training


title: animal_31_timeT1

description: validation


title: animal_26_timeT1

description: validation


title: animal_27_timeT1

description: training


title: animal_24_timeT1

description: validation


title: animal_35_timeT0

description: training


title: animal_25_timeT1

description: validation


title: animal_29_timeT0

description: validation


title: animal_23_timeT1

description: validation


title: animal_22_timeT1

description: validation


title: Late harvested  20kPa 3 days 0ºC replicate 2

city: Spain

first: M. Teresa

last: Sanchez-Ballesta

address: Jose Antonio Novais 10

country: Spain

institute: ICTAN-CSIC

description:
Vc_8
Gene expression data from the skin of grapes at early maturity stage stored 3 days 20kPa CO2 0ºC

hyb_protocol: CNB Grapegen Affymetrix hybridization

scan_protocol: CNB Grapegen Affymetrix scanning

data_processing: The data were analyzed using Robust Multichip Average (RMA) Express (v.1.0.4) using Affymetrix default analysis settings and quantile as normalization method.

organism: Vitis vinifera

source_name: Late harvested  20kPa 3 days 0ºC

label_protocol: CNB Grapegen Affymetrix labeling

growth_protocol: Table grapes cv. Cardinal were harvested from a commercial orchard in Sevilla (Spain) twice over 3 weeks. The first harvest began on the 13th June 2005 (early harvested) and the second on the 5th July 2005 at commercial maturity (late harvested).

extract_protocol: Total RNA was extracted from skin samples according to Zeng and Yang (2002). RNA samples were treated with DNase I recombinant-RNase free according to suppliers’ instructions (Roche). RNA purification was performed using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Table grapes were randomly divided into two lots. One was stored in air at 0ºC during 3 days (non-treated) and the other one, with same size, was kept under a gas mixture of 20 kPa CO2 + 20 kPa O2 + 60 kPa N2 (CO2-treated fruit) for up to 3 days

tag: cultivar

value: Cardinal

tag: maturity stage

value: late

tag: postharvest storage condition

value: 20 kPa CO2 at 0ºC for 3 days

value: skin


title: Late harvested  20kPa 3 days 0ºC replicate 3

description:
Vc_9
Gene expression data from the skin of grapes at early maturity stage stored 3 days 20kPa CO2 0ºC


title: animal_21_timeT1

description: validation

source_name: whole blood

value: gelding


title: animal_20_timeT0

description: training

value: female

value: AR


title: animal_20_timeT1

description: training


title: Late harvested Time zero replicate 3

description:
Vc_3
Gene expression data from the skin of time zero grapes at late maturity stage

source_name: Late harvested Time zero

value: Time zero


title: Late harvested air 3 days 0ºC replicate 3

description:
Vc_45
Gene expression data from the skin of grapes at late maturity stage stored 3 days air 0ºC

source_name: Late harvested air 3 days 0ºC

value: air 3 days 0ºC


title: Late harvested  20kPa 3 days 0ºC replicate 1

description:
Vc_7
Gene expression data from the skin of grapes at late maturity stage stored 3 days 20kPa CO2 0ºC


title: Late harvested air 3 days 0ºC replicate 1

description:
Vc_43
Gene expression data from the skin of grapes at late maturity stage stored 3 days air 0ºC


title: animal_2_timeT1

description: training


title: Late harvested Time zero replicate 2

description:
Vc_2
Gene expression data from the skin of time zero grapes at late maturity stage


title: animal_2_timeT0

description: training


title: Late harvested air 3 days 0ºC replicate 2

description:
Vc_44
Gene expression data from the skin of grapes at late maturity stage stored 3 days air 0ºC


title: animal_18_timeT0

description: validation


title: animal_19_timeT1

description: validation


title: animal_16_timeT0

description: validation


title: animal_15_timeT0

description: validation


title: animal_17_timeT1

description: validation


title: Late harvested Time zero replicate 1

description:
Vc_1
Gene expression data from the skin of time zero grapes at late maturity stage


title: Early harvested air 3 days 0ºC replicate 3

description:
Vc_12
Gene expression data from the skin of grapes at early maturity stage stored 3 days air 0ºC

source_name: Early harvested air 3 days 0ºC

value: early


title: Early harvested  20kPa 3 days 0ºC replicate 2

description:
Vc_29
Gene expression data from the skin of grapes at early maturity stage stored 3 days 20kPa CO2 0ºC

source_name: Early harvested  20kPa 3 days 0ºC


title: animal_14_timeT0

description: validation

value: DSA


title: animal_13_timeT0

description: validation


title: Early harvested  20kPa 3 days 0ºC replicate 3

description:
Vc_30
Gene expression data from the skin of grapes at early maturity stage stored 3 days 20kPa CO2 0ºC


title: Early harvested Time zero replicate 3

description:
Vc_27
Gene expression data from the skin of time zero grapes at early maturity stage

source_name: Early harvested Time zero


title: Early harvested air 3 days 0ºC replicate 1

description:
Vc_10
Gene expression data from the skin of grapes at early maturity stage stored 3 days air 0ºC


title: Early harvested Time zero replicate 2

description:
Vc_26
Gene expression data from the skin of time zero grapes at early maturity stage


title: animal_10_timeT0

description: validation


title: animal_1_timeT1

description: validation


title: Early harvested Time zero replicate 1

description:
Vc_25
Gene expression data from the skin of time zero grapes at early maturity stage


title: Early harvested  20kPa 3 days 0ºC replicate 1

description:
Vc_28
Gene expression data from the skin of grapes at early maturity stage stored 3 days 20kPa CO2 0ºC


title: Early harvested air 3 days 0ºC replicate 2

description:
Vc_11
Gene expression data from the skin of grapes at early maturity stage stored 3 days air 0ºC


title: animal_12_timeT1

description: validation


title: MDA urothelial conventional bladder tumor MDA cUC 88

status: Public on Sep 03 2016

city: Houston

state: TX

address: 1400 Pressler, unit 1410

department: Bioinformatics

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Quantile normalization in the Linear Model for Microarray Data (LIMMA)

source_name: Bladder tumor tissue embeded in parffin block

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

extract_protocol: RNA was extracted with MasterPure Complete Purification Kit from Epicentre in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: conventional urothelial carcinomas


title: MDA urothelial conventional bladder tumor MDA cUC 84


title: MDA urothelial conventional bladder tumor MDA cUC 80


title: MDA urothelial conventional bladder tumor MDA cUC 75


title: MDA urothelial conventional bladder tumor MDA cUC 83


title: MDA urothelial conventional bladder tumor MDA cUC 89


title: MDA urothelial conventional bladder tumor MDA cUC 86


title: MDA urothelial conventional bladder tumor MDA cUC 82


title: MDA urothelial conventional bladder tumor MDA cUC 76


title: MDA urothelial conventional bladder tumor MDA cUC 87


title: MDA urothelial conventional bladder tumor MDA cUC 69


title: MDA urothelial conventional bladder tumor MDA cUC 79


title: MDA urothelial conventional bladder tumor MDA cUC 72


title: MDA urothelial conventional bladder tumor MDA cUC 73


title: MDA urothelial conventional bladder tumor MDA cUC 71


title: MDA urothelial conventional bladder tumor MDA cUC 85


title: MDA urothelial conventional bladder tumor MDA cUC 81


title: MDA urothelial conventional bladder tumor MDA cUC 77


title: MDA urothelial conventional bladder tumor MDA cUC 78


title: MDA urothelial conventional bladder tumor MDA cUC 68


title: animal_55_timeT1

description: validation

value: AA


title: MDA urothelial conventional bladder tumor MDA cUC 70


title: MDA urothelial conventional bladder tumor MDA cUC 64


title: MDA urothelial conventional bladder tumor MDA cUC 74


title: MDA urothelial conventional bladder tumor MDA cUC 67


title: MDA urothelial conventional bladder tumor MDA cUC 66


title: MDA urothelial conventional bladder tumor MDA cUC 65


title: MDA urothelial conventional bladder tumor MDA cUC 63


title: MDA urothelial conventional bladder tumor MDA cUC 62


title: MDA urothelial conventional bladder tumor MDA cUC 60


title: MDA urothelial conventional bladder tumor MDA cUC 52


title: MDA urothelial conventional bladder tumor MDA cUC 58


title: MDA urothelial conventional bladder tumor MDA cUC 56


title: MDA urothelial conventional bladder tumor MDA cUC 59


title: MDA urothelial conventional bladder tumor MDA cUC 54


title: MDA urothelial conventional bladder tumor MDA cUC 61


title: MDA urothelial conventional bladder tumor MDA cUC 55


title: MDA urothelial conventional bladder tumor MDA cUC 51


title: MDA urothelial conventional bladder tumor MDA cUC 57


title: MDA urothelial conventional bladder tumor MDA cUC 50


title: MDA urothelial conventional bladder tumor MDA cUC 48


title: MDA urothelial conventional bladder tumor MDA cUC 44


title: MDA urothelial conventional bladder tumor MDA cUC 47


title: MDA urothelial conventional bladder tumor MDA cUC 43


title: MDA urothelial conventional bladder tumor MDA cUC 45


title: MDA urothelial conventional bladder tumor MDA cUC 38


title: MDA urothelial conventional bladder tumor MDA cUC 53


title: MDA urothelial conventional bladder tumor MDA cUC 36


title: MDA urothelial conventional bladder tumor MDA cUC 39


title: animal_28_timeT0

description: validation


title: MDA urothelial conventional bladder tumor MDA cUC 34


title: MDA urothelial conventional bladder tumor MDA cUC 35


title: MDA urothelial conventional bladder tumor MDA cUC 41


title: MDA urothelial conventional bladder tumor MDA cUC 46


title: MDA urothelial conventional bladder tumor MDA cUC 49


title: MDA urothelial conventional bladder tumor MDA cUC 40


title: MDA urothelial conventional bladder tumor MDA cUC 33


title: MDA urothelial conventional bladder tumor MDA cUC 32


title: MDA urothelial conventional bladder tumor MDA cUC 42


title: MDA urothelial conventional bladder tumor MDA cUC 29


title: MDA urothelial conventional bladder tumor MDA cUC 31


title: MDA urothelial conventional bladder tumor MDA cUC 25


title: MDA urothelial conventional bladder tumor MDA cUC 30


title: MDA urothelial conventional bladder tumor MDA cUC 26


title: MDA urothelial conventional bladder tumor MDA cUC 13


title: MDA urothelial conventional bladder tumor MDA cUC 23


title: MDA urothelial conventional bladder tumor MDA cUC 5


title: MDA urothelial conventional bladder tumor MDA cUC 21


title: MDA urothelial conventional bladder tumor MDA cUC 11


title: MDA urothelial conventional bladder tumor MDA cUC 15


title: MDA urothelial conventional bladder tumor MDA cUC 22


title: MDA urothelial conventional bladder tumor MDA cUC 17


title: MDA urothelial conventional bladder tumor MDA cUC 27


title: MDA urothelial conventional bladder tumor MDA cUC 14


title: MDA urothelial conventional bladder tumor MDA cUC 19


title: MDA urothelial conventional bladder tumor MDA cUC 16


title: MDA urothelial conventional bladder tumor MDA cUC 12


title: MDA urothelial conventional bladder tumor MDA cUC 6


title: MDA urothelial conventional bladder tumor MDA cUC 10


title: MDA urothelial conventional bladder tumor MDA cUC 7


title: MDA urothelial conventional bladder tumor MDA cUC 24


title: MDA urothelial conventional bladder tumor MDA cUC 20


title: MDA urothelial conventional bladder tumor MDA cUC 28


title: MDA urothelial conventional bladder tumor MDA cUC 9


title: MDA urothelial conventional bladder tumor MDA cUC 18


title: MDA urothelial conventional bladder tumor MDA cUC 4


title: MDA urothelial conventional bladder tumor MDA cUC 1


title: MDA urothelial conventional bladder tumor MDA cUC 8


title: MDA Micropapillary bladder tumor MDA MP43

value: micropapillary bladder tumors


title: MDA urothelial conventional bladder tumor MDA cUC 2


title: MDA Micropapillary bladder tumor MDA MP40


title: MDA Micropapillary bladder tumor MDA MP36


title: MDA Micropapillary bladder tumor MDA MP35


title: MDA Micropapillary bladder tumor MDA MP39


title: MDA Micropapillary bladder tumor MDA MP41


title: MDA Micropapillary bladder tumor MDA MP42


title: MDA Micropapillary bladder tumor MDA MP34


title: MDA Micropapillary bladder tumor MDA MP33


title: MDA Micropapillary bladder tumor MDA MP37


title: MDA Micropapillary bladder tumor MDA MP38


title: NIL-Bph6-RNAi leaf shealth with 6h BPH infestation, biological rep2

city: Wuhan

first: Jianping

last: Guo

address: Wuhan University

department: College of Life Sciences

institute: National Key Laboratory of Hybrid Rice

description: Gene expression data from NIL-BPH9 leaf shealth with 3h BPH infestation.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079,Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara,CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0  (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Plants were grown in a controlled growth chamber. The fourth leaf of 3-week-old young plants were used as the material in all experiments.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad,CA, US)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: Treat plants with BPH in different time points (as indicated) then sampled in the same time points.

value: leaf shealth

tag: genotype

value: Susceptible to BPH

tag: age

value: four-leaf stage


title: NIL-Bph6-RNAi leaf shealth with 48h BPH infestation, biological rep1

description: Gene expression data from NIL-BPH9 leaf shealth with 6h BPH infestation.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0

tag: tissue


title: MDA Micropapillary bladder tumor MDA MP32

scan_protocol: Standard Illumina scanning protocol


title: NIL-Bph6 leaf shealth with 48h BPH infestation, biological rep2

description: Gene expression data from 9311 leaf shealth with 6h BPH infestation.

value: Resistant to BPH


title: NIL-Bph6-RNAi leaf shealth without BPH infestation (at 0h), biological rep2

description: Gene expression data from NIL-BPH9 leaf shealth without BPH infestation (at 0h).


title: NIL-Bph6-RNAi leaf shealth without BPH infestation (at 0h), biological rep1


title: NIL-Bph6-RNAi leaf shealth without BPH infestation (at 0h), biological rep3


title: NIL-Bph6-RNAi leaf shealth with 6h BPH infestation, biological rep3


title: NIL-Bph6-RNAi leaf shealth with 48h BPH infestation, biological rep2


title: NIL-Bph6-RNAi leaf shealth with 48h BPH infestation, biological rep3


title: MDA Micropapillary bladder tumor MDA MP30


title: MDA Micropapillary bladder tumor MDA MP27


title: MDA Micropapillary bladder tumor MDA MP31


title: MDA Micropapillary bladder tumor MDA MP29


title: NIL-Bph6 leaf shealth with 6h BPH infestation, biological rep3

description: Gene expression data from 9311 leaf shealth with 3h BPH infestation.


title: NIL-Bph6 leaf shealth without BPH infestation (at 0h), biological rep3

description: Gene expression data from 9311 leaf shealth without BPH infestation (at 0h).


title: MDA Micropapillary bladder tumor MDA MP26


title: NIL-Bph6 leaf shealth with 6h BPH infestation, biological rep2


title: NIL-Bph6 leaf shealth with 48h BPH infestation, biological rep3


title: NIL-Bph6 leaf shealth with 48h BPH infestation, biological rep1


title: MCK-miR-499, biological rep3

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

description: Muscle RNA from muscle-specific miR-499 overexrpessing transgenic mouse

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data was analyzed using RMA algorithm using the Expression Console software Version 1.1 default settings.

source_name: Gastrocnemius muscle from miR-499 overexpressing mouse

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

extract_protocol: RNAzol B -followed manufacturers protocol

value: Gastrocnemius muscle for transgenic mouse overexpressing miR-499 in a skeletal muscle-specific manner

value: Transgenic mouse overexpressing miR-499 in a skeletal muscle-specific manner

value: 8 weeks of age


title: Non-transgenic mouse, biological rep2

description: Muscle RNA from littermate control mice for muscle-specific miR-499 overexrpessing transgenic mice

source_name: Gastrocnemius muscle from wild-type mouse

value: Gastrocnemius muscle wild-type mouse - control mouse for miR-499 overexpressing

value: Wild-type mouse - control mouse for miR-499 overexpressing


title: MCK-miR-499, biological rep1


title: NIL-Bph6 leaf shealth without BPH infestation (at 0h), biological rep1


title: NIL-Bph6 leaf shealth with 6h BPH infestation, biological rep1


title: Non-transgenic mouse, biological rep3


title: MCK-miR-499, biological rep2


title: NIL-Bph6-RNAi leaf shealth with 6h BPH infestation, biological rep1


title: Non-pregnant-mock

first: Lars

last: Dölken

state: Cambridgeshire

address: Addenbrookes Hospital, Hills Road

department: Medicine

institute: University of Cambridge

description: Affymetrix Mouse Gene 1.0 ST

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST arrays using manufacturer's equipment.

scan_protocol: Affymetrix Facility equipment (Technical University of Munich, Germany)

data_processing: RMA normalisation

source_name: ovary

label_protocol: Samples were labeled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction

growth_protocol: To ensure the same stage of the estrus cycle, non-pregnant mice were hormonally treated by sequential administration of pregnant mare's serum gonadotropin (PMSG) (Folligon, Intervet) and human chorionic gonadotropin (hCG) (Chorullon, Intervet).

extract_protocol: Equal amounts of RNA from 5 BALB/c mice per group isolated using Trizol (Invitrogen) were pooled.

treatment_protocol: Mice were infected 9.5 days post conception with 2x10e05 PFU MCMV i.v.. RNA was prepared at 5 days post infection (14.5 days post conception).

value: Balb/c

value: female

tag: condition

value: non-pregnant

tag: infection

value: mock-infected


title: MDA Micropapillary bladder tumor MDA MP24


title: MDA Micropapillary bladder tumor MDA MP25


title: MDA Micropapillary bladder tumor MDA MP23


title: Pregnant-mock

description: Affymetrix Mouse Gene 1.0 ST

value: pregnant

value: mock infected


title: Corpus luteum_day9-12_cow6

city: UNIVERSITY PARK

first: Samar

middle: and animal

last: Maalouf

state: Pennsylvania

address: 324 Henning Building

department: Animal Science

institute: Pennsylvania state university

hyb_protocol: According to standard protocols followed at Pennsylvania State University Expression Analysis, Genomics Core Facility

data_processing: Microarray Dat files were converted to Cel files, normalized to background controls, and analyzed using the Affymetrix miRNA QC Tools software.  Background hybridization value cut off was 4.  Intensities with a p-value < 0.06 were considered true values (above background). Labeling controls (Genisphere, Hatfield, PA) and hybridization control probes were used to determine successful labeling and efficient hybridization of RNA samples to microarray chips, respectively. Only miRNA with true values in all three replicates of either developing (D4) and/or midcycle (MC) CL were further analyzed.

label: Biotin

organism: Bos taurus

source_name: Corpus luteum, day 10 of estrous cycle or day 11 of estrous cycle

label_protocol: RNA with quality index (RIN) >8 were polyadenylated and biotinylated using the Genisphere Flash Tag Biotin RNA labeling kit (Genisphere Inc., Hatfield, PA).  Labeled miRNA were hybridized onto an Affymetrix Genechip miRNA microarray chip (Affymetrix, Santa Clara, CA) and miRNA expression was compared in day 4 (D4) vs. midcycle (day 9-12; MC) CL

growth_protocol: Handling of animals and surgical procedures were conducted according to protocols approved by the Institutional Animal Care and Use Committee (IACUC) at Pennsylvania State University, Pennsylvania, USA.

extract_protocol: Total RNA (including microRNA) were isolated from frozen luteal tissue using the MirVana miRNA isolation kit (Life Technologies) according to the manufacturer’s protocol. RNA quality was examined using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol:
The estrous cycle was synchronized in 6 cows using vaginally inserted Control Internal Drug Release (CIDR; Pharmacia & Upjohn Company LLC, New York, NY) devices that release progesterone, and injections of 25 mg of prostaglandin F2alpha (PGF2A), commercially available as Lutalyse (Pharmacia & Upjohn Company LLC).
CIDR devices were inserted vaginally for a period of 7 days.
PGF2A injection was administered on day 6, one day before CIDR removal, to induce luteal regression.
The three cows designated for early-cycle (day 4) time point received an injection of gonadotropin releasing hormone (GnRH; Factrel; Zoetis, Florham Park, NJ) to synchronize the ovulation of a dominant follicle, and were slaughtered 4 days later to collect a day 4 CL.
The three cows designated for midcycle CL collection were observed after CIDR removal to determine the onset of estrus, and on days 9-12 of the estrous cycle, the CL was collected by culpotomy.
All corpora lutea were quartered and immediately frozen in liquid nitrogen and stored at -80oC.

value: corpus luteum

tag: breed

value: Holstein

tag: day(s) of estrus


title: Pregnant-MCMV

description: Affymetrix Mouse Gene 1.0 ST

tag: strain

value: MCMV infected


title: MDA Micropapillary bladder tumor MDA MP20

value: micropapillary bladder tumors


title: Non-transgenic mouse, biological rep1


title: MDA Micropapillary bladder tumor MDA MP28


title: Non-pregnant-MCMV

description: Affymetrix Mouse Gene 1.0 ST

value: MCMV-infected


title: MDA urothelial conventional bladder tumor MDA cUC 37

value: conventional urothelial carcinomas


title: Corpus luteum_day4_cow3

scan_protocol: According to standard protocols followed at Pennsylvania State University Expression Analysis, Genomics Core Facility

source_name: Corpus luteum, day 4 of estrous cycle


title: Kupffer cell SR1078 rep 2

city: Seoul

first: Yong-Hyun

last: Han

state: Seoul

address: Daehak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
replicate 2
SAMPLE 12

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: Primary Mouse Kupffer cell

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: Kupffer cells were isolated from 8 weeks old, male C57BL/6 mice by perfusion of liver using collagenase type IV. For isolation of Kupffer cells, non-parenchymal sufficient supernatant was centrifuged in 50%/25% percoll  The layer containing Kupffer cells was plated with RPMI 1640 with 10% FBS.

extract_protocol: Cells were harvested in RLT buffer and RNA was extracted from cultured kupffer cells using the RNeasy micro KIT (Qiagen, Valencia, CA).

treatment_protocol: KCs were treated with 10 ng/ml LPS (M1), 20 ng/ml IL-4 (M2), DMSO (Veh), 10 mM SR3335, or 5 mM SR1078 for 24 h in RPMI medium.

value: Male

value: 8 weeks

tag: cell type

value: Primary cultured Kupffer cells


title: Corpus luteum_day9-12_cow4


title: Corpus luteum_day4_cow2


title: MDA Micropapillary bladder tumor MDA MP21


title: MDA Micropapillary bladder tumor MDA MP19


title: MDA Micropapillary bladder tumor MDA MP22


title: Corpus luteum_day9-12_cow5


title: MDA Micropapillary bladder tumor MDA MP16


title: Kupffer cell SR3335 rep 1

description:
replicate 1
SAMPLE 9

tag: gender


title: Kupffer cell SR3335 rep 2

description:
replicate 2
SAMPLE 10


title: MDA Micropapillary bladder tumor MDA MP18


title: MDA Micropapillary bladder tumor MDA MP15


title: Kupffer cell Veh rep 1

description:
replicate 1
SAMPLE 7


title: Kupffer cell SR1078 rep 1

description:
replicate 1
SAMPLE 11


title: Corpus luteum_day4_cow1


title: 5 v 15

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description: 5 v 15

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf

scan_protocol: Pixel Size : 5 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505C Scanning software : ChipScan Scanning software version : A.8.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 10.5.1.1
Datafile type : Agilent result file

organism: Saccharomyces cerevisiae

growth_protocol: OD : midlog

extract_protocol:
Extracted molecule : Total RNA
Extraction method : acid phenol prep http://dunham.gs.washington.edu/MDyeastRNA.pdf

tag: strain name

value: W303 WT


title: 16 v 15

description: 16 v 15

label_protocol: reference URL : http://dunham.gs.washington.edu/MDAgilentRNA.pdf

value: W303 DyNatA


title: Kupffer cell Veh rep 2

description:
replicate 2
SAMPLE 8


title: 17 vs 15

description: 17 vs 15

value: W303 yNatA::hNatA WT


title: Kupffer cell M2 IL-4 rep 1

description:
replicate 1
SAMPLE 5


title: 8 vs 5

description: 8 vs 5

value: W303 yNatA::hNatA S37P


title: 18 vs 15

description: 18 vs 15


title: Kupffer cell M1 LPS rep 1

description:
replicate 1
SAMPLE 3


title: MDA Micropapillary bladder tumor MDA MP13

first: Li


title: Kupffer cell M2 IL-4 rep 2

description:
replicate 2
SAMPLE 6


title: MDA Micropapillary bladder tumor MDA MP14


title: 7 vs 5

description: 7 vs 5


title: MDA Micropapillary bladder tumor MDA MP12


title: MDA urothelial conventional bladder tumor MDA cUC 3