title: DisColoEpithelium_miRNA_Control_rep3

city: Harbin

first: yanqiao

last: zhang

state: Heilongjiang

address: Haping Road # 150, Nangang District,Harbin, Heilongjiang Province, P. R. China

institute: Harbin Medical University Cancer Hospital

description: miRNA microarray of mouse colon epithelial tissue at day 100 in Control group

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Agilent)in hybridization Oven(Agilent)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Thermo Shandon, US) with Gene Expression Wash Buffer Kit(Agilent).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Agilent)and Feature Extraction software 10.7 (Agilent)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0  (Agilent).

source_name: Distal Colorectal Epithelial Tissue, 100day, Control, replicate 3

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Agilent)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Ambion, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent).

treatment_protocol: The epithelial tissue from the AOM, DSS and Control groups was scraped using a slide and kept in Trizol reagent (Invitrogen, Carlsbad, US). The AOM/DSS group neoplasm samples were clipped using ophthalmic scissors and kept in RNA storage solution (Tiangen, Peking, China).

value: Distal Colorectal Epithelial Tissue

value: female

tag: group

value: control


title: DisColoEpithelium_miRNA_Control_rep2

status: Public on May 10 2013

type: RNA

country: China

molecule: total RNA

organism: Mus musculus

source_name: Distal Colorectal Epithelial Tissue, 100day, Control, replicate 2

tag: tissue

tag: gender


title: AGS-004-004-010-003

city: Durham

first: Irina

middle: Yurievna

last: Tcherepanova

state: NC

address: 4233 Technology Drive

department: REsearch and Development

country: USA

institute: Argos Therapeutics Inc.

description: starting RNA for amplification sample 010-003

hyb_protocol: hybridization was performed according to standard Agilent procedures for 4X44K array. The arrays were custom made (Agilent) using probes generated for RCC genelist (Agilent) to correspond to 5' end, middle and 3' end of each transcript.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: RCC tumor_starting RNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total or amplified RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was checked using Bioanalyzer 2100.

extract_protocol:
RNA was extracted from homogenate made in RLT buffer using Qiagen Rneasy mini kit according to manufacturers instructions. The RNA was eluted in water. After verification of its integrity on denaturing agarose gel,  Total RCC RNA, were amplified according to the following procedure (Harris et al 2005) via cDNA intermediate.

Arm 2 [original amplification protocol]: Briefly, 2 μg of RNA 64T + oligo primer and 2 µM Capswitch RNA block primer 2 μM final concentration each were mixed in 40 µl total volume reaction.  Primers were allowed to annealed to the RNA templates at 72C for 2 min prior to addition of 16 µl 5X First Strand Buffer, 8 µl 100 mM DTT, 8 µl 10 mM dNTPs and 8 µl Superscript II Reverse Transcriptase (200 U/μl; Invitrogen).  Reverse transcription was carried out for 1 hour at 42C.  20 µl of the reverse transcription reaction was added to a mixture containing 819 µl water, 105 µl 10X Advantage 2  PCR Buffer, 21 µl 10 mM dNTPs, 42 µl 10 µM 64T + oligo primer, and 21 µl 20 uM of Capswitch primer (5’ – TAATACG ACTCACTATAGGGAGGAAGCAGTGGTAACAACGCAGAG T – 3’) instead of Capswitch primer. Advantage 2 Polymerase (Clonetech).  100 µl of PCR reaction mix were aliquotted into 10 PCR tubes and PCR was carried out using the following program:  95C 1 min then 20 cycles of 95C 5 s, 65C 5 s, 68C 6 min 4 º C hold.  All amplified cDNAs were purified over Qiagen PCR purification column and eluted in water. For the generation of RNA, in vitro transcription was carried out from using AmpliCap™ T7 High Yield Message Maker Kit from Epicentre Biotechnologies as per the manufacturer’s instructions

Arm 5 [improved amplification protocol] utilized a different PCR enzyme Fast Start High Fidelity enzyme (Roche) at the PCR step and a new primer. The conditions were as follows: 8 μg RNA with annealed primers in a 40 µl reaction. After annealing to each 20 µl of RNA solution  16 µl 5X First Strand Buffer, 8 µl 100 mM DTT, 8 µl 10 mM dNTPs and 8 µl Superscript II Reverse Transcriptase (200 U/μl; Invitrogen) were added and volume adjusted with water to 80 µl. The first strand synthesis was carried out at 45oC for one hour. 4 µl of each RT reaction was taken into 100 uL PCR reaction (multiple reactions were set, depending on the cDNA amount needed) containing FSFH reaction buffer with MgCl2, 4 µl of μM 10  64T+ oligo, 2 μM of 20 Powerswitch T7 primer, 2 µl of PCR nucleodide mix (10 mM each) and 2 µl of FSHF enzyme and 21 µl 20 µM T7 Powerswitch primer (5’-GAATTTAATACG ACTCACTATAGG TAGGAAGCAGTGGTAACAACGCAGAG T – 3’) instead of Capswitch primer. PCR was carried out using the following program:  95C  for 5 min followed by 10 cycles 95C 30 s, 65C 30s and 67C 6 min, then 10 cycles of 95C 30 s, 65C 30 s, 67C 6 min with 5 s increase each cycle, followed by 67C hold for 7 min and 4C hold. All amplified cDNAs were purified over Qiagen PCR purification column and eluted in water. For the generation of RNA, in vitro transcription was carried out using AmpliScribe™ T7-Flash™ Transcription Kit from Epicentre Biotechnologies as per the manufacturer’s instructions to generate uncapped RNA.  The uncapped RNAs were then post-transcriptionally capped using Epicentre Biotechnologies’ ScriptCap™ m7G Capping System in conjunction with ScriptCap™ 2'-O-Methyltransferase to generate type I 5’ end cap structure.
The cDNA was then in vitro transcribed and RNA capped. The final in vitro transcribed RNA was purified using Qiagen RNeasy Maxi column according to manufacturing instructions for RNA cleanup and eluted in water. individual aliquots of total and amplified RNA were stored in liquid nitrogen.

treatment_protocol: RCC tumor tissue was cut into 5 mm cubes and placed into RNAlater stabilizing solution at a bedside. The stabilized tumor tissue was stored refrigerated. Tumor tissue was homogenized using Pro homogenizer fitted with a steel blade in the RLT solution (Qiagen, RNeasy kit)

value: renal cell carcinoma (RCC) tumor

tag: molecule subtype

value: total RNA


title: DisColoEpithelium_miRNA_Control_rep1

source_name: Distal Colorectal Epithelial Tissue, 100day, Control, replicate 1


title: Non-smoker female, NSCLC, aCGH [PAT5N]

type: genomic

city: Daejeon

first: Sanghyuk

last: Lee

address: 125 Gwahak-ro

department: KOBIC

country: South Korea

institute: KRIBB

hyb_protocol: Hybridization was performed using Oligo aCGH Hybridization Kit at 65℃ and 20 rpm for 40 hours, enclosed in Agilent SureHyb-enabled hybridization chambers

scan_protocol: Images were scanned on the Agilent G2505 C Scanner and quantified using the Agilent Feature Extraction Software (version 10.7.3.1).

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

molecule: genomic DNA

source_name: human genomic female DNA: Promega G1521

label_protocol: 3 µg of gDNA were digested each  0.5 µl of AluⅠ(10U/ µl) and RsaⅠ(10U/µl) restriction enzyme at 37°C for 120 min, 65°C for 20 min then fluorescent labeled at 37°C for 120 min, 65°C for 10 min in Exo-Klenow Fragment enzyme and 2.5mM each dNTP with 1.0mM Cyanine 3-dUTP and 1.0mM Cyanine 5-dUTP

extract_protocol: genomic DNA prep: Standard protocol by phenol extraction

tag: reference

value: pooled female genomic DNA

source_name: Non-smoker female, NSCLC

tag: disease

value: Adenocarcinoma, NSCLC

tag: patient

tag: tissue type

value: normal

tag: Stage

value: IB

tag: age

value: 44 years

tag: smoker

value: non-smoker


title: white adipose_HFD F1_9months_mix4

city: Wuhan

first: Ling

last: Zheng

email: lzheng@whu.edu.cn, ywding0628@gmail.com

address: Wuhan University

department: College of Life Science

institute: Wuhan University

description:
9FF1
Mixed 4 samples.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using BeadArray Reader, and raw intensities were extracted and background-corrected using Illumina BeadStudio Amplification.

data_processing: The intensity data were normalized using the average normalization algorithm (GenomeStudio (V2010.2), Gene Expression Module (v1.8.0)).

label: biotin

source_name: white adipose, HFD, fed for 9 months, F1 generation

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Mice were fed with normal chow or a high fat diet (60% Kcal fat).

extract_protocol: Total RNA was extracted with RNAiso Plus (Takara Biotechnology Co., Dalian, China).

tag: strain

value: 9 months

tag: generation

tag: treatment

value: high fat diet

value: white adipose tissue


title: DisColoEpithelium_miRNA_DSS_rep2

description: miRNA microarray of mouse colon epithelial tissue at day 100 by given DSS

source_name: Distal Colorectal Epithelial Tissue, 100day, DSS, replicate 2

value: DDS


title: DisColoEpithelium_miRNA_DSS_rep1

source_name: Distal Colorectal Epithelial Tissue, 100day, DSS, replicate 1


title: Non-smoker female, NSCLC, aCGH [PAT8T]

value: tumor

value: IA

value: 62 years


title: DisColoEpithelium_miRNA_AOMDSS_rep3

description: miRNA microarray of mouse colon epithelial tissue at day 100 by given AOM and DSS

source_name: Distal Colorectal Epithelial Tissue, 100day, AOM/DSS, replicate 3

value: Distal Colorectal Epithelial Tissue

value: female

value: AOM/DDS


title: DisColoEpithelium_miRNA_AOM_rep3

description: miRNA microarray of mouse colon epithelial tissue at day 100 by given AOM

source_name: Distal Colorectal Epithelial Tissue, 100day, AOM, replicate 3

value: AOM


title: DisColoEpithelium_miRNA_AOMDSS_rep2

source_name: Distal Colorectal Epithelial Tissue, 100day, AOM/DSS, replicate 2


title: DisColoEpithelium_miRNA_AOM_rep2

source_name: Distal Colorectal Epithelial Tissue, 100day, AOM, replicate 2


title: DisColoEpithelium_miRNA_AOM_rep1

source_name: Distal Colorectal Epithelial Tissue, 100day, AOM, replicate 1


title: Non-smoker female, NSCLC, aCGH [PAT6T]

value: pooled female genomic DNA

value: IIB

value: 70 years


title: Non-smoker female, NSCLC, aCGH [PAT5T]

value: Adenocarcinoma, NSCLC

value: IIA


title: Non-smoker female, NSCLC, aCGH [PAT3T]

value: 53 years

value: non-smoker


title: white adipose_HFD F2_9months_mix4

description:
9FF2
Mixed 4 samples.

source_name: white adipose, HFD, fed for 9 months, F2 generation

value: 9 months

value: high fat diet


title: DisColoEpithelium_Control_rep2

description: Gene expression of mouse colon epithelial tissue at day 100 in Control group

hyb_protocol: Each  Slide  was  hybridized  with  1.65μg  Cy3-labeled  cRNA  using  Gene  Expression Hybridization Kit (Agilent) in Hybridization Oven (Agilent), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes  (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Agilent), followed the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent) with default settings，Dye channel: Green, Scan resolution=5μm, PMT 100%，10%，16bit.

data_processing: Feature Extraction software 10.7 (Agilent) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0  (Agilent).

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit(QIAGEN, GmBH, Germany) following the manufacturer's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent).

value: control


title: DisColoEpithelium_Control_rep3


title: Non-smoker female, NSCLC, aCGH [PAT8N]

value: normal

value: IB


title: Non-smoker female, NSCLC, aCGH [PAT4N]

value: 60 years


title: DisColoEpithelium_DSS_rep2

description: Gene expression of mouse colon epithelial tissue at day 100 by given DSS

value: Distal Colorectal Epithelial Tissue

value: DSS


title: DisColoEpithelium_Control_rep1

value: female


title: Non-smoker female, NSCLC, aCGH [PAT6N]


title: Non-smoker female, NSCLC, aCGH [PAT1T]

value: tumor

value: 44 years


title: DisColoEpithelium_AOM_rep2

description: Gene expression of mouse colon epithelial tissue at day 100 by given AOM

value: AOM


title: DisColoEpithelium_miRNA_AOMDSS_rep1

source_name: Distal Colorectal Epithelial Tissue, 100day, AOM/DSS, replicate 1

value: AOM/DDS


title: DisColoEpithelium_DSS_rep3

source_name: Distal Colorectal Epithelial Tissue, 100day, DSS, replicate 3


title: DisColoEpithelium_AOMDSS_rep1

description: Gene expression of mouse colon epithelial tissue at day 100 by given AOM and DSS

value: AOM/DSS


title: DisColoEpithelium_AOM_rep3


title: DisColoEpithelium_AOMDSS_rep2


title: DisColoEpithelium_AOM_rep1


title: DisColoEpithelium_DSS_rep1


title: KO at 1110

status: Public on May 09 2013

city: Fort Pierce

first: muqing

state: Florida

address: 2199 South Rock Road

institute: University of Florida

description: Hyberscore data from KO-treatment at time point 3

hyb_protocol: Labeled products were hybridized with PhyloChip™ Array, version G3, overnight at 48°C and 60 rpm.

scan_protocol: PhyloChip arrays were washed, stained, and scanned using a GeneArray® scanner (Affymetrix). Each scan is captured  using standard Affymetrix software (GeneChip® Microarray Analysis Suite).

data_processing:
Samples are processed in a Good Laboratory Practices (GLP) compliant service laboratory running Quality Management  Systems for sample and data tracking. The laboratory implements detailed SOPs, equipment and process validation,  training, audits and document control measures. QC and QA metrics are maintained for all sample handling, processing  and storage procedures.Details on probe selection, probe scoring, data acquisition, and preliminary data analysis are presented in Hazen et al. (2010) and premilary analyses were performed by Second Genome (San Bruno, CA, USA). In brief, two criteria were met when the probe pairs scored as positive: (i) the PM (Perfect Match) probe’s intensity of fluorescence was greater than 1.3 times that from the MM (Mismatch) control and (ii) the difference in intensity, PM minus MM, was at least 500 times greater than the squared noise value (>500 N2), which was the variation in pixel intensity signals observed by the scanner as it read the array surface. An OTU was considered present in the sample when over 90% of its assigned probe pairs were positive.
A hybridization intensity score (HybScore) was calculated in arbitrary units for each probe set as the trimmed average (maximum and minimum values removed before averaging) of the PM minus MM intensity differences across the probe pairs in a given probe set. The values of the present OTUs used for each taxa-sample intersection were populated in two distinct ways. In the first case, the abundance metrics were used directly (AT). In the second case, binary metrics were created where 1’s represented presence, 0’s indicated absence (BT).

organism: Citrus sinensis

source_name: Time point-3 at of KO-treatment (KO) in Oct. 2011

label_protocol: The 16S rRNA amplicons and a mixture of amplicons at known concentrations were combined, fragmented using DNAseI (Invitrogen, Carlsbad, CA), and biotin-labeled using the recommended protocol for Affymetrix Prokaryotic Arrays.

growth_protocol: HLB-affected, 7-year-old citrus trees (a unique hybrid, 10c-5-58, which is an open-pollinated seedling from the combination of Lee mandarin × Orlando tangelo) were planted at the USHRL farm, Fort Pierce, FL.

extract_protocol: Qiagen Plant Mini extraction of total DNA was performed according to the manufacturer's instructions.

treatment_protocol: The antibiotic treatments were conducted on the randomized complete block design with four replicates. For each replicate, five HLB-affected, 7-year-old citrus trees (a unique hybrid, 10c-5-58, which is an open-pollinated seedling from the combination of Lee mandarin × Orlando tangelo) at the USHRL farm, 10 cm in diameter, were injected with either 100 ml of the antibiotic combination treatment PS (5 g of penicillin G potassium + 0.5 g of Streptomycin per tree) or the antibiotic treatment KO (2 g of oxytetracycline + 1.0 g of kasugamycin per tree). Five trees were injected with water as injection controls (CK). Injections were made using an Avo-Ject syringe injector (a catheter-tipped 60 ml syringe; Aongatete Coolstores Ltd., NZ) beginning in August of 2010. The tapered tip was firmly fitted into a 19/64-in (7.5 mm) diameter hole, ≈3 cm deep, drilled into the tree. The injector was kept in the tree and the treatment lasted for one week in each injection-trunk. Treatments were repeated every 2 months for one year and ceased in August of 2011.

value: midrib of leaf

tag: genotype

value: citrus unique hybrid, 10c-5-58

value: HLB-affected, 7-year-old citrus trees


title: Disease control

description: Hyberscore data from DNA extracted from scions in the inoculated healthy plants grafted from Las-infected scions treated with water

data_processing:
Samples are processed in a Good Laboratory Practices (GLP) compliant service laboratory running Quality Management  Systems for sample and data tracking. The laboratory implements detailed SOPs, equipment and process validation,  training, audits and document control measures. QC and QA metrics are maintained for all sample handling, processing  and storage procedures.Preliminary data analyses were performed by Second Genome (San Bruno, CA) as described in Hazen et al. (2010) .Briefly, to calculate the summary intensity for each feature on each array, the central nine pixels of individual features were ranked by intensity and the 75th percentile was used. Probe intensities were background-subtracted and scaled to the PhyloChip™ Control Mix. Array fluorescence intensity was collected as integer values ranging from 0 to 65,536. Fluorescence intensities for sets of probes complementing an OTU were averaged after discarding the highest and lowest, and the means were log2 transformed. Thus, they are decimal numbers ranging from 0 to 16. For compatibility with some statistical operations, the HybScore was multiplied by 1000 and then rounded to the nearest integer allowing a range of 0 to 16,000. Thus, if an OTU’s HybScore changes by 1000, it indicates a doubling in the fluorescence intensity. An OTU is defined by a group of highly similar 16S rRNA gene sequences. In most OTUs, the intra-OTU similarity is >99%. The data was reduced to only the bacterial OTUs meeting criteria for confirmed presence as described in Hazen et al. (2010)
Hybridization values, the fluorescence intensity, for each taxon were calculated as a trimmed average, with maximum and minimum values removed before averaging .After the OTUs were identified for inclusion in the analysis, the values used for each OTU-sample intersection were populated in two distinct ways: i) Abundance metrics were used directly (AT); ii) Binary metrics were created where 1’s represent presence and 0’s indicate absence (BT).

organism: Citrus limonia

source_name: PT11-2090, inoculated diseased plants grafted from Las-infected scions treated with water

growth_protocol: The budsticks were grafted onto two-year-old healthy grapefruit (Citrus paradisi ‘Duncan’) rootstocks and covered using plastic tape for three weeks. Each experiment was replicated with 45 scions. To improve scion growth, new flush from the rootstocks was removed after grafting and then allowed to grow. All experimental plants were grown in an insect-proof greenhouse.

treatment_protocol: HLB-affected budsticks were sampled from severely HLB-affected field rough lemons (cv. Lemon #76) at the USDA-ARS-USHRL farm in Fort Pierce, FL and tested positive for Las by real-time qPCR. They were soaked in the antibiotic treatments; ampicillin sodium at a concentration of 1.0 g/L (Amp, Sigma-Aldrich, St. Louis, MO) or gentamicin sulfate at a concentration of 100 mg/L (Gm, Sigma-Aldrich, St. Louis, MO) and water as the diseased control (CK1), overnight in a fume hood under ventilation and lighting. Las-free budsticks, which tested negative by qPCR from healthy rough lemons, were also soaked in water as the healthy control (CK2).

value: scions from citrus rough lemon; rootstock from citrus grapefruit (cv. Duncan)

value: two-years old rootstocks


title: DisColoEpithelium_AOMDSS_rep3


title: PS at 1110

description: Hyberscore data from PS-treatment at time point 3

source_name: Time point-3 of PS-treatment (PS) in Oct. 2011


title: Gm-treatment

description: Hyberscore data from DNA extracted from scions in the inoculated diseased plants grafted from Las-infected scions treated with gentamicin

source_name: PT11-2088, inoculated disease plants grafted from Las-infected scions treated with Gentamicin


title: Healthy control

description: Hyberscore data from DNA extracted from scions in the inoculated healthy plants grafted from Las-free scions treated with water

source_name: PT11-2089, inoculated healthy plants grafted from Las-free scions treated with water


title: Amp-treatment

description: Hyberscore data from DNA extracted from scions in the inoculated healthy plants grafted from Las-infected scions treated with Ampicillin

source_name: PT11-2087, inoculated healthy plants grafted from Las-infected scions treated with Ampicillin


title: KO at 1104

description: Hyberscore data from KO-treatment at time point 2

source_name: Time point-2 at of KO-treatment (KO) in April, 2011


title: CK at 1104

description: Hyberscore data from control at time point 2

source_name: Time point-2 of water control (CK) in April, 2011


title: KO at 1010

description: Hyberscore data from KO-treatment at time point 1

source_name: Time point-1 of KO-treatment (KO) in Oct. 2010


title: Non-smoker female, NSCLC, aCGH [PAT1N]

source_name: human genomic female DNA: Promega G1521

value: pooled female genomic DNA

source_name: Non-smoker female, NSCLC

value: Adenocarcinoma, NSCLC

value: non-smoker


title: PS at 1104

description: Hyberscore data from PS-treatment at time point 2

source_name: Time point-2 of PS-treatment (PS) in April, 2011


title: PS at 1010

description: Hyberscore data from PS-treatment at time point 1

source_name: Time point-1 of PS-treatment (PS) in Oct. 2010


title: CK at 1110

description: Hyberscore data from control at time point 3

source_name: Time point-3 of water control (CK) in Oct. 2011


title: Toledo-WT 72hr

city: Seoul

first: Sanghyun

address: 599 Gwanak-ro, Gwanak-gu

department: Department of biology

institute: Seoul National University

hyb_protocol: Using Agilent hybridization system

scan_protocol: Image and signal data extraction with Agilent scanner & Feature Extraction v10.7.3.1.

data_processing: The scanned images were analyzed with GeneSpring GX v11.0, Variance Stabilization Normalization

source_name: fibroblast_Toledo-WT-infected 72hpi

label_protocol: 500ng total RNA direct labeling with Cy3, for one color hybridization.

growth_protocol: Human foreskin fibroblasts (HFFs) (ATCC, passages 10–15) were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin, and 50 µg/mL streptomycin.

extract_protocol: Total RNAs from HFFs  were isolated using the Trizol reagent.

treatment_protocol: HFFs were infected with HCMV Toledo-WT or Toledo-delta15kb at 2 MOI.

tag: primary cell type

value: human foreskin fibroblast (HFF)

tag: infected with

value: HCMV clinical strain Toledo-WT

tag: hour post infection (hpi)


title: Toledo-delta15kb 72hr

value: HCMV clinical strain ToledoΔ15kb


title: Toledo-delta15kb 24hr


title: Schistosoma japonicum post-infection at 8 week Replicate 2

city: Taipei

first: Po-Ching

last: Cheng

address: 250 Wuxing St,

department: Department of Parasitology, College of Medicine

country: Taiwan

institute: Taipei Medical University

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to ¬¬¬Agilent custom mouse oligo microarray (Agilent Technologies, USA) for 17 h at 60°C.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm and 625 nm for Cy3 and Cy5, respectively. Scanned images are analyzed by Feature extraction 9.1 software (Agilent Technologies, USA),

data_processing: an image analysis and normalization software were used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: Splenic Macrophage Cells

label_protocol: 0.5 μg of total RNA was amplified by a low RNA input fluor linear amp kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer, USA) during the in vitro transcription process. RNA from infected test group was labeled with Cy5 , and control group’s RNA was Cy3. 2μg of Cy-labled cRNA was fragmented to an average size of 50-100 nucleotides by incubation with fragmentation buffer for 30 min at 60oC.

growth_protocol: 8-week-old male C57BL/6j mice were infected with 35 cercariae via abdominal skin. Mice were sacrificed and spleens were collected for subsequent microarray test at the time points of 1, 4.5, 8, 12, and 18 weeks after infection. The control groups with the same number of normal mice were used.

extract_protocol: The preparation of macrophage RNA for microarray experiment was commissioned to Welgene Biotech, Co., Ltd. Total RNA was extracted from the MASC-purified macrophage by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany). RNA quality and quantity were determined by ND-1000 spectrophotometer (Nanodrop Technology, USA) and with RNA 6000 nano labchip kit (Agilent Technologies, USA) by using a Bioanalyzer 2100 (Agilent Technology, USA), respectively.

treatment_protocol: Spleen cells were resuspended with MACS separation buffer (containing 2 mM EDTA and 0.5% BSA in PBS). Anti-CD11b microbeads (Miltenyi Biotec, Germany) were added and reacted for 25 min at 4℃. MS separation columns (Miltenyi Biotec, Germany) were rinsed with 1.5 ml MACS buffer first, and the mixture of beads and cells was washed with MACS buffer twice and applied into MS separation columns. Then the columns were washed with 2 ml MACS buffer to remove the CD11b free cells. Finally the columns were moved from of the magnetic field, and CD11b+ cells were eluted with 1 ml MACS buffer. The survival rate and purity of purified cells were determined by Trypan Blue and flow cytometry, respectively.

tag: cell type

value: Splenic Macrophage Cells

tag: sample type

value: mouse infected S. j at 8wks

tag: infection

value: S. japonicum

tag: time

value: 8 wk

tag: tissue

value: spleen

source_name: pooled whole mouse splenic macrophages

value: pooled whole mouse splenic macrophages

value: normal mouse

value: uninfected control


title: Schistosoma japonicum post-infection at 8 week Replicate 1


title: Schistosoma japonicum post-infection at 1 week Replicate 1

value: mouse infected S. j at 1wk

value: 1 wk


title: DisColoEpithelium_miRNA_DSS_rep3

description: miRNA microarray of mouse colon epithelial tissue at day 100 by given DSS

source_name: Distal Colorectal Epithelial Tissue, 100day, DSS, replicate 3

value: Distal Colorectal Epithelial Tissue

tag: gender

value: female

tag: group

value: DDS


title: Schistosoma japonicum post-infection at 4.5 week Replicate 1

value: mouse infected S. j at 4.5wks


title: Schistosoma japonicum post-infection at 1 week Replicate 2


title: Schistosoma japonicum post-infection at 18 week Replicate 2

value: mouse infected S. j at 18wks

value: 18 wk


title: Toledo-WT 24hr

source_name: fibroblast_Toledo-WT-infected 24hpi

value: human foreskin fibroblast (HFF)

value: HCMV clinical strain Toledo-WT


title: Schistosoma japonicum post-infection at 18 week Replicate 1

value: Splenic Macrophage Cells


title: Schistosoma japonicum post-infection at 12 week Replicate 1

value: mouse infected S. j at 12wks

value: S. japonicum

value: 12 wk


title: Schistosoma japonicum post-infection at 12 week Replicate 2

value: spleen

value: pooled whole mouse splenic macrophages


title: H49_control

city: Campinas

first: Paulo

middle: R

last: Viadanna JR

state: Sao Paulo

address: Rua Francisco Otaviano, 62

country: Brazil

institute: Scylla Bioinformatics

description: Control

hyb_protocol: Each sample was hybridized to a GeneChip® miRNA Array at 48°C and 60 rpm for 16 h, subsequently washed and stained using a Fluidics Station 450

scan_protocol: Scanned on a GeneChip® Scanner 3000 7G. The image data were analyzed with the miRNA QC Tool software for quality control.

data_processing: Summarized probe set data was generated by using R/Bioconductor (v.2.8), using built-in processing from affy package (v.1.30.0). Welch's t test and ANOVA were use for statistical analysis.

source_name: Excised prostate tissue in open surgery

label_protocol: For each sample, 2 μg of total RNA was subjected to a tailing reaction (incubated in 2.5 mM MnCl 2, ATP and Poly A Polymerase for 15 min at 37°C) followed by ligation of the biotinylated signal molecule to the target RNA sample (1X Flash Tag ligation mix, biotin and T4 DNA ligase, incubated for 30 min at RT) and the addition of stop solution.

extract_protocol: One cm2 of fresh prostate tissue was excised immediately after gland removal and stored at 80°C. A similar fragment was formalin-fixed, routinely processed and stained with hematoxylin and eosin to guarantee that at least 75% of the sample was tumor tissue. The whole gland was fixed in formalin.

value: male

tag: age (yrs)

tag: gleason score

tag: tumor stage

tag: psa level (ng/ml)

value: prostate tissue


title: Schistosoma japonicum post-infection at 4.5 week Replicate 2

tag: strain

value: normal mouse

value: uninfected control


title: H88_control

description: Control


title: 568_pT3a

description: Tissue excised in radical prostatectomy

source_name: Excised prostate tissue after gland removal


title: Noninfected control

value: none (negative control)


title: Rehydrated_30min_rep2

type: mixed

city: Dublin

first: Sarah

last: Finn

address: University College Dublin

department: School of Public Health, Physiotherapy and Population Science

country: Ireland

institute: Centre for Food Safety

hyb_protocol: 1) Prepared Cy 5 labelled gDNA (6 µl) was added to Cy3 labelled cDNA (18 µl) for a total volume of 24 µl. 2) To each sample, 6µl of blocking solution (Agilent 5188-5973) and 30 µl of :hybridisation buffer (Agilent 5188-6420) were added. 3) Samples were boiled for 2 min at 95oC and centrifuged for 1 min at 13000 rpm. 4) The gasket slide was placed in hybridization chamber rubber and 50 µl of sample placed directly into centre of gasket slide. 5) When all samples were dispensed the array slide was inserted into the hybridisation chamber, sealed and placed in pre-heated hybridisation over (65˚C) at 10 rpm overnight. 6) Slides were removed from chamber washed according to manufacturer’s instructions (http://www.chem.agilent.com/Library/usermanuals/Public/G2534-90004_HybridizationChamber_User.pdf). 7) Array slides were cleaned with inert gas before measurement.

scan_protocol: Scans were carried out using an Agilent DNA Microarray Scanner, Model G2565, at at 5 µm resolution with Green and Red PMT values set to 100 % and an XDR value of 0.1.  Images generated were saved as multi-image .tiff files.

data_processing: Agilent Feature extraction software was used to process the scanned images of the arrays.  The data generated was then analysed using GeneSpring version 7.3 (Agilent Technologies, Santa Clara, California) based on the log ratio of median Cy3/Cy5 signal normalised to the 50th percentile.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

source_name: Rehydrated cells (30 min)

label_protocol: 1) Random priming reactions were set up in 1.5 ml microfuge tubes. Total RNA (10 µg) and 5 µg of random hexamers (Invitrogen, Cat: 48190011) were added to a final volume of 9.4 µl in RNase free water. 2) Samples incubated at 70 ˚C for 5 min and chilled on ice for 10 min. 3) RT reaction mix prepared by using the Stratagene AffinityScript multi-temperature Reverse Transcriptase by adding the following to each tube: 2 µl of 10 X RT buffer; 2 µl of 0.1 M DDT; 0.6 µl of 50 X dNTP’s (25 mM dATP, dGTP, dTTP and 10 mM dCTP[GE Healthcare Lifesciences, Cat: 27-2035-02]); 2 µl of Cy3 dCTP (1 mM stock, GE Healthcare Lifesciences, Cat: PA55321); 4 µl of reverse transcriptase. 4) Samples were vortexed to mix and incubated shaking at 25 ˚C for 10 min. 5) Samples then incubated overnight at 42 ˚C. 6) Freshly prepared 0.1 M NaOH (15 µl) was added and the RNA hydrolysed at 70 ˚C for 10 min. Freshly prepared 0.1 M HCl (15 µl) was added to neutralise the alkali. Samples were placed on ice to cool to room temperature.  7) Qia-quick PCR purification kit (Qiagen, Cat: 28104) was used to remove unincorporated/quenched cy dyes.  Samples eluted into 40 µl RNase free water and dried-down on speed vac to 18 µl.

growth_protocol: 10 ml of early stationary phase culture of Salmonella Typhimurium ST4/74 (grown statically at 24˚C in LB), centrifuged and resuspended in 1 ml LB.  This cell suspension was then dispensed across 10 stainless steel coupons and allowed to air-dry for 4 h.  Cells were then rehydrated with sterile water for 30 min.

extract_protocol: 1) Cells that had been rehydrated for 30 min were harvested by centrifugation the majority of the supernatant was discarded and the cell pellet re-suspended in the remaining liquid and transferred to a 1.5 ml microfuge tube.  The suspension was centrifuged at 20,800 xg after which the supernatant was discarded. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions.

tag: protocol

value: air-dried onto stainless steel for 4 h, then subsequently rehydrated with water for a 30 min period

tag: biological replicate

source_name: Salmonella genomic DNA (reference)

label_protocol: 1) Chromosomal DNA (2 µg) added to sterile microfuge tube and brought to 21 µl with RNase free water (Sigma, W4502-1L). 2) 20 µl each of 2.5 X Random primer/reaction buffer mix from the Invitrogen BioPrime® DNA Labelling System (18094011) was added to sample and boiled for 5 min, then put on ice for 5 min. 3) On ice, 5 µl of 10X dNTP mix (10X dNTP mix: 1.2 mM each dATP, dGTP, dTTP; 0.6 mM dCTP; 10 mM Tris pH 8.0; 1 mM EDTA;); 3 µl of Cy5 dCTP (1 mM stock, GE Helathcare Lifesciences, Cat: PA55321); and 1 µl Klenow enzyme from the kit were added. 4) Samples were spun briefly and the reaction mix incubated at 37 ˚C overnight. 5) A Qia-quick PCR purification kit (Qiagen Cat: 28104) was used to remove unincorporated/quenched Cy dyes.  Samples were eluted into 80 µl of RNase free water.  This protocol supplies sufficient labelled DNA for 9 hybridisations.  Samples adjusted to a volume of 50 µl using speed vac.

growth_protocol: Salmonella enterica serovar Typhimurium ST4/74 grown to stationary phase at 37˚C

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns).

value: comparator/reference


title: H80_control

description: Control


title: H46_control

description: Control


title: Desiccated_4h_rep2

source_name: Desiccated cells (4 h)

growth_protocol: 10 ml of early stationary phase culture of Salmonella Typhimurium ST4/74 (grown statically at 24˚C in LB), centrifuged and resuspended in 1 ml LB.  This cell suspension was then dispensed across 10 stainless steel coupons and allowed to air-dry for 4 h.

extract_protocol: 1) Dried samples were placed in 20 ml RNAlater® (Ambion) to stabilize the RNA and incubated for 30 min at 24˚C until cells had been removed.  The resulting suspension was centrifuged for 15 min at 3200 xg, the majority of the supernatant was discarded and the cell pellet re-suspended in the remaining liquid and transferred to a 1.5 ml microfuge tube. The suspension was centrifuged at 20,800 xg after which the supernatant was discarded. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions.

value: air-dried onto stainless steel for 4 h


title: Rehydrated_30min_rep1


title: 544_pT2

description: Tissue excised in radical prostatectomy


title: 556_pT3a

description: Tissue excised in radical prostatectomy


title: 547_pT2

description: Tissue excised in radical prostatectomy


title: Desiccated_4h_rep1


title: 554_pT3b

description: Tissue excised in radical prostatectomy


title: MCK-PPARa, biological rep3, array A

city: Orlando

first: Zhenji

last: Gan

state: FL

address: 6400 Sanger Rd

institute: SBMRI

description:
MCK-PPARa-rep3
Muscle RNA from muscle-specific PPARa-overexpressing transgenic mouse.

data_processing:
Software: RQ Manager 1.2
Normalization method: delta Ct
Normalization controls: snoRNA202-4380914
Undetermined Ct values were replaced by Ct 40.

label: FAM

source_name: Soleus muscle from PPARa-overexpressing mouse

label_protocol: Standard Taqman Assay: Quantitative real-time PCR was performed using the Applied Biosystems 7900HT system and a TaqMan Universal PCR Master Mix using the following conditions: 10 min at 94.5°C followed by 40 cycles of 97°C for 30 s and 59.7°C for 1 min.

extract_protocol: RNAzol B following the manufacturer's protocol.

tag: genotype/variation

value: PPARa transgenic

value: soleus muscle

tag: age

value: 12 weeks


title: 534_pT3a

description: Tissue excised in radical prostatectomy


title: Early stationary phase_rep2

source_name: Early stationary phase inoculum culture

growth_protocol: Salmonella Typhimurium ST4/74 grown to early stationary phase in LB, statically at 24˚C

extract_protocol: 1) Early stationary phase culture (10 ml) was harvested by centrifugation. 2) The cell pellet was dissolved in 1 ml TRIzol on ice (Invitrogen, Cat: 15596026). 3) The Trizol/RNA solution was transferred to Phase-Lock-Tubes (5Prime, Cat: 2302830), 400 µl CHCl3 was added and tube inverted for 6-8 times; samples were then incubated for 2-5 min at room temperature. 2) Samples were centrifuged for 15 min at 15°C at full speed and the aqueous phase transferred to a new 1.5 ml microfuge tube. 3) Isopropanol (450 µl) was added to the sample and immediately mixed by inverting and incubated at-20°C overnight. 4) Samples were centrifuged for 30 min at full speed, the supernatant discarded and the pellet washed with 350µl 70 % EtOH, and centrifuged for 10 min (4°C) full speed. The supernatant was discarded and pellet air-dired. 5) The RNA pellet was re-suspended in 80 µl RNase free water, heated to 65˚C for 10 min at 850 rpm in a shaking heat block and nucleotide concentration measured on Nanodrop. 6) Samples were treated with DNase I (Fermentas, EN0521) and Supease-In RNAse Inhibitor (1 µl; Ambion, AM2694).  Samples were adjusted to a concentration > 1,300 ng/l with RNase free water.  7) A NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, Delaware, USA) was used to quantify RNA concentrations.  The Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) was used to assess RNA quality according to manufacturer’s instructions

value: early stationary phase culture


title: 543_pT2

description: Tissue excised in radical prostatectomy


title: MCK-PPARa, biological rep2, array A

description:
MCK-PPARa-rep2
Muscle RNA from muscle-specific PPARa-overexpressing transgenic mouse.


title: 639_pT2

description: Tissue excised in radical prostatectomy


title: 533_pT2

description: Tissue excised in radical prostatectomy


title: Non-transgenic mouse a, biological rep3, array A

description:
NTGa-rep3
Muscle RNA from littermate control mice for muscle-specific PPARa-overexpressing transgenic mice.

source_name: Soleus muscle from wild-type mouse

value: wild-type


title: 535_pT3a

description: Tissue excised in radical prostatectomy


title: 527_pT2

description: Tissue excised in radical prostatectomy


title: Early stationary phase_rep1


title: 526_pT2

description: Tissue excised in radical prostatectomy


title: Non-transgenic mouse a, biological rep2, array A

description:
NTGa-rep2
Muscle RNA from littermate control mice for muscle-specific PPARa-overexpressing transgenic mice.


title: 532_pT2

description: Tissue excised in radical prostatectomy


title: 525_pT3b

description: Tissue excised in radical prostatectomy


title: 523_pT3a

description: Tissue excised in radical prostatectomy


title: 528_pT2

description: Tissue excised in radical prostatectomy


title: 524_pT3a

description: Tissue excised in radical prostatectomy


title: MCK-PPARa, biological rep1, array A

description:
MCK-PPARa-rep1
Muscle RNA from muscle-specific PPARa-overexpressing transgenic mouse.


title: Non-transgenic mouse a, biological rep1, array A

description:
NTGa-rep1
Muscle RNA from littermate control mice for muscle-specific PPARa-overexpressing transgenic mice.


title: 522_pT3b

description: Tissue excised in radical prostatectomy


title: 521_pT3a

description: Tissue excised in radical prostatectomy


title: 519_pT3bN1

description: Tissue excised in radical prostatectomy


title: 618_pT3a

description: Tissue excised in radical prostatectomy


title: 515_pT3aN1

description: Tissue excised in radical prostatectomy


title: MCK-PPARb, biological rep3, array A

description:
MCK-PPARb-rep3
Muscle RNA from muscle-specific PPARb-overexpressing transgenic mouse.

source_name: Soleus muscle from PPARb-overexpressing mouse

value: PPARb transgenic


title: 514_pT2

description: Tissue excised in radical prostatectomy


title: 538_pT3b

description: Tissue excised in radical prostatectomy


title: 508_pT2

description: Tissue excised in radical prostatectomy


title: MCK-PPARb, biological rep1, array A

description:
MCK-PPARb-rep1
Muscle RNA from muscle-specific PPARb-overexpressing transgenic mouse.


title: 509_pT2

description: Tissue excised in radical prostatectomy


title: Non-transgenic mouse b, biological rep3, array A

description:
NTGb-rep3
Muscle RNA from littermate control mice for muscle-specific PPARb-overexpressing transgenic mice.


title: 507_pT2

description: Tissue excised in radical prostatectomy


title: MCK-PPARb, biological rep2, array A

description:
MCK-PPARb-rep2
Muscle RNA from muscle-specific PPARb-overexpressing transgenic mouse.


title: 506_pT2

description: Tissue excised in radical prostatectomy


title: 505_pT2

description: Tissue excised in radical prostatectomy


title: 512_pT2

description: Tissue excised in radical prostatectomy


title: 500_pT2

description: Tissue excised in radical prostatectomy


title: Non-transgenic mouse b, biological rep1, array A

description:
NTGb-rep1
Muscle RNA from littermate control mice for muscle-specific PPARb-overexpressing transgenic mice.


title: Non-transgenic mouse b, biological rep2, array A

description:
NTGb-rep2
Muscle RNA from littermate control mice for muscle-specific PPARb-overexpressing transgenic mice.


title: 497_pT3a

description: Tissue excised in radical prostatectomy


title: 503_pT2

description: Tissue excised in radical prostatectomy


title: 496_pT2

description: Tissue excised in radical prostatectomy


title: H9-T3_card A

city: Adelaide

first: Victoria

last: Nisenblat

address: Frome road

country: Australia

institute: University of Adelaide

description:
H9-T3
SAMPLE 47

data_processing:
Raw quantification cycle (Cq) values were obtained using SDS v.2.3 and RQ Manager v.1.2 software (automatic baseline, threshold = 0.1). Only miRNA detectors that showed a Cq ≤ 32.0 were considered to be expressed and all detectors with Cq > 32.0 or that failed amplification were excluded. Technical replicate Cq values were averaged if the standard deviation (SD) of all replicates was < 0.5. If the SD was > 0.5 outlier replicates were excluded from the analysis if a triplicate or analysed separately if a duplicate. Detectors expressed in less than 50% of samples were removed from the data. The data was normalised by using Quantile normalisation method.
Matrix non-normalized worksheet reports all non-expressed values (Cq > 32 or undetected) as Cq=33
Matrix normalized worksheet reports quantile normalized Cq values. Only microRNAs expressed in > 50% samples were selected for normalisation and further analyses.
Matrix Template1 contains data from array card A
Matrix Template2 contains data from array card B

source_name: Control

label_protocol: Sample RNA (3 µl) was reverse-transcribed and then pre-amplified in 25 µl reactions according to manufacturer’s protocols (Applied Biosystems). The pre-amplified cDNA was diluted with 75 μl of nuclease-free water and stored at -20°C before amplification with Megaplex human pool PCR primers using an ABI 7900HT Thermal Cycler (Applied Biosystems).

extract_protocol: Total RNA was extracted by using Trisol LS protocol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions

value: Plasma

tag: menstrual cycle stage

value: mid luteal


title: CK at 1010

description: Hyberscore data from control at time point 1

source_name: Time point-1 of water control (CK) in Oct. 2010

value: midrib of leaf

tag: genotype

value: citrus unique hybrid, 10c-5-58

value: HLB-affected, 7-year-old citrus trees


title: H9-T2_card A

description:
H9-T2
SAMPLE 46

value: late proliferative


title: 480_pT2

description: Tissue excised in radical prostatectomy

value: male

value: prostate tissue


title: 488_pT3a

description: Tissue excised in radical prostatectomy


title: 470_pT3a

description: Tissue excised in radical prostatectomy


title: 498_pT3a

description: Tissue excised in radical prostatectomy


title: H6-T3_card A

description:
H6-T3
SAMPLE 44


title: 450_pT2

description: Tissue excised in radical prostatectomy


title: 449_pT3b

description: Tissue excised in radical prostatectomy


title: H6-T2_card A

description:
H6-T2
SAMPLE 43


title: H6-T1_card A

description:
H6-T1
SAMPLE 42

value: early proliferative


title: 447_pT3a

description: Tissue excised in radical prostatectomy


title: 446_pT3a

description: Tissue excised in radical prostatectomy


title: 448_pT3a

description: Tissue excised in radical prostatectomy


title: 445_pT3a

description: Tissue excised in radical prostatectomy


title: MCK-PPARa, biological rep3, array B


title: 487_pT2

description: Tissue excised in radical prostatectomy


title: H5-T3_card A

description:
H5-T3
SAMPLE 41


title: 442_pT3a

description: Tissue excised in radical prostatectomy


title: MCK-PPARa, biological rep2, array B


title: 490_pT3a

description: Tissue excised in radical prostatectomy


title: 443_pT2

description: Tissue excised in radical prostatectomy


title: 436_pT2

description: Tissue excised in radical prostatectomy


title: H5-T2_card A

description:
H5-T2
SAMPLE 40


title: MCK-PPARa, biological rep1, array B


title: 432_pT3a

description: Tissue excised in radical prostatectomy


title: H5-T1_card A

description:
H5-T1
SAMPLE 39


title: 433_pT3a

description: Tissue excised in radical prostatectomy


title: H15-T3_card A

description:
H15-T3
SAMPLE 38


title: Non-transgenic mouse a, biological rep2, array B


title: Non-transgenic mouse a, biological rep3, array B


title: Hsp730_1

city: Saint Paul

first: María

last: Muñoz-Amatriaín

state: MN

address: 411 Borlaug Hall, 1991Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description:
log2ratios(Hsp730.1/Morex)
Hsp730_1: 501145_2011-12-01_532.pair
Morex: 501145_2011-12-01_635.pair

hyb_protocol: 34ug of labeled DNA were hybridized to the array according to the manufacturer instructions (NimbleGen CGH User Guide version 9.1)

scan_protocol: Arrays were scanned iat 2 μm resolution on the MS 200 Microarray Scanner (Roche NimbleGen) according to the manufacturer instructions (NimbleGen CGH User Guide version 9.1)

data_processing:
Array images were quantified and data were processed using NimbleScan software (Roche NimbleGen). Pair reports containing the raw signal intensities for each probe on the array were produced for each array, one for the Cy3 and one for the Cy5 images. Pair files exported from NimbleScan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Array hybridization values were normalized to correct for inter-array and intra-array signal variations using Variance stabilization and calibration for microarray data (vsn, Huber et al. 2002).
Then, for all samples, the log2(sample/Morex) were calculated. Normalized probe values were averaged across replicated samples and also across contig fragments for downstream analysis.

organism: Hordeum vulgare subsp. vulgare

source_name: Hsp730, leave tissue

label_protocol: 0.5ug of genomic DNA were labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide version 9.1.

extract_protocol: The CTAB method (Saghai-Maroof et al.1984) was used for DNA isolation

tag: wild barley accession

value: leaves

source_name: Morex, leave tissue

tag: cultivar

value: Morex


title: Hsp462_1

description:
log2ratios(Hsp462.1/Morex)
Hsp462_1: 501055_2011-10-24_532.pair
Morex: 501055_2011-10-24_635.pair

source_name: Hsp462, leave tissue


title: 489_pT3a

description: Tissue excised in radical prostatectomy


title: H15-T2_card A

description:
H15-T2
SAMPLE 37


title: Non-transgenic mouse a, biological rep1, array B


title: H14-T3_card A

description:
H14-T3
SAMPLE 35


title: MCK-PPARb, biological rep3, array B


title: Hsp357_1

description:
log2ratios(Hsp357.1/Morex)
Hsp357_1: 501054_2011-10-24_532.pair
Morex: 501054_2011-10-24_635.pair

source_name: Hsp357, leave tissue


title: H9-T1_card A

description:
H9-T1
SAMPLE 45


title: D4

city: Beijing

first: Huimin

last: Kang

state: Beijing

address: Beijing

institute: China Agriculture University

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48℃, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on iScan (Illumina Inc.)(Illumina).

data_processing: BeadStudio (Illumina Inc.) software were used to genotyped the SNPs .

organism: Sus scrofa

source_name: ear tissue

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA for each  individuals was extracted from the ear tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany).

tag: breed

value: Duroc

tag: Sex

value: female

value: ear tissue


title: H15-T1_card A

description:
H15-T1
SAMPLE 36

tag: tissue


title: C3

value: Landrace


title: H14-T2_card A

description:
H14-T2
SAMPLE 34


title: MCK-PPARb, biological rep1, array B

value: soleus muscle

tag: gender

value: 12 weeks


title: Hsp278_1

description:
log2ratios(Hsp278.1/Morex)
Hsp278_1: 500968_2011-10-17_532.pair
Morex: 500968_2011-10-17_635.pair

source_name: Hsp278, leave tissue


title: H14-T1_card A

description:
H14-T1
SAMPLE 33

value: Plasma


title: 431_pT3a

description: Tissue excised in radical prostatectomy

tag: age (yrs)


title: Hsp248_2

description:
log2ratios(Hsp248.2/Morex)
Hsp248_2: 501025_2011-10-17_532.pair
Morex: 501025_2011-10-17_635.pair

source_name: Hsp248, leave tissue


title: H13-T3_card A

description:
H13-T3
SAMPLE 32

value: mid luteal


title: A1

value: wild pig


title: MCK-PPARb, biological rep2, array B

value: PPARb transgenic


title: Igri_1

description:
log2ratios(Igri.1/Morex)
Igri_1: 501127_2012-02-04_532.pair
Morex: 501178_2011-10-31_635.pair

source_name: Igri, leave tissue

value: Igri


title: Steptoe_1

description:
log2ratios(Steptoe.1/Morex)
Steptoe_1: 501038_2011-12-01_532.pair
Morex: 501038_2011-12-01_635.pair

source_name: Steptoe, leave tissue

value: Steptoe


title: Hsp357_2

description:
log2ratios(Hsp357.2/Morex)
Hsp357_2: 500967_2011-11-07_532.pair
Morex: 500967_2011-11-07_635.pair


title: Y2

value: Yorkshire


title: Non-transgenic mouse b, biological rep1, array B

value: wild-type

value: male


title: H13-T1_card A

description:
H13-T1
SAMPLE 30

value: early proliferative


title: Steptoe_2

description:
log2ratios(Steptoe.2/Morex)
Steptoe_2: 501127_2012-02-04_635.pair
Morex: 501178_2011-10-31_635.pair

value: leaves

value: Morex


title: D2

value: Duroc

value: female


title: H9-T2_card B

description:
H9-T2
SAMPLE 46

value: late proliferative


title: H11-T3_card A

description:
H11-T3
SAMPLE 29


title: H11-T2_card A

description:
H11-T2
SAMPLE 28


title: H9-T1_card B

description:
H9-T1
SAMPLE 45


title: Haruna_Nijo_1

description:
log2ratios(Haruna_Nijo.1/Morex)
Haruna_Nijo_1: 501089_2011-12-01_532.pair
Morex: 501089_2011-12-01_635.pair

source_name: Haruna_Nijo, leave tissue


title: R2

value: Rongchang pig

value: ear tissue


title: Bowman_2

description:
log2ratios(Bowman.2/Morex)
Bowman_2: 501179_2012-02-04_635.pair
Morex: 501178_2011-10-31_635.pair

source_name: Bowman, leave tissue

value: Bowman


title: Harrington_1

description:
log2ratios(Harrington.1/Morex)
Harrington_1: 501132_2012-02-04_635.pair
Morex: 501178_2011-10-31_635.pair

source_name: Harrington, leave tissue

value: Harrington


title: H6-T3_card B

description:
H6-T3
SAMPLE 44

value: Plasma

value: mid luteal


title: Hsp248_1

description:
log2ratios(Hsp248.1/Morex)
Hsp248_1: 500958_2011-10-31_532.pair
Morex: 500958_2011-10-31_635.pair


title: MS8

value: Meishan pig


title: Z2

value: Tibetan pig


title: Non-transgenic mouse b, biological rep3, array B

description:
NTGb-rep3
Muscle RNA from littermate control mice for muscle-specific PPARb-overexpressing transgenic mice.

value: soleus muscle

value: 12 weeks


title: Hsp278_2

description:
log2ratios(Hsp278.2/Morex)
Hsp278_2: 501178_2011-10-31_532.pair
Morex: 501178_2011-10-31_635.pair


title: H10-T3_card A

description:
H10-T3
SAMPLE 26


title: H6-T2_card B

description:
H6-T2
SAMPLE 43


title: DN5

value: Diannan small-ear pig


title: Bowman_1

description:
log2ratios(Bowman.1/Morex)
Bowman_1: 500980_2011-11-26_532.pair
Morex: 500980_2011-11-26_635.pair


title: W1

value: Daweizi pig


title: H6-T1_card B

description:
H6-T1
SAMPLE 42

value: early proliferative


title: MS7


title: H10-T1_card A

description:
H10-T1
SAMPLE 24


title: H10-T2_card A

description:
H10-T2
SAMPLE 25


title: H11-T1_card A

description:
H11-T1
SAMPLE 27


title: H5-T2_card B

description:
H5-T2
SAMPLE 40


title: E8-T3_card A

description:
E8-T3
SAMPLE 23

source_name: Endometriosis


title: Betzes_1

description:
log2ratios(Betzes.1/Morex)
Betzes_1: 501104_2011-12-01_532.pair
Morex: 501104_2011-12-01_635.pair

source_name: Betzes, leave tissue

value: Betzes

value: leaves

value: Morex


title: Franka_1

description:
log2ratios(Franka.1/Morex)
Franka_1: 501132_2012-02-04_532.pair
Morex: 501178_2011-10-31_635.pair

source_name: Franka, leave tissue

value: Franka


title: H5-T1_card B

description:
H5-T1
SAMPLE 39

source_name: Control


title: Non-transgenic mouse b, biological rep2, array B

description:
NTGb-rep2
Muscle RNA from littermate control mice for muscle-specific PPARb-overexpressing transgenic mice.

source_name: Soleus muscle from wild-type mouse

value: wild-type

value: male


title: E8-T1_card A

description:
E8-T1
SAMPLE 22


title: E7-T3_card A

description:
E7-T3
SAMPLE 21


title: H15-T1_card B

description:
H15-T1
SAMPLE 36


title: H5-T3_card B

description:
H5-T3
SAMPLE 41


title: M2

value: Min pig

value: female

value: ear tissue


title: E7-T2_card A

description:
E7-T2
SAMPLE 20

value: Plasma

value: late proliferative


title: DN1


title: H14-T3_card B

description:
H14-T3
SAMPLE 35

value: mid luteal


title: genotype: nts1007 - inoculation: + - tissue type name: shoot - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: entire shoot (upstream of the cotelydons) of a Rhizophagus irregularis-inoculated nark mutant (nts1007) plant (May still include original submitter created errors/discrepancies)

hyb_protocol: Hybridization (AtlasBiolabs)

scan_protocol: Scanning (AtlasBiolabs)

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. This data set used only soybean probe sets for normalization and hence will have expression values only for a subset (Affy. control and soybean probe sets) of the total number of probe sets in the platform.

organism: Glycine max

source_name: shoot (genotype: nts1007 - inoculation: + - tissue type name: shoot)

label_protocol: Labelling (AtlasBiolabs)

growth_protocol: Growth Description:  Soybean seeds were surface-sterilized with 1.5% sodium hypochlorite for 5 min, washed with distilled water, and germinated in wet expanded clay at conditions descibed below in a phyto-chamber. After 6 days of germination, the main root of seedlings was cut off around 2 cm below the shoot basis and seedlings were further cultivated under the conditions described below. After 2 days, plants were transferred to the split-root system by dividing the arising lateral roots onto two individual pots connected to each other (each 9 x 9 x 9.5 cm). In doing so, mycorrhizal plants were inoculated on one root-part (A) with 20% (v/v) Rhizophagus irregularis inoculum. The other root-part (B) and both root-parts of control plants stayed non-infected. All plants were watered with distilled water and fertilized with Long Ashton with 20% of the regular phosphate content during cultivation. Plants were havested nineteen days after inoculation.  Environmental Conditions:  Plants were cultivated in a phyto-chamber with 16 h light (200 µmol m-2 s-1) at 26°C and 8 h dark at 22°C with a relative humidity of 60-65%.

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: germplasm name

value: derived from seeds

tag: ecotype

value: Bragg

tag: organism part

value: shoot

tag: development stage

value: 27-day-old plant

value: 27 days after sowing

tag: growth media

value: expanded clay of 2-5 mm particle size

tag: inoculated

value: yes


title: E7-T1_card A

description:
E7-T1
SAMPLE 19

value: early proliferative


title: H14-T2_card B

description:
H14-T2
SAMPLE 34


title: E6-T3_card A

description:
E6-T3
SAMPLE 18


title: genotype: nts1007 - inoculation: + - tissue type name: shoot - rep3

tag: genotype/variation


title: H13-T3_card B

description:
H13-T3
SAMPLE 32


title: E6-T2_card A

description:
E6-T2
SAMPLE 17


title: H13-T2_card B

description:
H13-T2
SAMPLE 31


title: genotype: nts1007 - inoculation: + - tissue type name: shoot - rep1

tag: age


title: H13-T2_card A

description:
H13-T2
SAMPLE 31

tag: menstrual cycle stage


title: E5-T3_card A

description:
E5-T3
SAMPLE 15


title: Barke_1

description:
log2ratios(Barke.1/Morex)
Barke_1: 501147_2011-11-26_532.pair
Morex: 501147_2011-11-26_635.pair

source_name: Barke, leave tissue

value: Barke

value: leaves

source_name: Morex, leave tissue

value: Morex


title: H11-T3_card B

description:
H11-T3
SAMPLE 29


title: E6-T1_card A

description:
E6-T1
SAMPLE 16


title: H9-T3_card B

description:
H9-T3
SAMPLE 47


title: genotype: nts1007 - inoculation: + - tissue type name: root-part B (non-myc) - rep3

description: non-mycorrhizal root-part of a Rhizophagus irregularis-inoculated nark mutant (nts1007) plant. (plant was cultivated in a split-root-system and only one part of the root-system was inoculated) (May still include original submitter created errors/discrepancies)

source_name: root (genotype: nts1007 - inoculation: + - tissue type name: root-part B (non-myc))


title: E5-T2_card A

description:
E5-T2
SAMPLE 14


title: genotype: nts1007 - inoculation: + - tissue type name: root-part B (non-myc) - rep1


title: genotype: nts1007 - inoculation: + - tissue type name: root-part A (myc) - rep2

description: mycorrhizal root-part of a Rhizophagus irregularis-inoculated nark mutant (nts1007) plant. (plant was cultivated in a split-root-system and only one part of the root-system was inoculated) (May still include original submitter created errors/discrepancies)

source_name: root (genotype: nts1007 - inoculation: + - tissue type name: root-part A (myc))


title: Z5

source_name: ear tissue

value: Tibetan pig


title: genotype: nts1007 - inoculation: + - tissue type name: root-part B (non-myc) - rep2


title: genotype: nts1007 - inoculation: + - tissue type name: root-part A (myc) - rep3


title: genotype: nts1007 - inoculation: + - tissue type name: root-part A (myc) - rep1


title: H11-T1_card B

description:
H11-T1
SAMPLE 27


title: E4-T3_card A

description:
E4-T3
SAMPLE 12


title: E4-T2_card A

description:
E4-T2
SAMPLE 11


title: H10-T1_card B

description:
H10-T1
SAMPLE 24


title: H10-T2_card B

description:
H10-T2
SAMPLE 25


title: H11-T2_card B

description:
H11-T2
SAMPLE 28


title: Hsp11_1

description:
log2ratios(Hsp11.1/Morex)
Hsp11_1: 501053_2011-11-07_532.pair
Morex: 501053_2011-11-07_635.pair

source_name: Hsp11, leave tissue


title: H13-T1_card B

description:
H13-T1
SAMPLE 30


title: E6-T1_card B

description:
E6-T1
SAMPLE 16


title: E5-T1_card A

description:
E5-T1
SAMPLE 13


title: E5-T3_card B

description:
E5-T3
SAMPLE 15


title: E4-T1_card A

description:
E4-T1
SAMPLE 10


title: E3-T3_card A

description:
E3-T3
SAMPLE 9


title: genotype: nts1007 - inoculation: - - tissue type name: shoot - rep1

description: entire shoot (upstream of the cotelydons) of a non-infected nark mutant (nts1007) plant (May still include original submitter created errors/discrepancies)

source_name: shoot (genotype: nts1007 - inoculation: - - tissue type name: shoot)

value: no


title: E3-T1_card A

description:
E3-T1
SAMPLE 7


title: E3-T2_card A

description:
E3-T2
SAMPLE 8


title: E5-T2_card B

description:
E5-T2
SAMPLE 14


title: E5-T1_card B

description:
E5-T1
SAMPLE 13


title: genotype: nts1007 - inoculation: - - tissue type name: root-parts A&B - rep3

description: non-mycorrhizal roots of a non-infected nark mutant (nts1007) plant. (plant was cultivated in a split-root-system; RNA of both non-inoculated root-parts was pooled) (May still include original submitter created errors/discrepancies)

source_name: root (genotype: nts1007 - inoculation: - - tissue type name: root-parts A&B)


title: genotype: nts1007 - inoculation: - - tissue type name: root-parts A&B - rep2


title: E4-T3_card B

description:
E4-T3
SAMPLE 12


title: genotype: nts1007 - inoculation: - - tissue type name: root-parts A&B - rep1


title: E2-T2_card A

description:
E2-T2
SAMPLE 5


title: genotype: nts1007 - inoculation: - - tissue type name: shoot - rep3


title: E4-T2_card B

description:
E4-T2
SAMPLE 11


title: genotype: Bragg wt - inoculation: + - tissue type name: shoot - rep3

description: entire shoot (upstream of the cotelydons) of a Rhizophagus irregularis-inoculated Bragg wild-type plant (May still include original submitter created errors/discrepancies)

source_name: shoot (genotype: Bragg wt - inoculation: + - tissue type name: shoot)

value: wild type


title: genotype: Bragg wt - inoculation: + - tissue type name: shoot - rep1


title: E4-T1_card B

description:
E4-T1
SAMPLE 10

value: Plasma


title: E1-T3_card A

description:
E1-T3
SAMPLE 3


title: genotype: nts1007 - inoculation: - - tissue type name: shoot - rep2


title: genotype: Bragg wt - inoculation: + - tissue type name: root-part B (non-myc) - rep3

description: non-mycorrhizal root-part of a Rhizophagus irregularis-inoculated Bragg wild-type plant. (plant was cultivated in a split-root-system and only one part of the root-system was inoculated) (May still include original submitter created errors/discrepancies)

source_name: root (genotype: Bragg wt - inoculation: + - tissue type name: root-part B (non-myc))


title: E2-T1_card A

description:
E2-T1
SAMPLE 4


title: E3-T3_card B

description:
E3-T3
SAMPLE 9


title: E1-T1_card A

description:
E1-T1
SAMPLE 1


title: E1-T2_card A

description:
E1-T2
SAMPLE 2

value: late proliferative


title: E3-T2_card B

description:
E3-T2
SAMPLE 8


title: E2-T3_card A

description:
E2-T3
SAMPLE 6

value: mid luteal


title: E2-T3_card B

description:
E2-T3
SAMPLE 6


title: genotype: Bragg wt - inoculation: + - tissue type name: shoot - rep2

value: derived from seeds


title: genotype: Bragg wt - inoculation: + - tissue type name: root-part A (myc) - rep3

description: mycorrhizal root-part of a Rhizophagus irregularis-inoculated Bragg wild-type plant. (plant was cultivated in a split-root-system and only one part of the root-system was inoculated) (May still include original submitter created errors/discrepancies)

source_name: root (genotype: Bragg wt - inoculation: + - tissue type name: root-part A (myc))

value: Bragg


title: genotype: Bragg wt - inoculation: + - tissue type name: root-part B (non-myc) - rep1


title: genotype: Bragg wt - inoculation: + - tissue type name: root-part B (non-myc) - rep2


title: genotype: Bragg wt - inoculation: + - tissue type name: root-part A (myc) - rep2


title: genotype: Bragg wt - inoculation: + - tissue type name: root-part A (myc) - rep1


title: E2-T1_card B

description:
E2-T1
SAMPLE 4

source_name: Endometriosis


title: E3-T1_card B

description:
E3-T1
SAMPLE 7


title: E1-T3_card B

description:
E1-T3
SAMPLE 3


title: E1-T2_card B

description:
E1-T2
SAMPLE 2


title: E1-T1_card B

description:
E1-T1
SAMPLE 1


title: E2-T2_card B

description:
E2-T2
SAMPLE 5


title: genotype: Bragg wt - inoculation: - - tissue type name: shoot - rep2

description: entire shoot (upstream of the cotelydons) of a non-infected Bragg wild-type plant (May still include original submitter created errors/discrepancies)

source_name: shoot (genotype: Bragg wt - inoculation: - - tissue type name: shoot)

value: shoot


title: UC MES_2 replicate

city: cusano milanino

first: Zulian

last: Alessandra

state: milano

address: via zucchi 18

country: Italy

institute: istituto auxologico italiano

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalitation

source_name: isolated adipocytes

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

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.

value: mesenteric adipocytes from 5 patients pooled

tag: disease state

value: ulcerative colitis


title: genotype: Bragg wt - inoculation: - - tissue type name: shoot - rep3

value: 27-day-old plant

value: 27 days after sowing

value: expanded clay of 2-5 mm particle size


title: GPR15positive CD4T in LILP rep2

city: New York

first: Dan

last: Littman

address: 540 First Avenue, SKI 2-17

institute: NYU School of Medicine

description: Gene expression data from GPR15+ CD4+ T cells in the large intestine lamina propria

hyb_protocol: According to Affymetrix protocols

scan_protocol: According to Affymetrix protocols

data_processing: The data were analyzed using Affymetrix default analysis and global scaling as normalization method.

source_name: GFPpositive CD4+ T cells in the large intestine lamina propria from GPR15-GFP knock-in heterozygous mice

label_protocol: According to Affymetrix protocols

growth_protocol: GFP+CD4+ T cells and GFP-CD4+ T cells were sorted after collagenase-mediated digestion of large intestine lamina propria.

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

tag: strain

value: 129/B6 mixed

tag: cell type

value: CD4+ T cells

tag: gfp status

value: GFP+ cells

value: large intestine lamina propria


title: UC OM_2 replicate

value: omental adipocytes from 5 patients pooled


title: CD MES_1 replicate

value: crohn's disease


title: UC OM_1 replicate


title: CD MES_2 replicate


title: GPR15negative CD4T in LILP rep2

description: Gene expression data from GPR15- CD4+ T cells in the large intestine lamina propria

source_name: GFPnegative CD4+ T cells in the large intestine lamina propria from GPR15-GFP knock-in heterozygous mice

value: GFP- cells


title: UC MES_1 replicate


title: CD OM_2 replicate


title: GPR15negative CD4T in LILP rep1


title: CD OM_1 replicate


title: genotype: Bragg wt - inoculation: - - tissue type name: root-parts A&B - rep3

description: non-mycorrhizal roots of a non-infected Bragg wild-type plant (plant was cultivated in a split-root-system; RNA of both non-inoculated root-parts was pooled) (May still include original submitter created errors/discrepancies)

source_name: root (genotype: Bragg wt - inoculation: - - tissue type name: root-parts A&B)

value: wild type

value: no


title: genotype: Bragg wt - inoculation: - - tissue type name: root-parts A&B - rep2

value: derived from seeds


title: GPR15positive CD4T in LILP rep1


title: genotype: Bragg wt - inoculation: - - tissue type name: root-parts A&B - rep1

value: Bragg


title: chronic myeloid leukemia stem, biological replicate 4

status: Public on May 08 2013

city: Baltimore

first: Jessica

last: Gucwa

state: MD

address: 1650 Orleans Street

institute: JHMI

description: CML

hyb_protocol: Samples were hybridized to Human Exon 1.0 ST whole genome gene expression microarrays (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocols at the Johns Hopkins Microarray facility.

scan_protocol: All arrays are scanned in the Affymetrix GeneChip Scanner 3000 and raw analysis performed with Affymetrix Command Console and Expression Console.

data_processing:
The microarray gene expression data was analyzed with Partek Genomic Suite software (http://www.partek.com/partekgs) using the exon array workflow with default conditions (data imported and normalized using log2 transformation, default RMA background correction and normalization, of core meta-probe sets).
HuEx-1_0-st-v2.r2.pgf
\HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: bone marrow

label_protocol: Samples were fragmented and biotin-end-labelled using the Encore Biotin Module (NuGEN).

extract_protocol: Total RNA from sorted cell populations was subjected to cDNA synthesis and linear amplification using the Ovation RNA Exon Module amplification system (NuGEN, San Carlos, CA) according to the manufacturer’s protocols.

tag: cell marker

value: chronic myeloid leukemia

value: chronic myeloid leukemia stem


title: normal stem, biological replicate 3

description: Normal

value: Normal

value: normal stem


title: chronic myeloid leukemia stem, biological replicate 3

description: CML


title: chronic myeloid leukemia stem, biological replicate 5

description: CML


title: normal stem, biological replicate 2

description: Normal


title: chronic myeloid leukemia stem, biological replicate 2

description: CML


title: chronic myeloid leukemia progenitor, biological replicate 4

description: CML

value: chronic myeloid leukemia progenitor


title: genotype: Bragg wt - inoculation: - - tissue type name: shoot - rep1

value: shoot

value: 27-day-old plant

value: 27 days after sowing

value: expanded clay of 2-5 mm particle size


title: normal progenitor, biological replicate 4

description: Normal

value: normal progenitor


title: chronic myeloid leukemia stem, biological replicate 1

description: CML


title: chronic myeloid leukemia progenitor, biological replicate 3

description: CML


title: normal progenitor, biological replicate 5

description: Normal


title: chronic myeloid leukemia progenitor, biological replicate 1

description: CML


title: chronic myeloid leukemia progenitor, biological replicate 5

description: CML


title: normal progenitor, biological replicate 2

description: Normal


title: normal progenitor, biological replicate 3

description: Normal


title: normal stem, biological replicate 5

description: Normal


title: normal progenitor, biological replicate 1

description: Normal


title: normal stem, biological replicate 4

description: Normal


title: chronic myeloid leukemia progenitor, biological replicate 2

description: CML


title: 11-1823_(miRNA-2_0)

city: Research Triangle Park

first: Zongli

last: Xu

address: 111 tw alexander Dr.

institute: NIH/NIEHS

description: microRNA expression analyzed from total RNA extracted from serum

hyb_protocol: RNA was hybridized for 42 hours to the GeneChip miRNA 2.0 array

scan_protocol: The arrays were washed and stained using standard Affymetrix protocols and scanned using the Affymetrix GCS 3000 7G Scanner. Feature intensities were extracted using the miRNA 2.0 array library files.

data_processing: MiRNA expression intensity values were background corrected and normalized across arrays using the Robust Multichip Average (RMA) method. The intensity data used in all analysis were log (2) transformed. For each array the miRNA probe set signals were compared to the distribution of signals for anti-genomic probes that had matching GC content (miRNA QC Tool, Version 1.0.33.0) and following the manufacture’s recommendation, Wilcoxon Rank-Sum test of  p<0.06 was used to identify miRNAs above background. Subsequent analysis was restricted to 414 miRNAs that exceeded background levels in at least 50 women. Conditional logistic regression was used to identify differentially expressed miRNA probes between cases and controls for those 414 probes.

source_name: Serum

label_protocol: 8µl of total RNA was directly labeled using The Flash Tag Biotin HSR Labeling kits following the manufacturer’s instructions. RNA was heated at 80° C for 10 min before labeling to inactivate any residual DNase activity.

extract_protocol: Total RNA was extracted in batches using the Total RNA purification kit. Each individual sample was split into two equal aliquots and then processed following the manufacture’s recommended protocol for total RNA purification from serum. An on-column DNase digestion was added before sample elution using the RNase-Free DNase I Kit, following the manufacturer’s instructions.

tag: batch

value: A

tag: status

tag: race


title: 11-1829_(miRNA-2_0)


title: 11-1822_(miRNA-2_0)


title: 11-1824_(miRNA-2_0)


title: 11-1710_(miRNA-2_0)

value: B

value: noncase

value: 4) Other


title: 11-1828_(miRNA-2_0)


title: 11-1826_(miRNA-2_0)


title: 11-1669_(miRNA-2_0)

value: 3) Hispanic


title: 11-1798_(miRNA-2_0)

value: case

value: 1) Non-Hispanic White


title: 11-1827_(miRNA-2_0)


title: 11-1559_(miRNA-2_0)


title: 11-1821_(miRNA-2_0)


title: 11-1652_(miRNA-2_0)


title: 11-1825_(miRNA-2_0)


title: 11-1706_(miRNA-2_0)


title: 11-1441_(miRNA-2_0)


title: 11-1636_(miRNA-2_0)


title: 11-1799_(miRNA-2_0)


title: 11-1488_(miRNA-2_0)


title: 11-1560_(miRNA-2_0)


title: 11-1493_(miRNA-2_0)


title: normal stem, biological replicate 1

description: Normal


title: 11-1492_(miRNA-2_0)


title: 11-1782_(miRNA-2_0)


title: 11-1435_(miRNA-2_0)


title: 11-1444_(miRNA-2_0)


title: 11-1437_(miRNA-2_0)


title: 11-1433_(miRNA-2_0)


title: 11-1422_(miRNA-2_0)

value: 2) Black


title: 11-1554_(miRNA-2_0)


title: 11-1675_(miRNA-2_0)


title: 11-1727_(miRNA-2_0)


title: 11-1708_(miRNA-2_0)


title: 11-1578_(miRNA-2_0)


title: 11-1431_(miRNA-2_0)


title: 11-1531_(miRNA-2_0)


title: 11-1810_(miRNA-2_0)


title: 11-1703_(miRNA-2_0)


title: 11-1604_(miRNA-2_0)


title: 11-1676_(miRNA-2_0)


title: 11-1816_(miRNA-2_0)


title: 11-1653_(miRNA-2_0)


title: 11-1465_(miRNA-2_0)


title: 11-1542_(miRNA-2_0)


title: 11-1580_(miRNA-2_0)


title: 11-1622_(miRNA-2_0)


title: 11-1438_(miRNA-2_0)


title: 11-1414_(miRNA-2_0)


title: 11-1588_(miRNA-2_0)


title: 11-1788_(miRNA-2_0)


title: 11-1461_(miRNA-2_0)


title: 11-1477_(miRNA-2_0)


title: 11-1641_(miRNA-2_0)


title: 11-1526_(miRNA-2_0)


title: 11-1446_(miRNA-2_0)


title: 11-1532_(miRNA-2_0)


title: 11-1514_(miRNA-2_0)


title: 11-1686_(miRNA-2_0)


title: 11-1660_(miRNA-2_0)


title: 11-1759_(miRNA-2_0)


title: 11-1775_(miRNA-2_0)


title: 11-1637_(miRNA-2_0)


title: 11-1552_(miRNA-2_0)


title: 11-1704_(miRNA-2_0)


title: 11-1620_(miRNA-2_0)


title: 11-1630_(miRNA-2_0)


title: 11-1455_(miRNA-2_0)


title: 11-1728_(miRNA-2_0)


title: 11-1764_(miRNA-2_0)


title: 11-1678_(miRNA-2_0)


title: 11-1419_(miRNA-2_0)


title: 11-1561_(miRNA-2_0)


title: 11-1520_(miRNA-2_0)


title: 11-1640_(miRNA-2_0)


title: 11-1635_(miRNA-2_0)


title: 11-1680_(miRNA-2_0)


title: 11-1516_(miRNA-2_0)


title: 11-1510_(miRNA-2_0)


title: 11-1464_(miRNA-2_0)


title: 11-1549_(miRNA-2_0)


title: 11-1742_(miRNA-2_0)


title: 11-1781_(miRNA-2_0)


title: 11-1623_(miRNA-2_0)


title: 11-1778_(miRNA-2_0)


title: 11-1456_(miRNA-2_0)


title: 11-1804_(miRNA-2_0)


title: 11-1694_(miRNA-2_0)


title: 11-1416_(miRNA-2_0)


title: 11-1551_(miRNA-2_0)


title: 11-1721_(miRNA-2_0)


title: 11-1501_(miRNA-2_0)


title: 11-1755_(miRNA-2_0)


title: 11-1756_(miRNA-2_0)


title: 11-1819_(miRNA-2_0)


title: 11-1467_(miRNA-2_0)


title: 11-1530_(miRNA-2_0)


title: 11-1687_(miRNA-2_0)


title: 11-1744_(miRNA-2_0)


title: 11-1553_(miRNA-2_0)


title: 11-1590_(miRNA-2_0)


title: 11-1672_(miRNA-2_0)


title: 11-1487_(miRNA-2_0)


title: 11-1767_(miRNA-2_0)


title: 11-1451_(miRNA-2_0)


title: 11-1515_(miRNA-2_0)


title: 11-1699_(miRNA-2_0)


title: 11-1787_(miRNA-2_0)


title: 11-1733_(miRNA-2_0)


title: 11-1479_(miRNA-2_0)


title: 11-1496_(miRNA-2_0)


title: 11-1646_(miRNA-2_0)


title: 11-1474_(miRNA-2_0)


title: 11-1780_(miRNA-2_0)


title: 11-1499_(miRNA-2_0)


title: 11-1779_(miRNA-2_0)


title: 11-1815_(miRNA-2_0)


title: 11-1784_(miRNA-2_0)


title: 11-1575_(miRNA-2_0)


title: 11-1538_(miRNA-2_0)


title: 11-1426_(miRNA-2_0)


title: 11-1794_(miRNA-2_0)


title: 11-1572_(miRNA-2_0)


title: 11-1502_(miRNA-2_0)


title: 11-1817_(miRNA-2_0)


title: 11-1475_(miRNA-2_0)


title: 11-1599_(miRNA-2_0)


title: 11-1418_(miRNA-2_0)


title: 11-1820_(miRNA-2_0)


title: 11-1428_(miRNA-2_0)


title: 11-1450_(miRNA-2_0)


title: 11-1448_(miRNA-2_0)


title: 11-1683_(miRNA-2_0)


title: 11-1750_(miRNA-2_0)


title: 11-1749_(miRNA-2_0)


title: 11-1517_(miRNA-2_0)


title: 11-1768_(miRNA-2_0)


title: 11-1666_(miRNA-2_0)


title: 11-1598_(miRNA-2_0)


title: 11-1482_(miRNA-2_0)


title: 11-1411_(miRNA-2_0)


title: 11-1723_(miRNA-2_0)


title: 11-1618_(miRNA-2_0)


title: 11-1483_(miRNA-2_0)


title: 11-1562_(miRNA-2_0)


title: 11-1524_(miRNA-2_0)


title: 11-1457_(miRNA-2_0)


title: 11-1689_(miRNA-2_0)


title: 11-1647_(miRNA-2_0)


title: 11-1709_(miRNA-2_0)


title: 11-1498_(miRNA-2_0)


title: 11-1432_(miRNA-2_0)


title: 11-1724_(miRNA-2_0)


title: 11-1806_(miRNA-2_0)


title: 11-1574_(miRNA-2_0)


title: 11-1658_(miRNA-2_0)


title: 11-1661_(miRNA-2_0)


title: 11-1548_(miRNA-2_0)


title: 11-1486_(miRNA-2_0)


title: 11-1596_(miRNA-2_0)


title: 11-1595_(miRNA-2_0)


title: 11-1688_(miRNA-2_0)


title: 11-1489_(miRNA-2_0)


title: 11-1765_(miRNA-2_0)


title: 11-1809_(miRNA-2_0)


title: 11-1805_(miRNA-2_0)


title: 11-1511_(miRNA-2_0)


title: 11-1803_(miRNA-2_0)


title: 11-1544_(miRNA-2_0)


title: 11-1671_(miRNA-2_0)


title: 11-1811_(miRNA-2_0)


title: 11-1786_(miRNA-2_0)


title: 11-1795_(miRNA-2_0)


title: 11-1582_(miRNA-2_0)


title: 11-1774_(miRNA-2_0)


title: 11-1601_(miRNA-2_0)


title: 11-1594_(miRNA-2_0)


title: 11-1626_(miRNA-2_0)


title: 11-1541_(miRNA-2_0)


title: 11-1413_(miRNA-2_0)


title: 11-1740_(miRNA-2_0)


title: 11-1691_(miRNA-2_0)


title: 11-1449_(miRNA-2_0)


title: 11-1668_(miRNA-2_0)


title: 11-1525_(miRNA-2_0)


title: 11-1654_(miRNA-2_0)


title: 11-1770_(miRNA-2_0)


title: 11-1535_(miRNA-2_0)


title: 11-1677_(miRNA-2_0)


title: 11-1690_(miRNA-2_0)


title: 11-1459_(miRNA-2_0)


title: 11-1447_(miRNA-2_0)


title: 11-1751_(miRNA-2_0)


title: 11-1600_(miRNA-2_0)


title: 11-1568_(miRNA-2_0)


title: 11-1534_(miRNA-2_0)


title: 11-1754_(miRNA-2_0)


title: 11-1586_(miRNA-2_0)


title: 11-1508_(miRNA-2_0)


title: 11-1760_(miRNA-2_0)


title: 11-1571_(miRNA-2_0)


title: 11-1645_(miRNA-2_0)


title: 11-1642_(miRNA-2_0)


title: 11-1484_(miRNA-2_0)


title: 11-1473_(miRNA-2_0)


title: 11-1717_(miRNA-2_0)


title: 11-1685_(miRNA-2_0)


title: 11-1633_(miRNA-2_0)


title: 11-1783_(miRNA-2_0)


title: 11-1421_(miRNA-2_0)


title: 11-1747_(miRNA-2_0)


title: 11-1651_(miRNA-2_0)


title: 11-1722_(miRNA-2_0)


title: 11-1518_(miRNA-2_0)


title: 11-1714_(miRNA-2_0)


title: 11-1452_(miRNA-2_0)


title: 11-1757_(miRNA-2_0)


title: 11-1734_(miRNA-2_0)


title: 11-1476_(miRNA-2_0)


title: 11-1632_(miRNA-2_0)


title: 11-1624_(miRNA-2_0)


title: 11-1711_(miRNA-2_0)


title: 11-1769_(miRNA-2_0)


title: 11-1472_(miRNA-2_0)


title: 11-1670_(miRNA-2_0)


title: 11-1533_(miRNA-2_0)


title: 11-1589_(miRNA-2_0)


title: 11-1536_(miRNA-2_0)


title: 11-1664_(miRNA-2_0)


title: 11-1625_(miRNA-2_0)


title: 11-1758_(miRNA-2_0)


title: 11-1504_(miRNA-2_0)


title: 11-1505_(miRNA-2_0)


title: 11-1527_(miRNA-2_0)


title: 11-1468_(miRNA-2_0)


title: 11-1442_(miRNA-2_0)


title: 11-1649_(miRNA-2_0)


title: 11-1583_(miRNA-2_0)


title: 11-1439_(miRNA-2_0)


title: 11-1812_(miRNA-2_0)


title: 11-1679_(miRNA-2_0)


title: 11-1818_(miRNA-2_0)


title: 11-1693_(miRNA-2_0)


title: 11-1507_(miRNA-2_0)


title: 11-1550_(miRNA-2_0)


title: 11-1460_(miRNA-2_0)


title: 11-1609_(miRNA-2_0)


title: 11-1800_(miRNA-2_0)


title: 11-1494_(miRNA-2_0)


title: 11-1657_(miRNA-2_0)


title: 11-1730_(miRNA-2_0)


title: 11-1420_(miRNA-2_0)


title: 11-1629_(miRNA-2_0)


title: 11-1573_(miRNA-2_0)


title: 11-1491_(miRNA-2_0)


title: 11-1576_(miRNA-2_0)


title: 11-1584_(miRNA-2_0)


title: 11-1557_(miRNA-2_0)


title: 11-1478_(miRNA-2_0)


title: 11-1763_(miRNA-2_0)


title: 11-1674_(miRNA-2_0)


title: 11-1443_(miRNA-2_0)


title: 11-1581_(miRNA-2_0)


title: 11-1665_(miRNA-2_0)


title: 11-1796_(miRNA-2_0)


title: 11-1440_(miRNA-2_0)


title: 11-1659_(miRNA-2_0)


title: 11-1543_(miRNA-2_0)


title: 11-1650_(miRNA-2_0)


title: 11-1412_(miRNA-2_0)


title: 11-1745_(miRNA-2_0)


title: 11-1621_(miRNA-2_0)


title: 11-1791_(miRNA-2_0)


title: 11-1610_(miRNA-2_0)


title: 11-1619_(miRNA-2_0)


title: 11-1748_(miRNA-2_0)


title: 11-1430_(miRNA-2_0)


title: 11-1429_(miRNA-2_0)


title: 11-1813_(miRNA-2_0)


title: 11-1716_(miRNA-2_0)


title: 11-1480_(miRNA-2_0)


title: 11-1719_(miRNA-2_0)


title: 11-1731_(miRNA-2_0)


title: 11-1585_(miRNA-2_0)


title: 11-1692_(miRNA-2_0)


title: 11-1648_(miRNA-2_0)


title: 11-1643_(miRNA-2_0)


title: 11-1436_(miRNA-2_0)


title: 11-1712_(miRNA-2_0)


title: 11-1490_(miRNA-2_0)


title: 11-1762_(miRNA-2_0)


title: 11-1631_(miRNA-2_0)


title: 11-1732_(miRNA-2_0)


title: 11-1617_(miRNA-2_0)


title: 11-1797_(miRNA-2_0)


title: 11-1509_(miRNA-2_0)


title: 11-1519_(miRNA-2_0)


title: 11-1423_(miRNA-2_0)


title: 11-1497_(miRNA-2_0)


title: 11-1545_(miRNA-2_0)


title: 11-1673_(miRNA-2_0)


title: 11-1462_(miRNA-2_0)


title: 11-1667_(miRNA-2_0)


title: 11-1597_(miRNA-2_0)


title: 11-1513_(miRNA-2_0)


title: 11-1569_(miRNA-2_0)


title: 11-1521_(miRNA-2_0)


title: 11-1564_(miRNA-2_0)


title: 11-1566_(miRNA-2_0)


title: 11-1614_(miRNA-2_0)


title: 11-1615_(miRNA-2_0)


title: 11-1684_(miRNA-2_0)


title: 11-1777_(miRNA-2_0)


title: 11-1603_(miRNA-2_0)


title: 11-1469_(miRNA-2_0)


title: 11-1695_(miRNA-2_0)


title: 11-1606_(miRNA-2_0)


title: 11-1773_(miRNA-2_0)


title: 11-1608_(miRNA-2_0)


title: 11-1656_(miRNA-2_0)


title: 11-1713_(miRNA-2_0)


title: 11-1611_(miRNA-2_0)


title: 11-1776_(miRNA-2_0)


title: 11-1663_(miRNA-2_0)


title: 11-1612_(miRNA-2_0)


title: 11-1485_(miRNA-2_0)


title: 11-1662_(miRNA-2_0)


title: 11-1720_(miRNA-2_0)


title: 11-1523_(miRNA-2_0)


title: 11-1702_(miRNA-2_0)


title: 11-1537_(miRNA-2_0)


title: 11-1471_(miRNA-2_0)


title: 11-1427_(miRNA-2_0)


title: 11-1453_(miRNA-2_0)


title: 11-1766_(miRNA-2_0)


title: 11-1729_(miRNA-2_0)


title: 11-1700_(miRNA-2_0)


title: 11-1752_(miRNA-2_0)


title: 11-1707_(miRNA-2_0)


title: 11-1577_(miRNA-2_0)


title: 11-1547_(miRNA-2_0)


title: 11-1741_(miRNA-2_0)


title: 11-1579_(miRNA-2_0)


title: 11-1425_(miRNA-2_0)


title: 11-1655_(miRNA-2_0)


title: 11-1613_(miRNA-2_0)


title: 11-1753_(miRNA-2_0)


title: 11-1445_(miRNA-2_0)


title: 11-1701_(miRNA-2_0)


title: Hal_Supernat_040minb_vs_NRC-1

city: Seattle

first: Monica

middle: V.

last: Orellana

state: WA

address: 401 Terry Ave North

institute: Institute for Systems Biology

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 40 minutes.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org for more details.

organism: Halobacterium salinarum NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 40 min. Replica

label_protocol: 5 ug quality-checked total RNA was direct-labeled with Cy3 and Cy5 dyes according to manufacturer's instructions (Kreatech, Alameda, CA).

growth_protocol: Halobacterium salinarum reference was grown in CM (Dassarma S, Fleischmann EM (1995) Archaea a Laboratory Manual: Halophiles: Cold Spring Harbor Laboratory Press) or in MM2 please check Orellana et al.2013). Dunaliella was grown in MM1 (check Orellana et al., 2011).

extract_protocol: RNA was prepared the following day using the Absolutely RNA miniprep kit according to manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). RNA quality was checked using an Agilent Bioanalyzer as described (Schmid et al., 2009). Freedom from DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR.

treatment_protocol: see characteristics:source

source_name: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: Hal_Supernat_080minb_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 80 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 80 min. Replica


title: Hal_Supernat_160minb_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples takean at 160 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 160 min. Replica


title: Hal_Supernat_010minb_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 10 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 10 min. Replica


title: Hal_Supernat_020minb_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples takean at 20 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 20 min. Replica


title: Hal_Supernat_005minb_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 5 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 5 min. Replica


title: Hal_Supernat_000minb_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at zero minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested immediately. Replica


title: 11-1705_(miRNA-2_0)


title: 11-1463_(miRNA-2_0)


title: 11-1587_(miRNA-2_0)


title: Hal_MM1_320minb_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples takean at 320 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 320 min. Replica


title: Hal_MM1_160minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested at 160 min. Replica


title: 11-1801_(miRNA-2_0)


title: 11-1539_(miRNA-2_0)


title: 11-1638_(miRNA-2_0)


title: 11-1607_(miRNA-2_0)


title: 11-1570_(miRNA-2_0)


title: 11-1726_(miRNA-2_0)


title: T2 D400, patient 12

city: Lørenskog

first: Ert

last: Kalanxhi

address: Lørenskog

department: Clinical and Molecular Oncology

country: Norway

institute: Akershus University Hospital

description:
PRAVO#12_3
Patient 12, 2 hours after 400 mg dose of vorinostat

hyb_protocol: Standard Illumina hybridization protocol - LastHybridizationProtocol.pdf.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalized using the lumiN method with the parameter quantile from the Lumi package in Bioconductor.

source_name: peripheral blood mononuclear cells, 400 mg vorinostat, 2 hours

label_protocol: Standard Illumina label protocol - IlluminaTotalPrep96RNAAmpKit.pdf.

extract_protocol: From each study patient at T0, T2, and T24, peripheral blood was drawn on PAXgene Blood RNA Tubes. Total RNA was isolated using PAXgene Blood RNA Kit, following the manufacturer's protocol. RNA concentration and integrity were assessed using NanoDrop 1000 and Agilent 2100 Bioanalyzer, respectively.

treatment_protocol: The biological samples were collected from the study patients at baseline (before commencement of study treatment; T0) and on-treatment the third treatment day of ten, two and 24 hours after the patient had received the preceding daily dose of vorinostat (T2 and T24), respectively. The patients were treated at one of four sequential dose levels of vorinostat, starting at 100 mg daily with dose escalation in increments of 100 mg (D100, D200, D300, and D400).

value: peripheral blood mononuclear cells

tag: gender

value: male

tag: age (years)

tag: primary tumor site

value: colon

tag: treatment

value: 400 mg vorinostat

tag: time point

value: 2 hours

tag: patient identifier


title: T2 D400, patient 13

description:
PRAVO#13_3
Patient 13, 2 hours after 400 mg dose of vorinostat

value: female

value: rectum


title: Hal_MM1_080minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 80 min. Replica


title: 11-1761_(miRNA-2_0)


title: 11-1424_(miRNA-2_0)


title: 11-1725_(miRNA-2_0)


title: Hal_MM1_040minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 40 min. Replica


title: T2 D400, patient 9

description:
PRAVO#09_3
Patient 9, 2 hours after 400 mg dose of vorinostat


title: Hal_Supernat_320minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested 320 min. Replica


title: 11-1540_(miRNA-2_0)


title: Hal_MM1_010minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested at 10 min. Replica.


title: T2 D400, patient 14

description:
PRAVO#14_3
Patient 14, 2 hours after 400 mg dose of vorinostat


title: 11-1503_(miRNA-2_0)


title: Hal_MM1_005minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested at 5 min. Replica


title: T2 D400, patient 15

description:
PRAVO#15_3
Patient 15, 2 hours after 400 mg dose of vorinostat


title: 11-1506_(miRNA-2_0)

source_name: Serum


title: 11-1495_(miRNA-2_0)


title: 11-1715_(miRNA-2_0)


title: 11-1466_(miRNA-2_0)


title: 11-1616_(miRNA-2_0)


title: 11-1634_(miRNA-2_0)


title: 11-1718_(miRNA-2_0)


title: 11-1567_(miRNA-2_0)


title: 11-1593_(miRNA-2_0)


title: T2 D300, patient 6

description:
PRAVO#06_3
Patient 6, 2 hours after 300 mg dose of vorinostat

source_name: peripheral blood mononuclear cells, 300 mg vorinostat, 2 hours

value: 300 mg vorinostat


title: 11-1639_(miRNA-2_0)


title: Hal_MM1_020minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 20 min. Replica

source_name: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: 11-1546_(miRNA-2_0)


title: 11-1746_(miRNA-2_0)


title: T2 D300, patient 16

description:
PRAVO#16_3
Patient 16, 2 hours after 300 mg dose of vorinostat


title: T2 D300, patient 11

description:
PRAVO#11_3
Patient 11, 2 hours after 300 mg dose of vorinostat


title: 11-1792_(miRNA-2_0)

description: microRNA expression analyzed from total RNA extracted from serum


title: Hal_Supernat_320mina_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested 320 min.