title: 2966.92hr R 2966.68hr V

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

institute: Laval University

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.)

data_processing: Images were quantified using ArrayPro 6.4 software (Media Cybernetics). Background subtracted, LOESS normalized, data obtained from log2 of processed Red signal/processed Green signal.

organism: Bos taurus

label_protocol: Samples were labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

growth_protocol: Holstein cycling cows were stimulated during 3 days with FSH given at 12 hr intervals, followed by a coasting period (no FSH) of 20, 44, 68 or 92 hours.

extract_protocol:
Total RNA extraction was performed using the PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA, USA), with DNase treatment on the purification column according to the manufacturer instructions. RNA was eluted in 11 µl of elution buffer. Quantity and quality of each pool of RNA was verified on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada). Samples were stored at -80°C.
RNA_amplication: Anti-sense RNA was produced using the RiboAmp HS RNA amplification kit (Applied Biosystems, Carlsbad, CA, USA). Quantity of aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Each cow was exposed to one of the 4 coasting conditions: 20, 44, 68 and 92 hours in a randomized design with at least one month between aech treatment. Cumulus-oocyte complexes (COC’s) were collected by transvaginal puncture (PTV). The COC’s were then washed three times to remove follicular fluid and were mechanically denuded to remove all the cumulus cells. Oocytes were then washed, collected in small volumes of PBS, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: sample type

tag: breed (cattle)

value: holstein

tag: time

value: 92 hours

tag: reproductive status (cattle)

value: 2nd Parity

tag: tissue or cell type

value: oocyte

value: 68 hours


title: NL25lung

status: Public on Jun 21 2013

type: RNA

city: Pittsburgh

first: Carol

last: Feghali-Bostwick

state: PA

address: MONF 628NW Pittsburgh

department: Medicine

country: USA

institute: University of Pittsburgh

description: NL

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using median normalization followed by square root transformation in caGEDA [Patel S, Lyons-Weiler J. caGEDA: a web application for the integrated analysis of global gene expression patterns in cancer. Appl Bioinformatics 2004;3(1):49-62]

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NL

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. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: Lung


title: NL22lung

description: NL


title: 2966.92hr R 2966.20hr V

country: Canada

value: 20 hours


title: LPR3rest

city: Cambridge

first: Yingting

last: Mok

address: Hills Road

department: Cambridge Institute for Medical Research

country: United Kingdom

institute: University of Cambridge

description: miRNA profiling

hyb_protocol: Oligonucleotide probes were coupled to color-coded polystyrene beads, allowing the simultaneous detection of about 90 different target oligonucleotides. To obtain expression profiles for 309 miRNAs, we created four distinct sets of bead-coupled miRNA probes. Each sample was hybridized to the four bead sets to generate a complete miRNA profile. Oligos were 5´-amino modified with a 6-carbon linker and conjugated to carboxylated xMAP beads (Luminex, Austin, TX, USA) in 96-well formats following the standard manufacturer's protocol. To generate bead set pools, 3 μl of each oligo-bead conjugate was mixed into 1 ml 1.5× TMAC buffer (4.5 M tetramethylammonium chloride, 0.15% sarkosyl, 75 mM Tris-HCl pH 8.0, 6 mM EDTA). Samples were hybridized in a 96-well format with two water-only blanks and at least three bead blanks containing water instead of the labeled sample for use as a background control. We included replicate probes and technical replicate samples across bead sets and sample plates, respectively, to aid quality control and data preprocessing. Hybridization was carried out overnight at 50°C with 33 μl of the bead pool and 15 μl of labeled sample.  Unbound sample was removed from beads by washing with 1 × TE and re-suspending in 1× TMAC buffer. SAPE, streptavidin-phycoerythrin, premium grade (Invitrogen) was added to the beads (1:100 dilution) and incubated for 10 minutes at 50°C to bind to biotin moieties on the cDNA. S

scan_protocol: Samples were processed on a Luminex 100 machine and median fluorescence intensity (MFI) values acquired using the StarStation software (ACS, Sheffield, UK).

data_processing: For the miRNA profiling of B cells across C57BL/6 and autoimmune strains of mice, well-to-well scaling was performed such that the total MFI of the post-labeling controls in each well was equal to the median value across all wells. Sample scaling was performed such that total MFI of the pre-labeling controls in each sample was equal to the median value across all samples. A threshold of 1 was applied and the data was log2-transformed. Filtering for ‘expressed’ miRNAs was performed by employing a cutoff value of three standard deviations above the median MFI of all readings. Differential gene expression between sample pairs was analysed by carrying out 1-way ANOVAs (1 way Analysis of Variance) for all combinations of sample pairs using Graphpad Prism. Combinations with p value <0.05 were then filtered to show only within-strain comparisons. Differential gene expression across all samples was analysed using GEPAS T-rex multi-class comparison (ANOVA) tool (Montaner et al, 2006), which provided P-values adjusted for multiple testing, with control of family-wise error rate  and false-discovery rate (Storey & Tibshirani, 2003).

organism: Mus musculus

label_protocol: After purification of 18-26 bp RNAs, adaptors were ligated at the 3´ and 5´ ends using T4 RNA ligase (Fermentas, Burlington, OT, CA), a RNA-DNA hybrid 5´-pUUUaaccgcgaattccagt-idT-3´ (Dharmacon; X = RNA, x = DNA, p = phosphate, idT = inverted [3´-3´ bond] deoxythymidine) was ligated to the 3´ end and 5´-acggaattcctcactAAA-3´ (Dharmacon) was ligated to the 5´ end using T4 RNA ligase. These bi-ligated products underwent reverse transcription using an adaptor specific primer (M37, 5´-pTACTGGAATTCGCGGTTA-3´) and then amplified and labeled using PCR (M37 and M33, 5´-biotin-CAACGGAATTCCTCACTAAA-3´). Amplification was performed on an Eppendorf thermal cycler at 95°C for 30 s, 50°C for 30 s and 72°C for 40 s for 18 cycles. PCR products were precipitated without glycogen and redissolved in 66 μl 1 × TE buffer containing 1 μl of three biotinylated post labeling controls (100 fmols each, FVR506, PTG20210, MRC677).

extract_protocol: MiRNAs were extracted from 5 μg of sample total RNA using denaturing PAGE.

tag: strain

value: MRL-lpr

tag: autoimmune strain

value: yes

tag: cell type

value: splenic B-cell

tag: treatment

value: rest


title: 2966.92hr R 2966.44hr V

value: 44 hours


title: NL24lung

description: NL


title: IPF78lung

description: IPF

source_name: IPF


title: 2966.68hr R 2966.92hr V


title: 2966.68hr R 2966.44hr V


title: NL16lung

description: NL


title: IPF73lung

description: IPF


title: Control DP thymocytes mouse #21

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

country: France

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

description:
Sample name: Mouse #21
purified CD8+CD4+ thymocytes, control mouse #1
gene expression data from DP thymocytes from a control mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 7G System

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Target intensity was set at 100.

label_protocol: cRNA were prepared according to MessageAmp™ Premier RNA Amplification Kit (Ambion) protocol from 0.1 ug total RNA.

extract_protocol: RNAs were extracted with the RNAeasy kit, following the manufacturer's instructions (including DNAse I treatment)

treatment_protocol: Thymus were dissected from euthanized mice and cells collected after tissue disruption.Thymocytes were stained with CD4 and CD8 conjugated antibodies and CD8+CD4+ DP cells were sorted and purified on FACSAriaII (purity>98%).

tag: genotype/variation

value: R26NC/NC CD4Cre-

tag: age

value: 6 weeks

value: purified CD8+CD4+ thymocytes

value: Thymus


title: 2966.68hr R 2966.20hr V


title: 2966.44hr R 2966.92hr V


title: LPR1rest

description: miRNA profiling


title: 2966.44hr R 2966.68hr V


title: IPF7lung

description: IPF


title: LPR1Fab

description: miRNA profiling

value: Fab


title: MRL3LPS

description: miRNA profiling

value: MRL

value: LPS


title: LPR2rest

description: miRNA profiling


title: BoneMarrowBisulfite1_rep1

type: genomic

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

hyb_protocol: Hyb protocol as per manufacturer's instructions, Illumina

scan_protocol: Scan protocol as per manufacturer's instructions, Illumina

data_processing: Raw data was read by the minfi package in R Development (2.12). The beta scores were calculated from the raw intensity values from each probe, no normalisation was performed.

molecule: genomic DNA

source_name: Bone Marrow from Mouse 88

label_protocol: Label protocol as per manufacturer's instructions, Illumina

extract_protocol: tail lysis buffer, proteinase K digestion, phenol chloroform extraction, ethanol precipitation

value: Bone Marrow


title: SSc15lung

description: SSc PF

source_name: SSc PF


title: MRL2Fab2

description: miRNA profiling


title: MRL3Fab2

description: miRNA profiling


title: MRL1LPS

description: miRNA profiling


title: MRL2LPS

description: miRNA profiling


title: MRL1Fab2

description: miRNA profiling


title: IPF66lung

description: IPF


title: MRL3rest

description: miRNA profiling


title: MLR2rest

description: miRNA profiling


title: 2966.20hr R 2966.68hr V

value: holstein

value: 2nd Parity

value: oocyte


title: MRL1rest

description: miRNA profiling


title: 2966.20hr R 2966.92hr V

value: 20 hours

value: 92 hours


title: 2966.44hr R 2966.20hr V


title: IPF63lung

description: IPF

value: Lung


title: WT1(delZ) rep2

city: Lund

first: Karina

last: Vidovic

address: Klinikgatan 26

department: Hematology and Transfusion Medicine

country: Sweden

institute: Lund University

description:
WT1 delZ 10.03.08-foV.a1.lbe1
replicate 2

hyb_protocol: Illumina hybridization protocol (Manuel 11322187 Revision A)

scan_protocol: Standard Illumina iScan N240 scanning protocol Direct Hyb

data_processing: The data were normalised using quantile normalisation with GenomeStudio Software (v.2011.1).

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevB, (Modification of Amplification kit v1.1)

growth_protocol: Human progenitor cells (CD34+) were cultured in StemSpan SFEM with addition of StemSpan CC100 cytokine cocktail and rhTPO 100 ng/ml

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

treatment_protocol: CD34+ progenitor cells extracted from cord blood cultured 14 days in vitro

tag: celll type

tag: transduced with

value: WT1-mutant lacking zinc-finger, WT1(delZ)


title: WT1(delZ) rep3

description:
WT1 delZ 11.03.11.a1.lbe1
replicate 3

value: CD34+ progenitor cells extracted from cord blood cultured 14 days in vitro


title: BL63LPS

description: miRNA profiling

value: no

value: splenic B-cell


title: IPF39lung

description: IPF


title: IPF58lung

description: IPF


title: WT1(delZ) rep1

description:
WT1 delZ 10.03.08-fo6.a1.lbe1
replicate 1


title: WT1 +/- rep3

description:
WT1 11.03.11.a1.lbe1
replicate 3

source_name: hematopoietic progenitor cells_WT1 +/-

value: full-length WT1(+/-)


title: CTRL_fem_64yrs

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Human Genome U133A 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

scan_protocol: Arrays were scanned  with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product and Significance Analysis of Microarray.

label_protocol: A 6μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Cell lines were thawed on the same date, and grown with the same batch of RPMI-1640 media supplemented with 10% Fetal Calf Serum, 2 mM L-glutamine,  0.1 mg/ml streptomycin and 100 U/ml penicillin, under identical conditions (5% CO2, 37°C) to approximately the same cell density (10^6 cells/ml).

extract_protocol: Total RNA was extracted from 5x10^6 lymphoblastoid cells using the Qiaquick RNA Easy plus extraction kit (Qiagen, Mannheim, Germany) according to manufacturer's instructions.

treatment_protocol: No treatment

tag: group

value: healthy control

tag: gender

value: female

value: Epstein–Barr Virus transformed lymphocytes


title: IPF47lung

description: IPF


title: IPF28lung

description: IPF


title: 2959.68hr R 2959.92hr V

value: 68 hours


title: WT1(delZ) rep4

description:
WT1 delZ 11.05.28.a1.lbe1
replicate 4


title: 2959.92hr R 2959.20hr V


title: WT1 +/- rep4

description:
WT1 11.05.28.a1.lbe1
replicate 4


title: Control rep4

description:
control 11.05.28.a1.lbe1
replicate 4

source_name: hematopoietic progenitor cells_Control

value: empty vector (control)


title: IPF35lung

description: IPF


title: 2959.92hr R 2959.44hr V

value: 44 hours


title: 2959.92hr R 2959.68hr V

value: holstein


title: IPF44lung

description: IPF


title: 2959.68hr R 2959.44hr V

value: 2nd Parity


title: 2959.68hr R 2959.20hr V

value: oocyte


title: 2966.20hr R 2966.44hr V

value: 20 hours


title: IPF25lung

description: IPF


title: BL61LPS

description: miRNA profiling

value: LPS


title: BL62LPS

description: miRNA profiling


title: WT1 +/- rep1

description:
WT1 10.03.08-fo6.a1.lbe1
replicate 1


title: BL62Fab

description: miRNA profiling

value: Fab


title: BL63Fab

description: miRNA profiling


title: 2959.44hr R 2959.92hr V

value: 92 hours


title: Control rep3

description:
control 11.03.11.a1.lbe1
replicate 3

value: CD34+ progenitor cells extracted from cord blood cultured 14 days in vitro


title: IPF23lung

description: IPF

value: Lung


title: BL63rest

description: miRNA profiling

value: no

value: splenic B-cell

value: rest


title: BL62rest

description: miRNA profiling


title: BL61rest

description: miRNA profiling


title: 2959.44hr R 2959.68hr V


title: BL61Fab

description: miRNA profiling


title: S101-120

city: Urbana

first: Sonia

middle: Josefina

last: Moisá

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: University of Illinois

description: Sample were total RNA from bovine skeletal muscle tissue (Longissimus dorsi) were used as reference (Cy5 in Ch1 and Cy3 in Ch2)

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 110 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

source_name: Longissimus dorsi, High Energy, 120 days

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Aberdeen Angus steers were fed 2 different diets (high grain and high by product) for a 112 d growing phase.

extract_protocol: A sample of Longissimus dorsi muscle was disected and snap-frozen in liquid nitrogen. Tissue was weighted (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)

value: Skeletal muscle

source_name: Reference

value: Mixture of tissues


title: S101-60

source_name: Longissimus dorsi, High Energy, 60 days

treatment_protocol: Aberdeen Angus steers were fed 2 different diets (high grain and high by product) for a 112 d growing phase.


title: 2959.20hr R 2959.92hr V


title: S101-0

source_name: Longissimus dorsi, High Energy, 0 days


title: Control rep2

description:
control 10.03.08-foV.a1.lbe1
replicate 2


title: 2959.44hr R 2959.20hr V


title: S101-220

source_name: Longissimus dorsi, High Energy, 220 days


title: Control rep1

description:
control 10.03.08 -fo6.a1.lbe1
replicate 1


title: S080-120


title: S080-60


title: 2959.20hr R 2959.68hr V

value: 68 hours


title: 2959.20hr R 2959.44hr V


title: S080-220


title: S080-0


title: 2719.92hr R 2719.68hr V


title: S068-220

source_name: Longissimus dorsi, High Fiber, 220 days


title: 2719.92hr R 2719.20hr V


title: S059-120

source_name: Longissimus dorsi, High Fiber, 120 days


title: 2719.68hr R 2719.20hr V


title: S068-0

source_name: Longissimus dorsi, High Fiber, 0 days


title: S068-120


title: 2719.68hr R 2719.44hr V


title: S042-60

source_name: Longissimus dorsi, High Fiber, 60 days


title: S042-0


title: 2719.44hr R 2719.68hr V


title: S059-0


title: 2719.20hr R 2719.92hr V


title: S037-0


title: 2719.44hr R 2719.20hr V


title: S032-220


title: S037-220


title: 2719.68hr R 2719.92hr V


title: S037-120


title: S068-60


title: S059-220


title: 2719.92hr R 2719.44hr V


title: 2719.44hr R 2719.92hr V


title: S037-60


title: S059-60


title: S042-120


title: S032-120


title: 2719.20hr R 2719.68hr V


title: S032-60


title: S029-220


title: S032-0


title: S029-120


title: S020-120


title: S020-60


title: S029-60


title: S020-220


title: S020-0


title: PEG-treated Germinated Arabidopsis seeds (Col-0), Desiccation-Tolerant, biological rep3

city: Wageningen

first: Wilco

last: Ligterink

address: Droevendaalsesteeg 1

department: Lab of Plant Physiology

country: Netherlands

institute: Wageningen University

description: Gene expression data of desiccation-tolerant germinated seeds.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing:
Custom R script for reading CEL files. In summary, the data was quantile normalized and then filtered and summarized with the following steps:
- selection of all probes in exon regions (containing tu in tu column of annotation)
- from these, select all anti-sense probes (select probes with complement in strand column in combination with forward in direction column, and probes with sense in strand column in combination with reverse in direction column)
- from these, take the mean of all probes for a specific gene (according to the gene column).

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana PEG-treated germinated seeds

label_protocol: Total RNA was processed to produce biotinylated cRNA targets according to the manufacturer’s instructions.

growth_protocol: Seeds of Arabidopsis thaliana, accession Columbia (Col-0), were cold stratified for 72h at 4oC in 9 cm Petri dishes on two layers of blue filter paper (Anchor paper Co.) and 10 ml of distilled water. After stratification to break residual dormancy, germination was performed at 22oC under constant white light. Seeds were collected upon germination.

extract_protocol: Total RNA was extracted according to the hot borate protocol modified from Wan and Wilkins (1994).

treatment_protocol: Collected seeds were used without treatment (DS samples) or after incubation for 3 days in the dark at 22oC, in 6-cm Petri dishes containing 1.2 ml of PEG solution (-2.5MPa) on one sheet of filter paper. After incubation, germinated seeds were rinsed thoroughly in distilled water (DT samples).

tag: ecotype

value: germinated seeds

value: polyethylene glycol (PEG)

tag: phenotype

value: desiccation tolerant


title: PEG-treated Germinated Arabidopsis seeds (Col-0), Desiccation-Tolerant, biological rep1


title: ICC_Tumoral_Stroma_Patient_P10

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µ of 2x Agilent hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (G2565) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09_ssSurrogates and Grid: 028004_D_F_20101102). Gene expression data were further analyzed by using the GeneSpring software (Agilent Technologies). Filtration by "flag" and "signal intensity" was applied. Briefly, were retained only the entities in which at least 50% of the values in any of the two conditions (Non Tumoral vs. Tumoral) had a "detected flag" (i.e. a positive  and significant feature as defined by GeneSpring). For the filtration by signal intensity, were retained the entities in which at least 50% of the values in any of the two conditions (Non Tumoral vs. Tumoral) were within the range of interest (i.e. 20-100th percentile).

source_name: Tumoral stroma (laser capture microdissected)

label_protocol: Total RNA was amplified and labeled with Cy3 fluorescent dye using Agilent one color low-input QuickAmp labeling kit following according to the manufacturer's instructions. Starting from 50 ng total RNA purified from LCM stroma, amplification yield was 1.8±0.7 μg cRNA and specific activity was 5.8±3.4 pmol Cy3 per μg cRNA.

growth_protocol: Following the resection the liver tissue samples were preserved at -80°C.

extract_protocol: Total RNA from laser capture microdissected stroma (or fibrous tissue in the adjacent non-tumor tissue) was extracted and purified using an Arcturus Picopure RNA isolation kit according to the manufacturer’s instructions (Applied Biosystems, Carlsbad, CA).  RNA was qualified using a Nanodrop 2000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA).

treatment_protocol: Tissue samples were subjected to laser capture microdissection (LCM). LCM was performed using the Arcturus veritas™ Microdissection system (Applied Biosystems, Carlsbad, CA). From frozen tissues, serial sections of 10 µm were prepared using a Leica 3050 S cryostat (Leica Microsystems, Wetzlar, Germany) and mounted onto a PEN membrane glass slide (Applied Biosystems). Tissue sections were dehydrated by successive immersions (30 sec. twice) in 70%, 90% and 100% ethanol solutions. Enzymatic activity was locked by the immersion in a xylene solution (1 min. twice). After drying, LCM of stroma was performed according to the manufacturer’s instructions.

value: Tumoral


title: S017-120


title: Untreated Germinated Arabidopsis seeds (Col-0), Desiccation-Sensitive, biological rep2

description: Gene expression data of desiccation-sensitive germinated seeds.

source_name: Arabidopsis thaliana untreated germinated seeds

value: desiccation sensitive


title: ICC_Tumoral_Stroma_Patient_P9


title: S017-0


title: Untreated Germinated Arabidopsis seeds (Col-0), Desiccation-Sensitive, biological rep3


title: S017-220


title: S029-0


title: S017-60


title: S011-120


title: PEG-treated Germinated Arabidopsis seeds (Col-0), Desiccation-Tolerant, biological rep2


title: ICC_Non_Tumoral_Stroma_Patient_P10

source_name: Non-tumoral fibrous tissue (from portal tracts in the adjacent non-tumor tissue) (laser capture microdissected)

value: Non-Tumoral


title: S011-60


title: S011-220


title: ICC_Non_Tumoral_Stroma_Patient_P8


title: ICC_Tumoral_Stroma_Patient_P7


title: Untreated Germinated Arabidopsis seeds (Col-0), Desiccation-Sensitive, biological rep1


title: ICC_Tumoral_Stroma_Patient_P8


title: ICC_Non_Tumoral_Stroma_Patient_P9


title: S011-0


title: ICC_Non_Tumoral_Stroma_Patient_P7


title: S010-220


title: ICC_Non_Tumoral_Stroma_Patient_P5


title: ICC_Tumoral_Stroma_Patient_P4


title: S010-0


title: ICC_Tumoral_Stroma_Patient_P6


title: ICC_Tumoral_Stroma_Patient_P5


title: S010-60


title: S010-120


title: S007-120


title: S007-220


title: ICC_Non_Tumoral_Stroma_Patient_P4


title: ICC_Non_Tumoral_Stroma_Patient_P6


title: S007-0


title: ICC_Tumoral_Stroma_Patient_P3


title: S007-60


title: ICC_Non_Tumoral_Stroma_Patient_P3


title: T+ Cy5

city: tianjin

first: huiyuan

last: zhao

address: weijin Road 94

country: China

institute: nankai university

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. capitalbio software was used.

source_name: CD8+IL-10- T cells

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Splencytes from tiger mice were stimulated by ConA+IL-2+IL-4 for 48hrs,expanded 2 days,PMA+ion restimulation for 6hrs,sorting CD8+IL-10+ T cells and CD8+IL-10- T cells by BD Arial

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

value: spleen

value: male

source_name: CD8+IL-10+ T cells


title: 2719.20hr R 2719.44hr V

tag: sample type

tag: breed (cattle)

value: holstein

value: 20 hours

value: 2nd Parity

value: oocyte

value: 44 hours


title: S003-220


title: ICC_Non_Tumoral_Stroma_Patient_P2


title: isw1∆2∆_Cells_Normal_Growth_Replicate-2

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

institute: MRC Human Genetics Unit, The University Of Edinburgh

hyb_protocol: Agilent ChIP-chip protocol V-10.0

scan_protocol: Agilent ChIP-chip protocol V-10.0

data_processing: Agilent Genomic Workbench Lite Edition 6.5 was used for blnk subtraction and LOWESS normalization

organism: Saccharomyces cerevisiae

source_name: Log-phase cells [nucDNA]

label_protocol: 2 microgram each of mononucleosomal and naked DNA was labelled with Cy5 and Cy3 respectively using Agilent ChIP-chip protocol V-10.0

growth_protocol: Cells were grown in 1x YEP medium with 2% Glucose at 30'C up to mid log-phase and fixed with formaldehyde (1% final conc.)

extract_protocol: Mononucleosomal and size matched naked DNA prepared from fixed cells and normal cells respectively as described by Yuan et al. 2005.

treatment_protocol: Cells were grown in 1XxYEP medium with 2% Glucose at 30'C up to mid log-phase and shifted to  0.15x YEP minus Glucose for 4 hours and fixed with formaldehyde (1% final conc.)

tag: growth protocol

value: Normal Growth in YEP at 30'C

source_name: Log-phase cells [naked DNA]


title: rsc4-∆4_Cells_Normal_Growth_Replicate-3


title: T+ Cy3


title: ICC_Tumoral_Stroma_Patient_P1


title: rsc4-∆4_Cells_Normal_Growth_Replicate-2


title: S003-120

value: Skeletal muscle


title: S003-60

value: Mixture of tissues


title: isw1∆2∆_Cells_Normal_Growth_Replicate-3


title: ICC_Tumoral_Stroma_Patient_P2


title: ICC_Non_Tumoral_Stroma_Patient_P1


title: rsc4-∆4_Cells_Normal_Growth_Replicate-1


title: WT_Cells_Nutrient_Starvation_Replicate-3

source_name: Log-phase cells starved for 4hrs [nucDNA]

value: WT

value: Nutrient starvation in 0.15x YEP minus the carbon source

source_name: Log-phase cells starved for 4hrs [naked DNA]


title: WT_Cells_Nutrient_Starvation_Replicate-1


title: 252047410001_1_2-DS/LOG[E(5)/E(3)]

status: Public on Jun 20 2013

first: Dawn

last: Thompson

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description:
PS
Biological replicate E, technical replicate 1

hyb_protocol: Standard Agilent protocols for Agilent 8x15K and 4x44K Oligo Microarrays

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.  Reported expression values for each gene are median log2 ratios across all probes.

organism: Saccharomyces mikatae

label_protocol: Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.

growth_protocol: Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days).  These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below.  Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: Glucose depletion: Samples from the BMW cultures were taken at: Lag, Log, Late log (LL), Diauxic shift (DS), Post shift (PS), and plateau (P) at the appropriate times for each species.  Samples were collected in 50 mL conicals filled with the appropriate amount of 100% methanol in a dry ice-ethanol bath to stop cellular processes and RNase activity at a temperature of – 40 ° C or lower to produce a 60/40 mixture once the sample is added. Cells were pelleted at 3000 rpm at -4°C, flash frozen with liquid N2, and stored at -80°C prior to total RNA extraction.

tag: phase

value: PS

tag: organism

value: Saccharomyces mikatae

value: LOG


title: isw1∆2∆_Cells_Normal_Growth_Replicate-1


title: WT_Cells_Nutrient_Starvation_Replicate-2


title: 252047410002_2_1-PS/LOG[E(3)/E(5)]

description:
PS
Biological replicate E, technical replicate 4 (dye swap)


title: 252047410003_1_4-LAG/LOG[E(5)/E(3)]

description:
LAG
Biological replicate E, technical replicate 1

value: LAG


title: 252047410002_2_4-DS/LOG[D(5)/D(3)]

description:
DS
Biological replicate D, technical replicate 3

value: DS


title: 252047410002_1_2-PS/LOG[F(5)/F(3)]

description:
PS
Biological replicate F, technical replicate 1


title: 252047410001_2_2-DS/LOG[E(3)/E(5)]

description:
PS
Biological replicate E, technical replicate 2 (dye swap)


title: WT_Cells_Normal_Growth_Replicate-1


title: 252047410004_2_3-LL/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 1

value: LL


title: 252047410004_2_4-LL/LOG[N(5)/N(3)]

description:
LL
Biological replicate N, technical replicate 1


title: WT_Cells_Normal_Growth_Replicate-3


title: S003-0

tag: tissue

source_name: Reference


title: 252047410001_2_3-DS/LOG[F(3)/F(5)]

description:
LL
Biological replicate F, technical replicate 2 (dye swap)


title: 252047410001_1_1-DS/LOG[D(5)/D(3)]

description:
DS
Biological replicate D, technical replicate 1


title: 252047410001_1_3-DS/LOG[F(5)/F(3)]

description:
LL
Biological replicate F, technical replicate 1


title: 252047410002_1_1-PS/LOG[E(5)/E(3)]

description:
PS
Biological replicate E, technical replicate 3


title: WT_Cells_Normal_Growth_Replicate-2


title: 252047410002_2_2-PS/LOG[F(3)/F(5)]

description:
PS
Biological replicate F, technical replicate 2 (dye swap)


title: 252047410003_2_4-PLAT/LOG[F(5)/F(3)]

description:
PLAT
Biological replicate F, technical replicate 1

value: PLAT


title: 252047410003_2_2-PLAT/LOG[E(5)/E(3)]

description:
PLAT
Biological replicate E, technical replicate 1


title: 252175810002_2_4-PS/LOG[N(3)/N(5)]

description:
DS
Biological replicate N, technical replicate 2 (dye swap)

organism: Lachancea kluyveri

value: Saccharomyces kluyveri


title: 3rd instar neuroblast replicate 1

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

description: Dam-Pol II / Dam-control in 3rd instar neuroblasts

hyb_protocol: Hybridisation has been done with HX1 mixer following Nimblegen's procedures

scan_protocol: Arrays were scanned on an Axon 4000B scanner following Nimblegen guidelines

data_processing: The  Dam-Pol II/Dam log2 ratios were median normalised using NimbleScan software (v.2.6, Nimblegen).

organism: Drosophila melanogaster

source_name: Dam-Pol II processed DNA from 3rd instar larval brains expressing LT3-Dam-Pol II in neuroblasts

label_protocol: Labeling has been done using the Nimbelgen Dual-Color Labeling Kit based on a Klenow enzymatic reaction following manufacturer's protocol

growth_protocol: Embryos were collected for 4-6 hours at 25°C, shifted to 18°C for 2 days, hatched larvae were transfered to a food plate for 5 days at 18°C, shifted to 29°C for 1 day.

extract_protocol: Tissues were dissected and placed in 180ul of PBS with 100mM EDTA before samples were processed as previously described (Choksi et al., 2006)

treatment_protocol: Brains were dissected from 3rd instar larvae

value: w-; insc-GAL4/+; tub-GAL80ts/UAS-LT3-Dam-Pol II

value: neuroblast cells

source_name: Dam-control processed DNA from 3rd instar larval brains expressing LT3-Dam in neuroblasts


title: 252175810001_1_4-PS/LOG[M(5)/M(3)]

description:
DS
Biological replicate M, technical replicate 1


title: 3rd instar neuroblast replicate 2


title: 252047410003_1_3-PLAT/LOG[D(5)/D(3)]

description:
PLAT
Biological replicate D, technical replicate 1


title: 252047410001_2_1-DS/LOG[D(3)/D(5)]

description:
DS
Biological replicate D, technical replicate 2 (dye swap)


title: 252047410001_2_4-PS/LOG[D(3)/D(5)]

description:
PS
Biological replicate D, technical replicate 2 (dye swap)


title: 252047410001_1_4-PS/LOG[D(5)/D(3)]

description:
PS
Biological replicate D, technical replicate 1


title: 3rd instar salivary gland replicate 2

description: Dam-Pol II / Dam-control in 3rd instar salivary glands

source_name: Dam-Pol II processed DNA from 3rd instar salivary glands expressing LT3-Dam-Pol II

growth_protocol: Grown at 25°C for 5 days.

treatment_protocol: Salivary glands were dissected from 3rd instar larvae

value: w-; +; sg-GAL4 (hs-GAL4)/UAS-LT3-Dam-Pol II

value: salivary gland cells

source_name: Dam-control processed DNA from 3rd instar salivary glands expressing LT3-Dam

value: w-; +; sg-GAL4 (hs-GAL4)/UAS-LT3-Dam


title: 252175810001_1_2-LL/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 1


title: 252175810004_1_2-LL/LOG[O(5)/O(3)]

description:
LL
Biological replicate O, technical replicate 1


title: 252047410003_1_1-LAG/LOG[D(5)/D(3)]

description:
LAG
Biological replicate D, technical replicate 1


title: 1st instar neuroepithelium replicate 2

description: Dam-Pol II / Dam-control in 1st instar neuroepithelial cells

source_name: Dam-Pol II processed DNA from 1st instar larval brains expressing LT3-Dam-Pol II in neuroepithial cells

growth_protocol: Embryos were collected for 4-6 hours at 25°C, shifted to 18oC for 2 days, hatched larvae were to 29°C for 1 day.

treatment_protocol: Brains were dissected from 1st instar larvae

value: w-; tub-GAL80ts/+; c855-GAL4/UAS-LT3-Dam-Pol II

value: neuroepithelial cells

source_name: Dam-control processed DNA from 1st instar larval brains expressing LT3-Dam in neuroepithial cells


title: 1st instar neuroepithelium replicate 1


title: 252175810002_2_1-DS/LOG[N(5)/N(3)]

description:
LL
Biological replicate N, technical replicate 3


title: 252175810004_1_1-DS/LOG[O(5)/O(3)]

description:
DS
Biological replicate O, technical replicate 1


title: 252175810002_2_3-DS/LOG[N(3)/N(5)]

description:
LL
Biological replicate N, technical replicate 5 (dye swap)


title: 252175810001_2_3-DS/LOG[M(3)/M(5)]

description:
LL
Biological replicate M, technical replicate 5 (dye swap)


title: 252175810001_1_3-DS/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 2


title: 252175810002_1_2-LL/LOG[N(5)/N(3)]

description:
LL
Biological replicate N, technical replicate 1


title: 252175810001_2_1-DS/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 3


title: 3rd instar salivary gland replicate 1


title: 3rd instar neuroepithelium replicate 3

description: Dam-Pol II / Dam-control in 3rd instar neuroepithelial cells

source_name: Dam-Pol II processed DNA from 3rd instar larval brains expressing LT3-Dam-Pol II in neuroepithial cells

source_name: Dam-control processed DNA from 3rd instar larval brains expressing LT3-Dam in neuroepithial cells


title: 252175810004_2_2-PLAT/LOG[O(5)/O(3)]

description:
PLAT
Biological replicate O, technical replicate 1


title: 252175810001_2_2-LL/LOG[M(3)/M(5)]

description:
LL
Biological replicate M, technical replicate 4 (dye swap)


title: 252175810004_1_4-LPS/LOG[O(5)/O(3)]

description:
PS
Biological replicate O, technical replicate 2


title: 252175810004_2_1-ELL/LOG[O(5)/O(3)]

description:
LL
Biological replicate O, technical replicate 2


title: 252175810003_2_1-LAG/LOG[M(5)/M(3)]

description:
LAG
Biological replicate M, technical replicate 1


title: 252175810001_2_4-PS/LOG[M(3)/M(5)]

description:
DS
Biological replicate M, technical replicate 2 (dye swap)


title: 3rd instar neuroepithelium replicate 2


title: 252175810004_2_4-LPS/LOG[N(5)/N(3)]

description:
PS
Biological replicate N, technical replicate 1


title: 252175810003_2_4-PLAT/LOG[N(5)/N(3)]

description:
PLAT
Biological replicate N, technical replicate 1


title: 252175810002_1_3-DS/LOG[N(5)/N(3)]

description:
LL
Biological replicate N, technical replicate 2


title: 252175810003_2_2-PLAT/LOG[M(5)/M(3)]

description:
PLAT
Biological replicate M, technical replicate 1


title: FAM22-02 Human peiripheral blood

type: SRA

city: La Jolla

first: Nongluk

last: Plongthongkum

state: California

address: 9500 Gilman Drive, MC0412, PFBH402

department: Bioengineering

institute: University of California, San Diego

library_source: genomic

data_processing:
The libraries were sequenced by Illumina HiSeq and GAII. Illumina OLB was used for base-calling.
Adaptor sequences (27bp from 5' end) were trimmed from bisulfite reads prior to mapping
Bisulfite reads were mapped using the protocol from Diep et al, Nature Methods 2012. Briefly, all 'C's were replaced by 'T's in reads and mapped to a reference with all 'C's converted to 'T's. After mapping, the modified reads were replaced by the original reads then pileup files were generated using SAMTOOLS
Methylation levels were calculated as the number of cytosines over the total thymines and cytosines for CpGs where at least 90% of base called were thymines and cytosines
CpG sites with at least 10 depth of coverage were reported in final processed file (BED format)
Genome_build: hg19
Supplementary_files_format_and_content: BED formated (tab-delimited) text files include chromosome position and methylation fraction value for each CpG in each subject

source_name: Human peiripheral blood

extract_protocol:
Genomic DNA was extracted from peripheral blood of 22 pedigrees, and approximately 1 µg of genomic DNA was bisulfite converted with EZ-96 Zymo DNA Methylation-Gold kit
Bisulfite padlock probes capture and sequencing (Diep et al, 2012). Briefly,  approximately 250ng of bisulfite converted genomic DNAs were mixed with normalized amount of genome-wide scale padlock probes and oligo suppressors. The padlock probes annealing to targets were polymerized and ligated resulting in circularized DNA. The bisulfite sequencing libraries were generated by library-free BSPP protocol as described (Dinh et al. 2012). Two-thirds of the circularized DNA of each captured reaction were directly amplified and barcoded. The bisulfite sequencing libraries were purified with AMPure magnetic beads, pooled in equimolar ratios, size selected with 6% polyacrylamide gel, and sequenced by Illumina HiSeq and GAIIx sequencers. We firstly sequenced the 96 pooled libraries with Illumina HiSeq. For those samples with number of reads than 22 millions (53 samples), we did 3 additional sequencings on the same libraries as indicated in the two columns below (HiSeq, GAIIx, and Hiseq).

value: Female


title: FAM22-04 Human peiripheral blood

description: In addition to HiSeq 2000, these Samples had to be furthered sequenced with (Hiseq2000 and  GAIIx) to obtain enough reads

tag: father

tag: mother


title: FAM22-01 Human peiripheral blood

value: Male


title: FAM22-03 Human peiripheral blood


title: FAM21-04 Human peiripheral blood


title: FAM21-02 Human peiripheral blood


title: FAM21-03 Human peiripheral blood


title: 3rd instar neuroepithelium replicate 1

tag: cell type


title: FAM21-01 Human peiripheral blood


title: FAM20-03 Human peiripheral blood


title: FAM20-04 Human peiripheral blood


title: 252175810002_1_4-PS/LOG[N(5)/N(3)]

description:
DS
Biological replicate N, technical replicate 1


title: FAM20-01 Human peiripheral blood


title: FAM20-02 Human peiripheral blood


title: FAM19-05 Human peiripheral blood


title: FAM19-04 Human peiripheral blood


title: FAM19-02 Human peiripheral blood


title: FAM19-01 Human peiripheral blood


title: 252175810003_2_3-LAG/LOG[N(5)/N(3)]

description:
LAG
Biological replicate N, technical replicate 1


title: FAM18-01 Human peiripheral blood


title: FAM18-02 Human peiripheral blood


title: FAM19-03 Human peiripheral blood


title: FAM18-04 Human peiripheral blood


title: FAM18-03 Human peiripheral blood


title: ec_glucose_heatshock_3

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

description: SAMPLE 6

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (aligned.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). (Please note that the original/unedited raw data files were named as  *_aligned because the hybridization images were aligned before being processed to generate .pair files.)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: M9 glucose with heatshock

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: E. coli K-12 MG1655 was grown to mid-log phase (O.D.600nm 0.6) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, then 42°C heatshock was applied to heatshock samples for 10 min.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: growth phase

tag: treated with

value: 42°C heatshock for 10min


title: miR1225 transfected MEG-01, biological replicate 4

first: Shilpa

last: Jain

address: 200 Lothrop Street

institute: Uinversity of Pittsburgh

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent 8X60K microarray. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters.
LincRNAs have been excluded from the normalization. Positive and negative controls are also removed.

source_name: Meg-01 cells, post-nucleofection

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng of total RNA

growth_protocol: The cells were subcultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin under 5% CO2 at 37 degrees Celsius.

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cultured MEG-01 cells were transfected with 200nM of upregulated pre-miRNA 1225-3p or negative control and left for incubation for 24 hours

tag: cell line

value: Meg-01 cells

tag: genotype/variation

value: miR1225 overexpression


title: FAM17-04 Human peiripheral blood


title: 252175810004_2_3-LPS/LOG[M(5)/M(3)]

description:
PS
Biological replicate M, technical replicate 1

value: PS

value: LOG


title: miR1225 transfected MEG-01, biological replicate 5


title: scrambled transfected MEG-01, biological replicate 3

source_name: Meg-01 cells, no treatment

value: control


title: scrambled transfected MEG-01, biological replicate 4


title: scrambled transfected MEG-01, biological replicate 5


title: scrambled transfected MEG-01, biological replicate 2


title: FAM17-02 Human peiripheral blood


title: miR1225 transfected MEG-01, biological replicate 1


title: miR1225 transfected MEG-01, biological replicate 3


title: ec_glucose_noheat_3

description: SAMPLE 3

source_name: M9 glucose without heatshock


title: ec_glucose_heatshock_1

description: SAMPLE 4


title: ec_glucose_noheat_1

description: SAMPLE 1


title: scrambled transfected MEG-01, biological replicate 1


title: miR1225 transfected MEG-01, biological replicate 2


title: ec_glucose_heatshock_2

description: SAMPLE 5


title: FAM17-01 Human peiripheral blood


title: FAM16-04 Human peiripheral blood


title: FAM16-03 Human peiripheral blood


title: FAM17-03 Human peiripheral blood


title: ec_glucose_noheat_2

description: SAMPLE 2


title: Water column DNA_ETSP_Station 26_20m

type: mixed

city: Princeton

first: Xuefeng

last: Peng

state: NJ

address: Guyot Hall

department: Geosciences

institute: Princeton University

description:
E26.20m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4200). Images were analyzed with GenePix Pro 6.0 software (Molecular Devices).

data_processing:
Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).
Cy3/Cy5 fluorescence intensities were standardized to the highest Cy3/Cy5 fluorescence across the AOA probe set (normalized fluorescence ratio; FRN).

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard + 70-mer

label_protocol: Hybridization targets were prepared by digesting environmental DNA with a four cutter restriction enzyme. The digested environmental DNA were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from the filters using the PureGene DNA kit (Gentra, Minneapolis, MN) or the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Ward 2008).

value: reference

organism: marine metagenome

source_name: Total DNA from water column, ETSP station 26, 20m

tag: location

value: Eastern Tropical South Pacific (ETSP) Station 26

tag: depth

value: environmental


title: FAM16-01 Human peiripheral blood

tag: gender


title: FAM15-04 Human peiripheral blood


title: FAM15-03 Human peiripheral blood


title: Water column DNA_ETSP_Station 26_260m

description:
E26.260m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 26, 260m


title: Water column DNA_ETSP_Station 24_20m

description:
E24.20m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 24, 20m

value: Eastern Tropical South Pacific (ETSP) Station 24


title: Water column DNA_ETSP_Station 24_260m

description:
E24.260m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 24, 260m


title: Water column DNA_ETSP_Station 20_260m

description:
E20.260m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 20, 260m

value: Eastern Tropical South Pacific (ETSP) Station 20


title: Water column DNA_ETSP_Station 20_20m

description:
E20.20m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 20, 20m


title: FAM16-02 Human peiripheral blood


title: Water column DNA_ETSP_Station 19_260m

description:
E19.260m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 19, 260m

value: Eastern Tropical South Pacific (ETSP) Station 19


title: Water column DNA_ETSP_Station 19_20m

description:
E19.20m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 19, 20m


title: FAM14-05 Human peiripheral blood


title: Water column DNA_ETSP_Station 14_260m

description:
E14.260m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 14, 260m

value: Eastern Tropical South Pacific (ETSP) Station 14


title: FAM15-01 Human peiripheral blood


title: FAM14-03 Human peiripheral blood


title: FAM14-04 Human peiripheral blood


title: FAM14-02 Human peiripheral blood


title: Water column DNA_ETSP_Station 12_20m

description:
E12.20m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 12, 20m

value: Eastern Tropical South Pacific (ETSP) Station 12


title: Water column DNA_ETSP_Station 14_20m

description:
E14.20m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 14, 20m


title: Water column DNA_ETSP_Station 12_260m

description:
E12.260m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, ETSP station 12, 260m


title: Water column DNA_Arabian Sea_Station 3_110m

description:
AS3.110m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 3, 110m

value: Arabian Sea Station 3


title: FAM15-02 Human peiripheral blood

description: In addition to HiSeq 2000, these Samples had to be furthered sequenced with (Hiseq2000 and  GAIIx) to obtain enough reads

source_name: Human peiripheral blood

value: Female


title: Water column DNA_Arabian Sea_Station 2_200m

description:
AS2.200m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 2, 200m

value: Arabian Sea Station 2


title: FAM13-05 Human peiripheral blood

value: Male


title: FAM14-01 Human peiripheral blood


title: Water column DNA_Arabian Sea_Station 3_150m

description:
AS3.150m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 3, 150m


title: FAM13-02 Human peiripheral blood


title: 252175810002_2_2-LL/LOG[N(3)/N(5)]

description:
LL
Biological replicate N, technical replicate 4 (dye swap)

value: Saccharomyces kluyveri

value: LL


title: Water column DNA_Arabian Sea_Station 2_150m

description:
AS2.150m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Universal Internal Standard + 70-mer

source_name: Total DNA from water column, Arabian Sea station 2, 150m


title: 252175810004_1_3-PS/LOG[O(5)/O(3)]

description:
PS
Biological replicate O, technical replicate 1

value: PS


title: FAM12-05 Human peiripheral blood


title: Water column DNA_Arabian Sea_Station 2_10m

description:
AS2.10m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 2, 10m


title: FAM13-03 Human peiripheral blood


title: FAM12-04 Human peiripheral blood


title: FAM12-03 Human peiripheral blood


title: Water column DNA_Arabian Sea_Station 1_175m

description:
AS1.175m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 1, 175m

value: Arabian Sea Station 1


title: FAM12-02 Human peiripheral blood


title: Water column DNA_Arabian Sea_Station 1_150m

description:
AS1.150m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 1, 150m


title: Water column DNA_Arabian Sea_Station 1_10m

description:
AS1.10m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 1, 10m


title: FAM12-01 Human peiripheral blood


title: FAM11-04 Human peiripheral blood


title: Water column DNA_Arabian Sea_Station 1_102m

description:
AS1.102m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 1, 102m


title: Water column DNA_Arabian Sea_Station 1_60m

description:
AS1.60m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 1, 60m


title: Water column DNA_Arabian Sea_Station 3_10m

description:
AS3.10m
This Sample represents 2 replicates.
DNA extracted from sterivex filter used to create 2 targets to run on duplicate arrays.

source_name: Total DNA from water column, Arabian Sea station 3, 10m


title: FAM11-03 Human peiripheral blood


title: 252035410005_1_2-DS/LOG[B(5)/B(3)]

description:
LL
Biological replicate B, technical replicate 1

organism: Kluyveromyces lactis

value: Kluyveromyces lactis

value: LOG


title: 252035410007_1_3-LPS/LOG[H(5)/H(3)]

description:
PS
Biological replicate H, technical replicate 1


title: FAM13-04 Human peiripheral blood


title: FAM11-02 Human peiripheral blood


title: FAM11-01 Human peiripheral blood


title: FAM13-01 Human peiripheral blood


title: FAM10-03 Human peiripheral blood


title: FAM10-04 Human peiripheral blood


title: FAM9-04 Human peiripheral blood


title: FAM10-01 Human peiripheral blood


title: FAM9-02 Human peiripheral blood


title: 252035410005_2_4-PS/LOG[A(3)/A(5)]

description:
LL
Biological replicate A, technical replicate 4 (dye swap)


title: FAM10-02 Human peiripheral blood


title: 252035410007_1_4-PLAT/LOG[H(5)/H(3)]

description:
PLAT
Biological replicate H, technical replicate 1

value: PLAT


title: 252035410007_2_4-LPS/LOG[I(5)/I(3)]

description:
PS
Biological replicate I, technical replicate 1


title: 252035410001_1_4-PS/LOG[G(5)/G(3)]

description:
DS
Biological replicate G, technical replicate 1

value: DS


title: 252035410001_1_2-LL/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 1


title: 252035410001_2_3-PLAT/LOG[G(5)/G(3)]

description:
PLAT
Biological replicate G, technical replicate 1


title: 252035410006_2_1-PS/LOG[B(3)/B(5)]

description:
LL
Biological replicate B, technical replicate 4 (dye swap)


title: 252035410006_1_2-PS/LOG[C(5)/C(3)]

description:
LL
Biological replicate C, technical replicate 3


title: 252035410007_1_2-PS/LOG[H(5)/H(3)]

description:
DS
Biological replicate H, technical replicate 1


title: 252035410007_2_3-PS/LOG[I(5)/I(3)]

description:
DS
Biological replicate I, technical replicate 1


title: 252035410005_1_3-DS/LOG[C(5)/C(3)]

description:
LL
Biological replicate C, technical replicate 1


title: FAM8-04 Human peiripheral blood


title: FAM8-02 Human peiripheral blood

description: In addition to HiSeq 2000, these Samples had to be furthered sequenced with (Hiseq2000 and  GAIIx) to obtain enough reads


title: FAM9-03 Human peiripheral blood


title: FAM8-05 Human peiripheral blood


title: FAM9-01 Human peiripheral blood


title: FAM8-01 Human peiripheral blood


title: 252035410006_2_4-DS/LOG[A(3)/A(5)]

description:
LL
Biological replicate A, technical replicate 5 (dye swap)


title: 252035410001_2_2-LAG/LOG[H(5)/H(3)]

description:
LAG
Biological replicate H, technical replicate 1

value: LAG


title: 252035410005_1_1-DS/LOG[A(5)/A(3)]

description:
LL
Biological replicate A, technical replicate 1


title: FAM7-02 Human peiripheral blood


title: FAM8-03 Human peiripheral blood


title: 252035410001_1_1-LAG/LOG[G(5)/G(3)]

description:
LAG
Biological replicate G, technical replicate 1


title: FAM7-05 Human peiripheral blood


title: FAM7-01 Human peiripheral blood


title: FAM7-03 Human peiripheral blood


title: 252035410005_1_4-PS/LOG[A(5)/A(3)]

description:
LL
Biological replicate A, technical replicate 2


title: 252035410006_1_1-PS/LOG[B(5)/B(3)]

description:
LL
Biological replicate B, technical replicate 3


title: 252035410005_2_1-DS/LOG[A(3)/A(5)]

description:
LL
Biological replicate A, technical replicate 3 (dye swap)


title: 252035410001_2_4-LPS/LOG[G(5)/G(3)]

description:
PS
Biological replicate G, technical replicate 1


title: FAM7-04 Human peiripheral blood


title: FAM6-02 Human peiripheral blood


title: FAM6-04 Human peiripheral blood


title: FAM6-03 Human peiripheral blood


title: FAM5-05 Human peiripheral blood


title: FAM6-01 Human peiripheral blood


title: FAM5-04 Human peiripheral blood


title: 251983910005_1_2-LL/LOG[F(5)/F(3)]

description:
LL
Biological replicate F, technical replicate 1

organism: Nakaseomyces glabratus

value: Candida glabrata


title: 251983910004_1_1-PS/LOG[E(5)/E(3)]

description:
PS
Biological replicate E, technical replicate 1


title: 251983910005_2_2-LL/LOG[F(3)/F(5)]

description:
LL
Biological replicate F, technical replicate 2 (dye swap)


title: 252035410005_2_2-DS/LOG[B(3)/B(5)]

description:
LL
Biological replicate B, technical replicate 2 (dye swap)


title: 251983910027_1_1-ELL/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 1


title: 251983910027_2_3-LL/LOG[O(5)/O(3)]

description:
DS
Biological replicate O, technical replicate 1


title: 252035410007_2_1-LAG/LOG[I(5)/I(3)]

description:
LAG
Biological replicate I, technical replicate 1


title: FAM5-01 Human peiripheral blood


title: FAM4-02 Human peiripheral blood


title: FAM4-01 Human peiripheral blood


title: 251983910012_1_1-DS/LOG[H(5)/H(3)]

description:
DS
Biological replicate H, technical replicate 1


title: FAM5-03 Human peiripheral blood

description: In addition to HiSeq 2000, these Samples had to be furthered sequenced with (Hiseq2000 and  GAIIx) to obtain enough reads


title: FAM5-02 Human peiripheral blood


title: 251983910012_2_3-PS/LOG[I(5)/I(3)]

description:
PS
Biological replicate I, technical replicate 1


title: 251983910001_1_4-PS/LOG[G(5)/G(3)]


title: FAM4-04 Human peiripheral blood


title: FAM4-03 Human peiripheral blood


title: 251983910001_2_3-PLAT/LOG[G(5)/G(3)]

description:
PLAT
Biological replicate G, technical replicate 1


title: 251983910028_1_2-LL/LOG[N(5)/N(3)]

description:
DS
Biological replicate N, technical replicate 1


title: 251983910004_1_4-DS/LOG[E(5)/E(3)]

description:
DS
Biological replicate E, technical replicate 1


title: FAM3-02 Human peiripheral blood


title: FAM3-05 Human peiripheral blood


title: FAM3-01 Human peiripheral blood


title: FAM3-03 Human peiripheral blood


title: 251983910003_1_4-PS/LOG[F(5)/F(3)]

description:
PS
Biological replicate F, technical replicate 1


title: 251983910028_1_1-ELL/LOG[N(5)/N(3)]

description:
LL
Biological replicate N, technical replicate 1


title: 251983910004_2_1-PS/LOG[E(3)/E(5)]

description:
PS
Biological replicate E, technical replicate 2 (dye swap)


title: 251983910027_1_2-LL/LOG[M(5)/M(3)]

description:
DS
Biological replicate M, technical replicate 1


title: FAM2-01 Human peiripheral blood


title: FAM2-04 Human peiripheral blood


title: 251983910003_2_1-PLAT/LOG[F(3)/F(5)]

description:
PLAT
Biological replicate F, technical replicate 2 (dye swap)


title: 252035410006_2_2-PS/LOG[C(3)/C(5)]

description:
LL
Biological replicate C, technical replicate 4 (dye swap)


title: FAM2-02 Human peiripheral blood


title: 251983910043_1_1-LAG/LOG[P(5)/P(3)]

description:
LAG
Biological replicate P, technical replicate 1


title: 251983910004_2_4-DS/LOG[E(3)/E(5)]

description:
DS
Biological replicate E, technical replicate 2 (dye swap)


title: FAM2-03 Human peiripheral blood


title: 251983910003_1_1-PLAT/LOG[F(5)/F(3)]

description:
PLAT
Biological replicate F, technical replicate 1


title: 251983910028_1_4-PS/LOG[N(5)/N(3)]

description:
PS
Biological replicate N, technical replicate 2


title: 251983910028_2_2-PLAT/LOG[N(5)/N(3)]

description:
PLAT
Biological replicate N, technical replicate 1


title: FAM3-04 Human peiripheral blood


title: FAM1-03 Human peiripheral blood


title: 251983910004_2_3-DS/LOG[F(3)/F(5)]

description:
DS
Biological replicate F, technical replicate 2 (dye swap)


title: FAM1-02 Human peiripheral blood


title: 251983910003_2_2-PLAT/LOG[E(3)/E(5)]

description:
PLAT
Biological replicate E, technical replicate 2 (dye swap)


title: 251983910003_1_3-PLAT/LOG[D(5)/D(3)]

description:
PLAT
Biological replicate D, technical replicate 1


title: 251983910005_2_3-LL/LOG[E(3)/E(5)]

description:
LL
Biological replicate E, technical replicate 2 (dye swap)


title: 251983910027_2_4-DS/LOG[O(5)/O(3)]

description:
PS
Biological replicate O, technical replicate 1


title: 251983910005_1_4-LL/LOG[D(5)/D(3)]

description:
LL
Biological replicate D, technical replicate 1


title: FAM1-01 Human peiripheral blood


title: 251983910012_2_2-DS/LOG[I(5)/I(3)]

description:
DS
Biological replicate I, technical replicate 1


title: 251983910001_1_2-LL/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 1


title: sickle cell disease 7, UPMC

description:
Platelets purified from whole blood
miRNA profiling

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55 C on Agilent- 021827 Human miRNA microarray V3. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15K array slides

data_processing: Agilent Feature Extraction v10.7.1.1 default parameters

source_name: Platelets

label_protocol: pCp-Cy3  labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA was extracted from platelets, obtained from 20ml of peripheral whole blood, using Trizol according to the manufacturer's instructions.

treatment_protocol: Control subjects: none. SCD subjects: Hydroxyurea or No Hydroxyurea.

tag: cohort

value: UPMC

tag: subject's disease state

value: Sickle Cell disease

tag: age (years)

tag: treatment

value: No Hydroxyurea

value: peripheral whole blood

value: platelet


title: 251983910004_1_3-DS/LOG[F(5)/F(3)]

description:
DS
Biological replicate F, technical replicate 1

tag: phase


title: FAM1-04 Human peiripheral blood

description: In addition to HiSeq 2000, these Samples had to be furthered sequenced with (Hiseq2000 and  GAIIx) to obtain enough reads


title: 251983910028_1_3-DS/LOG[N(5)/N(3)]

description:
PS
Biological replicate N, technical replicate 1

tag: organism


title: 251983910003_2_3-PLAT/LOG[D(3)/D(5)]

description:
PLAT
Biological replicate D, technical replicate 2 (dye swap)


title: 251983910005_1_3-LL/LOG[E(5)/E(3)]

description:
LL
Biological replicate E, technical replicate 1


title: sickle cell disease 6, UPMC

value: Female

tag: tissue


title: sickle cell disease 5, UPMC

value: Male


title: sickle cell disease 4, UPMC

value: Hydroxyurea


title: 251983910003_1_2-PLAT/LOG[E(5)/E(3)]

description:
PLAT
Biological replicate E, technical replicate 1


title: 251983910004_2_2-PS/LOG[D(3)/D(5)]

description:
PS
Biological replicate D, technical replicate 2 (dye swap)


title: 251983910027_2_2-PLAT/LOG[M(5)/M(3)]

description:
PLAT
Biological replicate M, technical replicate 1


title: 251983910003_2_4-PS/LOG[F(3)/F(5)]

description:
PS
Biological replicate F, technical replicate 2 (dye swap)


title: 251983910027_1_4-PS/LOG[M(5)/M(3)]

description:
PS
Biological replicate M, technical replicate 2


title: 251983910004_1_2-PS/LOG[D(5)/D(3)]

description:
PS
Biological replicate D, technical replicate 1


title: 252061210003_1_3-PS/LOG[P(5)/P(3)]

description:
DS
Biological replicate P, technical replicate 1

organism: Debaryomyces hansenii

value: Debaryomyces hansenii


title: sickle cell disease 3, UPMC


title: sickle cell disease 2, UPMC


title: 252061210001_2_3-PLAT/LOG[C(3)/C(5)]

description:
LL
Biological replicate C, technical replicate 1 (dye swap)

value: LL


title: sickle cell disease 1, UPMC


title: 251983910043_1_2-LAG/LOG[Q(5)/Q(3)]

description:
LAG
Biological replicate Q, technical replicate 1


title: Control 6, UPMC

value: control


title: 252061210002_1_1-LAG/LOG[A(5)/A(3)]

description:
LAG
Biological replicate A, technical replicate 1


title: 252061210004_1_4-LL/LOG[R(5)/R(3)]

description:
LL
Biological replicate R, technical replicate 2


title: 251983910001_1_3-DS/LOG[G(5)/G(3)]

description:
DS
Biological replicate G, technical replicate 1


title: 251983910005_2_4-LL/LOG[D(3)/D(5)]

description:
LL
Biological replicate D, technical replicate 2 (dye swap)


title: 252061210004_1_3-ELL/LOG[R(5)/R(3)]

description:
LL
Biological replicate R, technical replicate 1


title: 251983910027_1_3-DS/LOG[M(5)/M(3)]

description:
PS
Biological replicate M, technical replicate 1

value: PS


title: Control 5, UPMC

description:
Platelets purified from whole blood
miRNA profiling


title: 251983910012_1_4-PLAT/LOG[H(5)/H(3)]

description:
PLAT
Biological replicate H, technical replicate 1

value: LOG


title: Control 2, UPMC


title: 252061210004_1_1-LPS/LOG[Q(5)/Q(3)]

description:
PS
Biological replicate Q, technical replicate 1


title: 252061210003_2_2-LL/LOG[Q(5)/Q(3)]

description:
LL
Biological replicate Q, technical replicate 2


title: 252061210004_2_3-LPS/LOG[R(5)/R(3)]

description:
PS
Biological replicate R, technical replicate 1


title: 252061210002_2_3-PLAT/LOG[C(5)/C(3)]

description:
LL
Biological replicate C, technical replicate 2


title: 251983910012_1_2-PS/LOG[H(5)/H(3)]

description:
PS
Biological replicate H, technical replicate 1


title: Control 3, UPMC


title: Control 1, UPMC


title: Human Mammary Epithelial Cells, control, IV

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description: Human Mammary Epithelial Cells with GFP overexpression, IV

hyb_protocol: Target samples were hybridized to Human Exon 1.0 ST v2 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw data was preprocessed using the RMA method. For transcript probe set definition the custom CDF package from the brainarray group (hugene10stv1enstcdf version 13, defining probe sets for transcripts from Ensembl core database version 58) was used.

source_name: HMEC_GFP control overexpression

label_protocol: Target RNA was labeled by addition of biotin-linked deoxynucleotides with terminal deoxynucleotidyl transferase according to the manufacturer's (Affymetrix) protocols. Washing and staining was performed in an Affymetrix 450S fluidics station.

growth_protocol: HMECs of 3 independent donors were seeded on a Transwell 0.4 µm Polyester Membrane (Costar) coated with Growth Factor Reduced Matrigel (BD Biosciences) diluted 1:40 in a serum free RPMI1640. Cell culture medium was exchanged daily. Until day 4-5 cells cells formed confluent monolayer and until day 12 they polarized. The polarization status of the culture was confirmed by transepithelial resistance measurement.

extract_protocol: RNA of HMECs (3 independent donors) with EpCAM/GFP adenoviruses was extracted using TRI-reagent (Sigma) acording to manufacture's protocol. After extraction, DNA was digested using Dnase I (Qisgen), RNA was purified using RNeasy kit (Qiagen).

treatment_protocol: HMECs were cultured on a transwells for 10 days until we polarized culture was obtained, medium was chcnged daily. On day 10 of culture cells were transfected for 32 hours with EpCAM adenoviruses (or GFP control adenoviruses) to obtain overexpression of this antigen. After 32 h of transfection, RNA was extracted.

value: human mammary epithelial cells

value: GFP control overexpression

tag: transfected with

value: GFP control adenoviruses

tag: sample/donor pairing

value: IV


title: Control 7, UPMC

value: UPMC

tag: cell type


title: Human Mammary Epithelial Cells, EPCAM overexpressing, IV

description: Human Mammary Epithelial Cells with EPCAM overexpression, IV

source_name: HMEC_EpCAM overexpression

value: EpCAM overexpression

value: EpCAM adenoviruses


title: sickle cell disease 19, NIH

value: NIH

value: Sickle Cell disease

value: No Hydroxyurea

value: peripheral whole blood


title: Human Mammary Epithelial Cells, EPCAM overexpressing, III

description: Human Mammary Epithelial Cells with EPCAM overexpression, III

value: III


title: Human Mammary Epithelial Cells, control, III

description: Human Mammary Epithelial Cells with GFP overexpression, III


title: Human Mammary Epithelial Cells, control, II

description: Human Mammary Epithelial Cells with GFP overexpression, II

value: II


title: 252061210002_1_4-PS/LOG[B(5)/B(3)]

description:
LL
Biological replicate B, technical replicate 1

value: LL

value: Debaryomyces hansenii


title: 252061210003_2_1-ELL/LOG[Q(5)/Q(3)]

description:
LL
Biological replicate Q, technical replicate 1


title: sickle cell disease 18, NIH

value: Female

value: platelet


title: sickle cell disease 16, NIH


title: 252061210004_2_2-PS/LOG[R(5)/R(3)]

description:
DS
Biological replicate R, technical replicate 1

value: DS

value: LOG


title: Control 4, UPMC

value: control

value: Male


title: Human Mammary Epithelial Cells, EPCAM overexpressing, II

description: Human Mammary Epithelial Cells with EPCAM overexpression, II

value: human mammary epithelial cells


title: sickle cell disease 15, NIH


title: sickle cell disease 13, NIH


title: CONTROL10

type: protein

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

institute: University of California Irvine

hyb_protocol: Serum samples were diluted 1:200 in Protein Array Blocking buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5α E. coli lysate (MCLAB, San Francisco, CA) and incubated on arrays over night at 4°C.  Microarray slides were incubated in biotin-conjugated anti-IgG Fc fragment secondary antibody (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer, and detected by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Columbia, MD). The slides were washed and air-dried by brief centrifugation.

scan_protocol: Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to Pf proteins on the microarray the following steps were taken: (i) the mean background signal of antibody binding to 31 control spots of in vitro transcription/translation reaction without DNA template (no DNA spots) were removed from each sera’s raw values of antibody binding measured as the mean pixel intensity of spots of printed protein; (ii) the average, 95% confidence intervals (CI) and Z-scores of antibody binding intensity for each study and control groups were calculated for each protein target on the array. A Z-score was the number of standard deviations above or below the mean of the control group. Protein targets were considered immunogenic if the following criteria were satisfied: (i) for each sera group, the average pixel intensity to the protein had to be above the group’s upper CI value of pixel intensity of no DNA spots; high reactant proteins were considered for further analysis if at least one study group satisfied this cutoff; (ii) the study group’s lower confidence interval for pixel intensity did not overlap with the control group’s upper confidence interval for each protein; the significant antigens were included in further analysis if this was true for at least one study group.

molecule: protein

source_name: serum

tag: serum type

value: Unexposed

tag: age group (years)

tag: season

tag: site

tag: molecule subtype

value: Total IgG


title: 252061210003_1_1-LL/LOG[P(5)/P(3)]

description:
LL
Biological replicate P, technical replicate 1


title: CONTROL8


title: 252061210003_2_4-PS/LOG[Q(5)/Q(3)]

description:
DS
Biological replicate Q, technical replicate 1


title: sickle cell disease 17, NIH

city: Pittsburgh

description:
Platelets purified from whole blood
miRNA profiling

value: NIH


title: CONTROL6


title: CONTROL5


title: CONTROL9


title: sickle cell disease 14, NIH

value: Sickle Cell disease


title: 252153310007_1_2-LAG/LOG[Q(5)/Q(3)]

city: Cambridge

description:
LAG
Biological replicate Q, technical replicate 1

organism: Vanderwaltozyma polyspora

value: LAG

value: Kluyveromyces polysporus


title: 252153310002_1_4-PS/LOG[L(5)/L(3)]

description:
PS
Biological replicate L, technical replicate 1

value: PS


title: sickle cell disease 12, NIH

value: No Hydroxyurea

value: peripheral whole blood


title: 252153310002_1_2-LL/LOG[L(5)/L(3)]

description:
LL
Biological replicate L, technical replicate 1

value: LL


title: CONTROL4


title: 252153310003_1_2-DS/LOG[J(5)/J(3)]

description:
LL
Biological replicate J, technical replicate 1


title: CONTROL3


title: sickle cell disease 11, NIH

value: Female


title: CONTROL2


title: CONTROL1


title: 252153310002_2_1-DS/LOG[L(5)/L(3)]

description:
DS
Biological replicate L, technical replicate 2


title: sickle cell disease 10, NIH

value: Hydroxyurea

value: platelet


title: 252153310002_2_2-LL/LOG[L(3)/L(5)]

description:
LL
Biological replicate L, technical replicate 2 (dye swap)

value: LOG


title: 3HD10

value: Exposed

value: DRY

value: HILLTOP


title: 3HD9


title: 252153310001_1_3-DS/LOG[K(5)/K(3)]

description:
LL
Biological replicate K, technical replicate 1


title: 3HD8


title: 252153310001_2_3-DS/LOG[K(3)/K(5)]

description:
LL
Biological replicate K, technical replicate 3 (dye swap)


title: sickle cell disease 8, NIH

value: Male


title: 3HD6

value: Total IgG


title: sickle cell disease 5, NIH

value: NIH


title: 252153310002_1_3-DS/LOG[L(5)/L(3)]

description:
DS
Biological replicate L, technical replicate 1

value: DS


title: sickle cell disease 7, NIH

value: Sickle Cell disease


title: sickle cell disease 4, NIH


title: CONTROL7

value: Unexposed


title: sickle cell disease 6, NIH


title: 252153310001_2_4-PS/LOG[K(3)/K(5)]

description:
PS
Biological replicate K, technical replicate 2 (dye swap)

value: Kluyveromyces polysporus

value: PS


title: 3HD7


title: 3HD5


title: 252153310003_2_2-PLAT/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 1

value: PLAT


title: 252153310003_1_3-PS/LOG[J(5)/J(3)]

description:
DS
Biological replicate J, technical replicate 1


title: 3HD4


title: sickle cell disease 3, NIH

value: peripheral whole blood


title: 3HD3


title: 252153310003_2_3-LPS/LOG[L(5)/L(3)]

description:
PS
Biological replicate L, technical replicate 3


title: 252153310002_2_3-DS/LOG[L(3)/L(5)]

description:
DS
Biological replicate L, technical replicate 3 (dye swap)


title: 3HD2


title: sickle cell disease 2, NIH

value: Female


title: sickle cell disease 1, NIH

value: Hydroxyurea


title: 3HD1


title: 252153310002_2_4-PS/LOG[L(3)/L(5)]

description:
PS
Biological replicate L, technical replicate 2 (dye swap)


title: control 10, NIH

value: control

value: platelet


title: 3HW10

value: Exposed

value: WET


title: control 9, NIH


title: 3HW9

value: HILLTOP


title: control 8, NIH


title: 252153310001_2_1-DS/LOG[K(5)/K(3)]

description:
LL
Biological replicate K, technical replicate 2

value: LL

value: LOG


title: 3HW8

value: Total IgG


title: IFN treatment with miR-203 inhibitor Replicate 2

city: Evanston

first: William

last: Buggele

address: 2200 Campus Dr.

institute: Northwestern University

description: A549 cells were transfected with 50nM miR-203 inhibitor using Lipofectamine 2000.  Fifteen hours after transfection, cells were treated with 1000 units/mL IFN_ for ten hours prior to RNA purification.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Quantile Normalization

source_name: A549 cells

label_protocol: standard as recommended by illumina

extract_protocol: Total RNA was prepared using Qiagen's miRNEasy kit

tag: cell line

value: IFNalpha


title: control 7, NIH

description:
Platelets purified from whole blood
miRNA profiling

value: NIH

tag: gender

value: Male


title: sickle cell disease 9, NIH

tag: cohort

value: Sickle Cell disease


title: Untreated Replicate 3

description: A549 cells were left untreated.

value: Untreated


title: IFN treatment with miR-203 mimic Replicate 2

description: A549 cells were transfected with 50nM miR-203 mimic using Lipofectamine 2000.  Fifteen hours after transfection, cells were treated with 1000 units/mL IFN_ for ten hours prior to RNA purification.


title: 252153310003_1_4-LPS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 1

value: PS

value: Kluyveromyces polysporus


title: 3HW7


title: control 6, NIH

tag: subject's disease state

value: Female

value: peripheral whole blood


title: 252153310001_1_4-PS/LOG[K(5)/K(3)]

description:
PS
Biological replicate K, technical replicate 1


title: IFN treatment with miR-203 mimic Replicate 3


title: IFN treatment Replicate 3

description: A549 cells were treated with 1000 units/mL IFN_ for 10 hours prior to RNA purification.


title: control 5, NIH

value: control

tag: age (years)


title: 3HW6


title: IFN treatment with miR-203 inhibitor Replicate 1

tag: treatment


title: IFN treatment with miR-203 inhibitor Replicate 3


title: 3HW5


title: Untreated Replicate 2

description: A549 cells were left untreated.


title: 252153310003_2_4-PLAT/LOG[L(5)/L(3)]

description:
PLAT
Biological replicate L, technical replicate 1

tag: phase

value: PLAT


title: 3HW4

value: Exposed


title: control 3, NIH

value: platelet


title: 252153310003_2_1-PLAT/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 1

tag: organism


title: 252153510001_2_4-PS/LOG[M(3)/M(5)]

description:
DS
Biological replicate M, technical replicate 2 (dye swap)

organism: Schizosaccharomyces japonicus

value: Schizosaccharomyces japonicus

value: DS


title: 252153310007_1_1-LAG/LOG[P(5)/P(3)]

description:
LAG
Biological replicate P, technical replicate 1

value: LAG

value: LOG


title: 252153510003_1_4-LAG/LOG[N(5)/N(3)]

description:
LAG
Biological replicate N, technical replicate 1


title: 252153510003_2_4-PS/LOG[O(5)/O(3)]

description:
DS
Biological replicate O, technical replicate 1


title: 3HW3

value: WET

value: HILLTOP

value: Total IgG


title: control 2, NIH

value: NIH

tag: tissue


title: IFN treatment Replicate 2

value: IFNalpha


title: Untreated Replicate 1

description: A549 cells were left untreated.

value: Untreated


title: IFN treatment with miR-203 mimic Replicate 1


title: IFN treatment Replicate 1


title: 252153510001_1_2-LL/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 1

value: LL


title: 3HW2


title: Sendai Virus Infected with miR-203 Inhibitor Replicate 1

description: A549 cells were transfected with 50nM miR-203 inhibitor using Lipofectamine 2000.  Fifteen hours after transfection, cells were infected with Sendai virus (Cantell strain, 5 pfu/cell) for 10 hours prior to RNA purification.

data_processing: quantile normalization

extract_protocol: Total RNA was purified using Qiagen's miRNEasy Kit

tag: infection

value: Sendai virus


title: Mock Infected Replicate 2

description: A549 cells were mock infected for 10 hours prior to RNA purification

value: Mock


title: control 1, NIH

value: control

value: Female

value: peripheral whole blood


title: 3VD10

value: Exposed

value: DRY

value: VALLEY


title: 3HW1


title: 252153510001_1_3-DS/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 2

value: Schizosaccharomyces japonicus


title: 3VD9


title: 3VD8


title: Sendai Virus Infected Replicate 1

description: A549 cells were infected with Sendai virus (Cantell strain, 5 pfu/cell) for 10 hours prior to RNA purification


title: 3VD7


title: 252153510002_1_1-DS/LOG[N(5)/N(3)]

description:
DS
Biological replicate N, technical replicate 1

value: DS

value: LOG


title: control 4, NIH

description:
Platelets purified from whole blood
miRNA profiling

value: Male

value: platelet


title: 252153510003_1_2-LPS/LOG[M(5)/M(3)]

description:
PS
Biological replicate M, technical replicate 1

value: PS


title: 252153510003_2_1-LPS/LOG[N(5)/N(3)]

description:
PS
Biological replicate N, technical replicate 3


title: 251507210453_1_1-LL/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 1

value: Saccharomyces cerevisiae


title: 252153510002_1_3-DS/LOG[N(3)/N(5)]

description:
DS
Biological replicate N, technical replicate 2 (dye swap)


title: 251507210458_1_1-LAG/LOG[J(5)/J(3)]

description:
LAG
Biological replicate J, technical replicate 1

value: LAG


title: 251507210517_1_3-DS/LOG[C(3)/C(5)]

description:
DS
Biological replicate C, technical replicate 2 (dye swap)


title: 251507210459_1_2-DS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 1


title: 252153510003_2_2-PLAT/LOG[N(5)/N(3)]

description:
PLAT
Biological replicate N, technical replicate 1

value: PLAT


title: 251507210522_1_3-PS/LOG[B(3)/B(5)]

description:
PS
Biological replicate B, technical replicate 1 (dye swap)


title: 3VD6

value: Total IgG


title: Sendai Virus Infected Replicate 3

value: Sendai virus


title: Sendai Virus Infected with miR-203 Mimic Replicate 2

description: A549 cells were transfected with 50nM miR-203 mimic using Lipofectamine 2000.  Fifteen hours after transfection, cells were infected with Sendai virus (Cantell strain, 5 pfu/cell) for 10 hours prior to RNA purification.


title: 252153510002_1_4-PS/LOG[N(3)/N(5)]

description:
PS
Biological replicate N, technical replicate 1 (dye swap)


title: Sendai Virus Infected with miR-203 Mimic Replicate 3


title: Sendai Virus Infected with miR-203 Inhibitor Replicate 2

description: A549 cells were transfected with 50nM miR-203 inhibitor using Lipofectamine 2000.  Fifteen hours after transfection, cells were infected with Sendai virus (Cantell strain, 5 pfu/cell) for 10 hours prior to RNA purification.


title: 251507210516_1_2-DS/LOG[B(5)/B(3)]

description:
DS
Biological replicate B, technical replicate 1


title: 3VD5


title: Mock Infected Replicate 1

description: A549 cells were mock infected for 10 hours prior to RNA purification

value: Mock


title: Sendai Virus Infected with miR-203 Inhibitor Replicate 3


title: 3VD4


title: 252153510001_2_1-DS/LOG[M(5)/M(3)]

description:
LL
Biological replicate M, technical replicate 3

value: LL


title: 3VD2


title: 3VD3


title: Sendai Virus Infected with miR-203 Mimic Replicate 1


title: 3VD1


title: 251507210454_1_4-PLAT/LOG[H(5)/H(3)]

description:
PLAT
Biological replicate H, technical replicate 1


title: 252153510002_2_2-LL/LOG[N(5)/N(3)]

description:
LL
Biological replicate N, technical replicate 2


title: 3VW10

value: WET


title: 252153510002_2_4-PS/LOG[N(5)/N(3)]

description:
PS
Biological replicate N, technical replicate 2


title: 252153510001_1_4-PS/LOG[M(5)/M(3)]

description:
DS
Biological replicate M, technical replicate 1


title: 252153510004_1_1-LAG/LOG[P(5)/P(3)]

description:
LAG
Biological replicate P, technical replicate 1


title: 3VW9

value: Exposed


title: 251507210455_1_1-PLAT/LOG[K(5)/K(3)]

description:
PLAT
Biological replicate K, technical replicate 1


title: 251507210455_1_4-LL/LOG[K(5)/K(3)]

description:
LL
Biological replicate K, technical replicate 1


title: 252153510003_1_3-PLAT/LOG[M(5)/M(3)]

description:
PLAT
Biological replicate M, technical replicate 1


title: 3VW8


title: 251507210454_1_2-DS/LOG[H(5)/H(3)]

description:
DS
Biological replicate H, technical replicate 1


title: 3VW6


title: 251507210523_1_2-PS/LOG[C(5)/C(3)]

description:
PS
Biological replicate C, technical replicate 2


title: 252153510002_2_3-DS/LOG[N(5)/N(3)]

description:
DS
Biological replicate N, technical replicate 3


title: 252153510001_2_2-LL/LOG[M(3)/M(5)]

description:
LL
Biological replicate M, technical replicate 4 (dye swap)


title: 252153510002_1_2-LL/LOG[N(3)/N(5)]

description:
LL
Biological replicate N, technical replicate 1 (dye swap)


title: 251507210453_1_3-PS/LOG[G(5)/G(3)]

description:
PS
Biological replicate G, technical replicate 1


title: 251507210455_1_2-DS/LOG[K(5)/K(3)]

description:
PS
Biological replicate K, technical replicate 1


title: 251507210454_1_3-PS/LOG[H(5)/H(3)]

description:
PS
Biological replicate H, technical replicate 1


title: 251507210458_1_4-PS/LOG[D(5)/D(3)]

description:
PS
Biological replicate D, technical replicate 1


title: 3VW4


title: 252153510003_1_1-LAG/LOG[M(5)/M(3)]

description:
LAG
Biological replicate M, technical replicate 1


title: 3VW5


title: 251507210517_1_2-DS/LOG[B(3)/B(5)]

description:
DS
Biological replicate B, technical replicate 2 (dye swap)


title: Mock Infected Replicate 3

description: A549 cells were mock infected for 10 hours prior to RNA purification


title: 251507210459_1_1-LL/LOG[J(5)/J(3)]

description:
LL
Biological replicate J, technical replicate 1


title: 252153510004_1_2-LAG/LOG[Q(5)/Q(3)]

description:
LAG
Biological replicate Q, technical replicate 1


title: 3VW3


title: Sendai Virus Infected Replicate 2

description: A549 cells were infected with Sendai virus (Cantell strain, 5 pfu/cell) for 10 hours prior to RNA purification


title: 3VW2


title: 3VW7


title: 252153510001_2_3-DS/LOG[M(3)/M(5)]

description:
LL
Biological replicate M, technical replicate 5 (dye swap)


title: 252061310004_1_4-PLAT/LOG[H(5)/H(3)]

description:
PLAT
Biological replicate H, technical replicate 1

organism: Schizosaccharomyces pombe

value: Schizosaccharomyces pombe


title: 252061310003_1_2-ELL/LOG[G(5)/G(3)]

description:
LL
Biological replicate G, technical replicate 1


title: 2HD6

value: DRY

value: HILLTOP


title: 3VW1

value: VALLEY


title: 2HD7


title: 2HD5


title: 252061310004_2_2-LL/LOG[I(5)/I(3)]

description:
DS
Biological replicate I, technical replicate 1

value: DS

value: LOG


title: 251507210522_1_2-PS/LOG[C(3)/C(5)]

description:
PS
Biological replicate C, technical replicate 1 (dye swap)


title: 252061310003_2_1-LAG/LOG[H(5)/H(3)]

description:
LAG
Biological replicate H, technical replicate 1


title: 2HD4


title: 252061310003_2_2-ELL/LOG[H(5)/H(3)]

description:
LL
Biological replicate H, technical replicate 1


title: 2HD2


title: 251507210455_1_3-PS/LOG[K(5)/K(3)]

description:
PS
Biological replicate K, technical replicate 2


title: 251507210453_1_4-PLAT/LOG[G(5)/G(3)]

description:
PLAT
Biological replicate G, technical replicate 1


title: 252061310003_1_1-LAG/LOG[G(5)/G(3)]

description:
LAG
Biological replicate G, technical replicate 1


title: 2HD1


title: 252061310004_2_1-ELL/LOG[I(5)/I(3)]

description:
LL
Biological replicate I, technical replicate 1


title: 252061310003_2_3-PLAT/LOG[I(5)/I(3)]

description:
PLAT
Biological replicate I, technical replicate 1


title: 252061310005_2_2-LAG/LOG[I(5)/G(3)]

description:
LAG
Biological replicate I/G, technical replicate 1


title: 251507210459_1_4-PLAT/LOG[J(5)/J(3)]

description:
PLAT
Biological replicate J, technical replicate 1


title: 2HW10


title: 251507210517_1_1-DS/LOG[A(3)/A(5)]

description:
PS
Biological replicate A, technical replicate 2 (dye swap)


title: 252061310005_2_4-DS/LOG[I(5)/I(3)]

description:
DS
Biological replicate I, technical replicate 3


title: 251507210523_1_3-PS/LOG[B(5)/B(3)]

description:
PS
Biological replicate B, technical replicate 2


title: 252061310005_1_3-PS/LOG[H(5)/H(3)]

description:
PS
Biological replicate H, technical replicate 2


title: 2HW9


title: 2HD3


title: 251507210459_1_3-PS/LOG[J(5)/J(3)]

description:
PS
Biological replicate J, technical replicate 2


title: 2HW8


title: 252061310005_1_4-PS/LOG[I(5)/I(3)]

description:
PS
Biological replicate I, technical replicate 1


title: 252061310004_1_1-LL/LOG[H(5)/H(3)]

description:
DS
Biological replicate H, technical replicate 1


title: 251507210454_1_1-LL/LOG[H(5)/H(3)]


title: 251507210453_1_2-DS/LOG[G(5)/G(3)]

description:
DS
Biological replicate G, technical replicate 1


title: 2HW6


title: 251507210516_1_1-DS/LOG[A(5)/A(3)]

description:
PS
Biological replicate A, technical replicate 1


title: 251507210519_1_2-PLAT/LOG[B(3)/B(5)]

description:
PLAT
Biological replicate B, technical replicate 1 (dye swap)


title: 2HW7


title: 251507210458_1_3-LL/LOG[D(5)/D(3)]

description:
LL
Biological replicate D, technical replicate 1


title: 2HW3


title: 252061310004_2_3-DS/LOG[I(5)/I(3)]

description:
DS
Biological replicate I, technical replicate 2


title: 2HW2


title: 252061310003_1_4-DS/LOG[G(5)/G(3)]

description:
DS
Biological replicate G, technical replicate 2


title: 252061310004_1_2-DS/LOG[H(5)/H(3)]

description:
PS
Biological replicate H, technical replicate 1


title: 2HW1


title: 251507210519_1_3-PLAT/LOG[C(3)/C(5)]

description:
PLAT
Biological replicate C, technical replicate 1 (dye swap)


title: 251507210523_1_4-PS/LOG[A(5)/A(3)]

description:
PS
Biological replicate A, technical replicate 4


title: 251507210522_1_4-PS/LOG[A(3)/A(5)]

description:
PS
Biological replicate A, technical replicate 3 (dye swap)


title: 2VD10


title: 252050510004_1_1-LAG/LOG[P(5)/P(3)]

description:
LAG
Biological replicate P, technical replicate 1

organism: Saccharomyces paradoxus

value: Saccharomyces paradoxus


title: 251507210458_1_2-LAG/LOG[K(5)/K(3)]

description:
LAG
Biological replicate K, technical replicate 1


title: 252050510010_1_2-PLAT/LOG[Q(5)/Q(3)]

description:
PLAT
Biological replicate Q, technical replicate 2


title: 251507210516_1_3-DS/LOG[C(3)/C(5)]

description:
DS
Biological replicate C, technical replicate 1 (dye swap)


title: 252061310005_1_1-PS/LOG[G(5)/G(3)]

description:
PS
Biological replicate G, technical replicate 1

value: PS


title: 252061310005_2_1-DS/LOG[G(5)/I(3)]

description:
DS
Biological replicate G/I, technical replicate 3


title: 2VD9

organism: Homo sapiens


title: 252050510008_1_2-PLAT/LOG[Q(5)/Q(3)]

description:
PLAT
Biological replicate Q, technical replicate 1


title: 2VD8


title: 252061310005_2_3-DS/LOG[H(5)/H(3)]

description:
PS
Biological replicate H, technical replicate 3


title: 2VD7


title: 252050510008_2_4-PLAT/LOG[R(5)/R(3)]

description:
PLAT
Biological replicate R, technical replicate 1


title: 252061310003_1_3-LL/LOG[G(5)/G(3)]

description:
DS
Biological replicate G, technical replicate 1


title: 252050510004_1_2-DS/LOG[P(5)/P(3)]

description:
LL
Biological replicate P, technical replicate 1


title: 2VD5