title: transgenic seedlings, normal conditions

city: shanghai

first: Mengfei

last: Yang

address: Handan Road 220

country: China

institute: Fudan university

description: Gene expression data from leaf tissues of 2-week-old seedlings (10 plants each).

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: 2-week-old transgenic seedlings without NaCl treatment

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

growth_protocol: Antisense-OsPDCD5 transgenic Zhonghua 11 and nontransgenic control Zhonghua 11 plants were grown in half-strength Murashige and Skoog medium under white ﬂuorescent light (a 14/10h light/dark cycle) at 28℃.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: 2-week-old seedlings were transferred into petri dishes ﬁlled with half-strength Murashige and Skoog (MS) medium containing 200 mM NaCl for 20mins and 3 hours.

tag: age


title: transgenic seedlings, 3 hours NaCl treatment

status: Public on Nov 01 2011

type: RNA

label: biotin

molecule: total RNA

source_name: 2-week-old transgenic seedlings 3 hours after 200mM NaCl treatment


title: Day 18 non-pregnant control, biological replicate 1

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

description: endometrial tissue sample collected at day 18 of estrous cycle after sham insemination

hyb_protocol: For the hybridization, wash and staining process the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) was used. GeneChips were processed using the Fluidics Station 450 (Affymetrix). All steps were done according to the manufacturer’s protocol.

scan_protocol: The processed arrays were scanned with a GeneChip® Scanner 3000 with AutoLoader (Affymetrix).

data_processing: Affymetrix CEL files were processed with the robust multi-array average (RMA) method (Irizarry et al. Biostatistics 2003). Quality control was done using a variety of tools, such as pseudo images (BioC package AffyPLM), RNA degradation plots (BioC package Affy), different box plots, distance matrices and heatmaps. Probe sets were filtered based on expression calls before significance analysis.

organism: Bos taurus

source_name: intercaruncular endometrium, day 18 of cycle

label_protocol: Preparation of hybridization probes (biotinylated cRNA) for Affymetrix GeneChip® Bovine Genome Arrays (Affymetrix, Santa Clara, USA) was performed using 10 µg total RNA and the One-Cycle Target Labeling and Control Reagent package (Affymetrix).

growth_protocol: Bavarian Simmental heifers, synchronized by an intramuscular injection of a single dose of 500 µg Cloprostenol (PGF2α, Estrumate®, Intervet, Munich, Germany) at diestrus

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen) according to the manufactorer's recommendations. The quantity and quality of total RNA were determined by spectrometry, agarose gel electrophoresis and Agilent 2100 Bioanalyzer, respectively.

treatment_protocol: Experiment I: In the IFNA treatment group, a rod-shaped human IFNA-releasing lipid extrudate was loaded in PBS into a 0.50-ml artificial insemination straw and non-surgically (via the cervix) transferred into the uterine horn ipsilateral to the functional CL on day 14 using an insemination pipette. The placebo group received only the rod-shaped lipid extrudate, whereas the control group received PBS only. Based on in vitro release experiments, IFNA concentration and lipid formulation was adjusted to release 8-9x107 IU of IFNA over a period of two days. On day 16 of the estrous cycle, uteri were non-surgically flushed with 10 ml of PBS using an embryo-flushing catheter (Minitüb, type Dissi, CH12, Tiefenbach, Germany). After flushing, six (±1) endometrial biopsy samples were collected per animal from the ipsilateral horn by the use of an uterine biopsy forceps (Richard Wolf, type 8151.07, 450 mm in length, 2.2 mm in diameter, Knittlingen, Germany), which was non-surgically inserted into the uterine horn through a self-shortened transcervical plastic cannula (Henry Schein, type bovivet, Hamburg, Germany) under rectal palpation control. Experiment II: Animals of the insemination group were inseminated on day 1 with cryo-conserved sperm (ejaculate + diluter 1:10) of the same bull and slaughtered at days 12, 15, or 18. Cyclic control animals received sperm-free supernatant of centrifuged sperm and were also slaughtered at days 12, 15, or 18. The sperm supernatant was refrigerated at -20°C and warmed up to room temperature before use. In animals slaughtered at day 12, the uteri were flushed with PBS before opening to determine the presence of a blastocyst. Immediately afterwards each uterine horn was prepared and opened longitudinally. The embryo was identified in the collection medium under a stereomicroscope and carefully transferred into RNAlater™. In animals slaughtered on days 15 and 18 after insemination, conceptuses were carefully removed after opening the uteri and stored in RNAlater™. Endometrial tissue samples were collected from the uterine horns ipsilateral to the functional CL; from the cranial uterine part for day 12 animals, from the middle part for day 15 animals, and from the caudal part for day 18 animals. Samples were carefully cut out from the lamina propria of the intercaruncular endometrium with a scalpel and immediately transferred into vials containing 4 ml RNAlater™.

tag: gender

value: female

tag: breed

value: Bavarian Simmental

tag: localization

value: ipsilateral, caudal

tag: treatment group

value: sham insemination

tag: pregnant

value: no


title: Day 15 pregnant, biological replicate 1

description: endometrial tissue sample collected at day 15 of pregnancy after artificial insemination

source_name: intercaruncular endometrium, day 15 of pregnancy

value: ipsilateral, medial

value: artificial insemination

value: yes


title: nontransgenic seedlings, 3 hours NaCl treatment

source_name: 2-week-old nontransgenic seedlings 3 hours after 200mM NaCl treatment


title: PeCDF 2 nM rat A -

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

country: USA

institute: The Dow Chemical Company

hyb_protocol: Using Agilent's hybridization protocol, in the hybridization reaction 0.75 ug of Alexa555 labeled cRNA and 0.75 ug of Alexa647 labeled cRNA were mixed together and allowed to co-hybridize on an Agilent Rat Whole Genome Oligo Microarray for 17 hours at 60°C. Slide was washed and dried according to Agilent's 60-mer Oligo microarray processing protocol for SSPE wash.

scan_protocol: Scanned with an Agilent G2565AA scanner, 10um resolution.  PMT settings were set at 100%.

data_processing: Images were quantified with Agilent Feature Extraction software, version 9.1 using local background subtraction and Linear & LOWESS normalization.

organism: Rattus norvegicus

source_name: 2 nM PeCDF treated primary rat hepatocytes

label_protocol: For each sample, Alexa555- and Alexa647-labeled aRNAs were generated from 500 ng of total RNA using the Epicentre One-Round amplification and Aminoallyl Labeling Kit.

growth_protocol: Hepatocytes were isolated from two adult female Sprague-Dawley rats (250-350 g; Harlan, Indianapolis, IN), as previously described (Runge-Morris et al., 1996). Following isolation, 3 million viable hepatocytes, as determined by trypan blue exclusion assessment, were plated onto 60-mm Matrigel-coated dishes. Cultures were maintained in MCM supplemented with ITS+ (6.25 ug/mL insulin, 6.25 ug/mL transferrin, and 6.25 ng/mL selenium) and 0.1 uM DEX for 48 h prior to treatment.

extract_protocol: Total RNA was purifed with the RNeasy Mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s protocol, after isolation with TRIzol Reagent® (Invitrogen). The protocol included DNase treatment. RNA quality was assessed using an Agilent Bioanalyzer. Extracted RNA from three dishes derived from one animal were pooled to create a hybridization sample.

treatment_protocol: Hepatocytes were untreated, treated with vehicle (0.1% DMSO) or treated with the test compounds (dissolved in DMSO and added to media for a concentration of 0.1% DMSO) for 24 h (n = 3 dishes per treatment and dose group per rat). Hepatocytes were treated with 2,3,7,8-TCDD (0.01nM, 1.0 nM), 2,3,7,8-TCDF (0.1nM, 10.0 nM), or 2,3,4,7,8-PeCDF (0.02 nM , 2.0 nM).

tag: cell type

value: hepatocyte

tag: strain

value: Sprague Dawley

tag: treatment

value: 2 nM PeCDF treated primary

tag: animal

value: A

source_name: DMSO control

value: DMSO control


title: Day 15 pregnant, biological replicate 2


title: nontransgenic seedlings, normal conditions

source_name: 2-week-old nontransgenic seedlings without NaCl treatment


title: Day 15 non-pregnant control, biological replicate 3

description: endometrial tissue sample collected at day 15 of estrous cycle after sham insemination

source_name: intercaruncular endometrium, day 15 of cycle


title: Day 15 pregnant, biological replicate 3


title: PeCDF 2 nM rat B +

value: B


title: transgenic seedlings, 20mins NaCl treatment

source_name: 2-week-old transgenic seedlings 20mins after 200mM NaCl treatment


title: PeCDF 2 nM rat B -


title: Day 15 non-pregnant control, biological replicate 1


title: nontransgenic seedlings, 20mins NaCl treatment

source_name: 2-week-old nontransgenic seedlings 20mins after 200mM NaCl treatment


title: E19.5_rep3 2 of 2

type: genomic

city: Boston

first: Maria

middle: Isabel

last: Ramirez

state: MA

address: 72 E. Concord St. E603

department: Medicine

institute: Boston University School of Medicine

scan_protocol: see protocol http://www.genomics.agilent.com/files/Manual/G4481-90010_MammalianProtocol_10.11.pdf. Arrays were scanned using an Agilent scanner model G2565BA.

data_processing: The image analysis was performed using Agilent’s Feature Extraction software v.9.5.3.1 set to the default ChIP protocol. To combine the replicates for each time point, the raw data was background subtracted and median normalized using limma library, part of the Bioconductor project, in the R statistical environment {Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80 and Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64}. The difference of binding between the IP and Input (Cy5/Cy3), for each probe/feature, was analyzed using empirical Bayes method implemented in the limma package. P-values obtained from the multiple comparison tests were corrected by false discovery rates. In addition, for the binding profiles, we calculated average binding ratio (Cy5/Cy3) for each probe by averaging the ratio between the candidate bound probe and the 2 closest neighboring probes.

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic lung day19.5

label_protocol: For chip-on-chip experiments we followed previously described methods {Lee, 2006 #26}. Briefly, immunoprecipitated DNA (IP) and whole cell extract DNA (input) were purified by treatment with RNAse A, proteinase K and multiple phenol: chloroform: isoamyl alcohol extractions. Purified DNA was blunt-ended and ligated to linkers, and amplified using a two-stage PCR protocol. Amplified DNA was labeled and purified by using Bioprime random primer labeling kits (Invitrogen). Immunoprecipitated DNA (IP) was labeled with Cy5 fluorophore, and whole cell extract DNA (input) was labeled with Cy3 fluorophore. Cy5 and Cy3 labeled DNAs were mixed (~5 μg of each) and hybridized to arrays in Agilent hybridization chambers for 40 hours at 40°C, washed and immediately scanned.

extract_protocol: Five to ten embryonic lungs were used for each immunoprecipitation. E11.5 and E19.5 lungs were dissected, minced and immediately immersed in 2 volumes of 1xPBS. Lungs were chemically cross linked by the addition of one-tenth volume of fresh 11% formaldehyde solution, and incubated for 10 minutes at room temperature. Formaldehyde was then quenched with 2.5M glycine and tissues rinsed twice with 1xPBS. Crosslinked lung samples were flashed frozen in liquid nitrogen and stored at –80ºC. Lungs were lysed and sonicated to solubilize and shear crosslinked DNA. We sonicated samples on ice in a Branson Ultrasonic Sonicator coupled to a Fisher Scientific Sonic dismembrator 500 power supply at 90% amplitude for 12 cycles of 30 second pulses with 60 second pause between pulses, yielding fragments of about 500 bp. Part of the whole cell extract was saved as input material and the rest was incubated overnight at 4°C with 100 μl of Dynal Protein G magnetic beads (Invitrogen) that had been pre-incubated with 10 μg of the a-Nkx2.1 antibody  (07-601, Upstate-Millipore) or IgG (Santa Cruz Biotechnologies, Inc). Conditions were optimized for binding to chromatin from embryonic mouse lung.  Beads were washed 4-5 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by addition of elution buffer and by heating at 65°C for 15 min with 2 minutes interval of vortexing. Crosslinking in the IP and input samples was reversed by overnight incubation at 65°C.

tag: developmental stage

tag: tissue

value: embryonic lung

tag: antibody

tag: antibody manufacturer

value: Upstate-Millipore

tag: antibody catalog #

tag: developmental time point

tag: sample type

value: input DNA


title: PeCDF 0.02 nM rat B -

source_name: 0.02 nM PeCDF treated primary rat hepatocytes

value: 0.02 nM PeCDF treated primary


title: PeCDF 2 nM rat A +


title: Day 12 pregnant, biological replicate 5

description: endometrial tissue sample collected at day 12 of pregnancy after artificial insemination

source_name: intercaruncular endometrium, day 12 of pregnancy

value: female

value: Bavarian Simmental

value: ipsilateral, distal


title: Day 15 non-pregnant control, biological replicate 2

value: sham insemination

value: no


title: Day 12 pregnant, biological replicate 4

value: artificial insemination


title: Day 12 pregnant, biological replicate 3

value: yes


title: E19.5_rep2 2 of 2


title: E11.5_rep1 2 of 2

source_name: Embryonic lung day11.5


title: Day 12 pregnant, biological replicate 1


title: E11.5_rep2 2 of 2


title: PeCDF 0.02 nM rat B +

value: hepatocyte


title: PeCDF 0.02 nM rat A -

value: Sprague Dawley


title: Day 12 non-pregnant control, biological replicate 5

description: endometrial tissue sample collected at day 12 of estrous cycle after sham insemination

source_name: intercaruncular endometrium, day 12 of cycle


title: E19.5_rep1 2 of 2


title: TCDF 0.1 nM rat B -

source_name: 0.1 nM TCDF treated primary rat hepatocytes

value: 0.1 nM TCDF treated primary


title: TCDF 0.1 nM rat B +


title: TCDF 10 nM rat A +

value: A

source_name: 10 nM TCDF treated primary rat hepatocytes

value: 10 nM TCDF treated primary


title: TCDF 10 nM rat B -

value: B

value: DMSO control


title: TCDF 0.1 nM rat A -


title: TCDF 0.1 nM rat A +


title: TCDF 10 nM rat A -


title: Day 12 non-pregnant control, biological replicate 4


title: TCDD 1 nM rat B -

source_name: 1 nM TCDD treated primary rat hepatocytes

value: 1 nM TCDD treated primary


title: Day 12 pregnant, biological replicate 2


title: TCDD 0.01 nM rat B -

source_name: 0.01 nM TCDD treated primary rat hepatocytes

value: 0.01 nM TCDD treated primary


title: PeCDF 0.02 nM rat A +

value: 0.02 nM PeCDF treated primary


title: TCDF 10 nM rat B +


title: TCDD 1 nM rat B +


title: TCDD 1 nM rat A -


title: Day 12 non-pregnant control, biological replicate 3

value: female


title: TCDD 0.01 nM rat A -


title: Day 12 non-pregnant control, biological replicate 2

value: Bavarian Simmental


title: TCDD 1 nM rat A +


title: TCDD 0.01 nM rat B +


title: PBS control, biological replicate 3

description: 6 endometrial biopsy samples collected on day 16 of the estrous cycle after intrauterine application of PBS on day 14

source_name: endometrial biopsies, day 16 of estrous cycle

value: ipsilateral, caudal

value: PBS control


title: Day 12 non-pregnant control, biological replicate 1

value: ipsilateral, distal

value: sham insemination

value: no


title: Placebo control, biological replicate 2

description: 6 endometrial biopsy samples collected after intrauterine application of placebo lipid extrudates fromat day 14-16 of the estrous cycle

value: placebo


title: Placebo control, biological replicate 3


title: Placebo control, biological replicate 1


title: untreated rat A -

source_name: untreated primary rat hepatocytes

value: hepatocyte

value: Sprague Dawley

value: untreated


title: PBS control, biological replicate 1


title: TCDD 0.01 nM rat A +

value: A


title: treatment with human IFNA, biological replicate 1

description: 6 endometrial biopsy samples collected after intrauterine application of IFNA-containing lipid extrudates fromat day 14-16 of the estrous cycle

value: IFNA


title: untreated rat A +

value: DMSO control


title: nontransgenic

city: Shanghai

first: weiwei

last: qi

address: 220#Handan road

description: Gene expression data from leaf tissues of one-month-stage seedlings (3 plants each).

hyb_protocol: Array hybridization and wash was performed by following the Agilent manufacturer’s instructions.

scan_protocol: Agilent Technologies Scanner G2505C.

data_processing:
Data points were extracted using Agilent Feature Extraction software (Version 10.7.1.1).
The genes with 2-fold differences in expression supported by a p-value of 0.05 or less are considered significant.

organism: Brassica napus

source_name: one-month-stage nontransgenic seedlings

label_protocol: Total RNA were amplified, labeled and purified by following the Agilent manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Control and the transgenic plants (20 plants each genotype) were grown at a density of 50 X 50 cm per plantunder in soid under white ﬂuorescent light (a 14/10h light/dark cycle) at 28℃.

value: leaf

tag: genetic background

value: Nannongyou of B. napus

tag: genotype

value: wild type

tag: age

value: one-month


title: untreated rat B +

source_name: DMSO control

value: B


title: untreated rat B -


title: PBS control, biological replicate 2

tag: gender

value: female

tag: breed

value: Bavarian Simmental

tag: localization

value: ipsilateral, caudal


title: Advanced IPF_explant_upper lobe_rep160

city: Durham

first: Eric

middle: B.

last: Meltzer

state: NC

department: Department of Medicine, Division of Pulmonary, Allergy and Critical Care

institute: Duke University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Array Scanner (7G).

data_processing: All pre-processing and data analyses were performed using R version 2.9 and the Bioconductor packages designed for use with Affymetrix microarray data.

organism: Homo sapiens

source_name: Whole lung tissue_advanced IPF_explant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA ( Affymetrix Technical Manual).

extract_protocol: Extraction of total RNA was performed with RNAqueous-4PCR kits (Ambion, Inc., Austin, TX) according to the manufacturer's instructions.

value: lung, upper lobe

tag: lung source

value: explant

tag: phenotype

value: advanced idiopathic pulmonary fibrosis (IPF)


title: treatment with human IFNA, biological replicate 3

tag: treatment group


title: treatment with human IFNA, biological replicate 2


title: transgenic A1-3

description: Gene expression data from leaf tissues of one-month-stage seedlings (4 plants each).

source_name: one-month-stage transgenic seedlings

value: csRRM2 transgenic


title: transgenic A19-1

description: Gene expression data from leaf tissues of one-month-stage seedlings (6 plants each).


title: Advanced IPF_explant_lower lobe_rep160

value: lung, lower lobe


title: Early IPF_surgical biopsy_upper lobe_rep159

source_name: Whole lung tissue_early IPF_biopsy

value: surgical biopsy

value: early idiopathic pulmonary fibrosis (IPF)

value: male


title: transgenic A1-5

description: Gene expression data from leaf tissues of one-month-stage seedlings (5 plants each).


title: Advanced IPF_explant_lower lobe_rep157


title: Advanced IPF_explant_lower lobe_rep158


title: Early IPF_surgical biopsy_lower lobe_rep159


title: Advanced IPF_explant_upper lobe_rep158


title: Advanced IPF_explant_upper lobe_rep152


title: Early IPF_surgical biopsy_upper lobe_rep149


title: Advanced IPF_explant_upper lobe_rep157


title: Early IPF_surgical biopsy_upper lobe_rep145


title: Early IPF_surgical biopsy_upper lobe_rep144


title: Advanced IPF_explant_lower lobe_rep146


title: Advanced IPF_explant_lower lobe_rep152


title: Early IPF_surgical biopsy_lower lobe_rep149


title: Healthy donor_biological replicate6

source_name: Whole lung tissue_healthy donor lung

value: lung

value: routine lung volume reduction

value: healthy

value: unknown


title: Early IPF_surgical biopsy_upper lobe_rep142


title: Early IPF_surgical biopsy_upper lobe_rep140


title: SKmel28(2)

city: ALLSTON

first: Nicolaos

middle: Jay

last: Palaskas

address: 15 North Beacon St #502

institute: UCLA

description: high

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: GCOS 1.3 was used to convert intensities using Expression Analysis settings :  Parameters -default  Baseline - default  Probemask - default  Normalization - all probe sets  Scaling - all probe sets

source_name: ATCC

growth_protocol: All cell line cultures were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) during FDG-uptake assays.

extract_protocol: QIAGEN Rneasy

treatment_protocol: In-vitro FDG uptake assays. 2 x 105 cells were seeded in triplicate on 6-well plates and incubated overnight in culture medium.  The next morning, the culture medium was removed from the 6-well plates and cells were incubated for 2 hours in fresh culture medium containing (18)F-FDG at a concentration of 0.5 μCi/ml.  The medium was aspirated, cells washed 3 times in PBS, trypsinized, and resuspended in culture medium.  Two thirds of the suspension was used for (18) F-FDG uptake determination by a gamma-counter (Wallac Wizard model 1480-11 with a 3” crystal). One third was reserved for viable cell number counts using the VI-Cell XR automated cell-viability analyzer (Beckmann Coulter).  Disintegrations per minute per cell were calculated for each well and the average of three wells was reported as the FDG uptake for each cell line.

tag: cell line

tag: fdg uptake

value: high


title: UACC812

description: prediction set

value: prediction set


title: ZR751

description: prediction set


title: U87(1)

description: high


title: Healthy donor_biological replicate4

tag: tissue


title: ZR7530

description: prediction set


title: Healthy donor_biological replicate5


title: U87(2)

description: high


title: Healthy donor_biological replicate2


title: Healthy donor_biological replicate3


title: Healthy donor_biological replicate1


title: Control neural progenitor cells, biol repl 3

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description:
Control
MB3_ctrl_Sox1+NPC.CEL

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data was processed with RMA using Affymetrix Power Tools and a custom CDF (Brainarray version 11.0.1, RefSeq).

source_name: Neural progenitor cells

label_protocol: Standard Affymetrix protocol.

growth_protocol: Sox1-GFP or Sox1-GFP/Nestin-Sox3 positive mouse ES-cells  were differentiated for 4 days with B27 and N2 supplement (GIBCO) as monolayers on gelatinized cellbinding surface (Corning) with 0.5uM retinoic acid (all-trans, Sigma) at day 0 and day 2.

extract_protocol: Qiagen mRNA preparation kit

treatment_protocol: Cells were trypsinized and FACS sorted at day 4.

tag: cell type

value: ES cell derived neural progenitor cells


title: SKmel28(1)

description: high


title: Control neural progenitor cells, biol repl 2

description:
Control
MB2_ctrl_Sox1+NPC.CEL


title: Control neural progenitor cells, biol repl 1

description:
Control
MB1_ctrl_Sox1+NPC.CEL


title: LAPC4(1)

description: low

source_name: SAWYERS LAB

value: low


title: LNCAP(1)

description: high

value: LNCAP


title: LAPC4(2)

description: low


title: MCF7

description: prediction set


title: Sox3 over-expression in neural progenitor cells, biol repl 3

description:
Sox3 over-expression
MB6_+Sox3_Sox1+NPC.CEL

value: Sox1-GFP and Nestin-Sox3


title: LNCAP(2)

description: high


title: SF268(1)

description: low


title: SF268(2)

description: low


title: HCC70

description: prediction set


title: CHL(2)

description: low

value: CHL


title: CHL(1)

description: low


title: HCC1500

description: prediction set


title: AA_FDG_low2

description: low

source_name: ANAPLASTIC ASTROCYTOMA

value: primary tumor


title: AA_FDG_low1

description: low


title: Sox3 over-expression in neural progenitor cells, biol repl 2

description:
Sox3 over-expression
MB5_+Sox3_Sox1+NPC.CEL


title: Sox3 over-expression in neural progenitor cells, biol repl 1

description:
Sox3 over-expression
MB4_+Sox3_Sox1+NPC.CEL


title: Mm mono-culture + hydrogen-limited FC45 FC46 FC50 gSet2

city: Berkeley

first: Adam

middle: P.

last: Arkin

state: CA

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: Syntrophically grown Desulfovibrio vulgaris and Methanococcus maripaludis compared against hydrogen-limited Methanococcus maripaludis

hyb_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J. 2005.  Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

scan_protocol: ImaGene software

data_processing: See Methods in: S. R. Chhabra, Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A.  . Arkin, and A. K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, J Bacteriol. 2006 March; 188(5): 1817-1828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16484192

organism: Methanococcus maripaludis S2

tag: strain

tag: culture

value: Methanococcus maripaludis mono-culture

tag: treatment

value: hydrogen limited


title: DvH + Mm co-culture hydrogen-limited FC36 FC38 FC44 gSet1

label_protocol: He, Z., Wu, L., Li, X., Fields, M., and Zhou, J.  2005. Empirical Establishment of Oligonucleotide Probe Design Criteria. Appl. Environ. Microbiol. 71:3753-3760.

value: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough and Methanococcus maripaludis co-culture


title: 14-day Gut WNV Infected, rep4

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

hyb_protocol: The Agilent Technologies in situ hybridization kit was used for hybridizations according to the manufacturer's instructions. After washes, the microarrays were instantaneously dried with pressurized air.

scan_protocol: Microarrays were scanned with an Axon GenePix 4200AL scanner using a 10 µm pixel size. Laser power was set to 60%, and the PMT was adjusted to maximize effective dynamic range and minimize pixel saturation (Axon Instruments, Union City, CA). Spot parameters were determined with the GenePix software Pro 6.0 algorithms, and potential misidentifications of spot locations and quality were corrected manually.

data_processing: TIGR

organism: Culex quinquefasciatus

source_name: 14-day gut WNV infected

label_protocol: The Agilent Technologies Low Input Linear Amplification RNA labeling kit was used to synthesize fluorochrome-labeled cRNA probes from 3 g of RNA according to the manufacturer's instructions. Probes were quantified with the Nanodrop spectrophotomer (ND1000, Thermo Scientific, Wilmington, DE). Technologies Low Input Linear Amplification RNA labeling kit was used to synthesize fluorochrome-labeled cRNA probes from 3 g of RNA according to the manufacturer's instructions. Probes were quantified with the Nanodrop spectrophotomer (ND1000, Thermo Scientific, Wilmington, DE).

extract_protocol: Carcasses and midguts from WNV-infected and uninfected (blood fed only) C. quinquefasciatus (Sebring colony) were collected at 7 and 14 days post-infection (per os, fed on viremic hamster). RNA was isolated using a QIAGEN kit.

value: Sebring

value: 14-day gut

value: West Nile virus (WNV) infection

source_name: 14-day gut

value: uninfected


title: AA_FDG_high1

description: high


title: AA_FDG_high2

description: high


title: 14-day Gut WNV Infected, rep3


title: 14-day Carcass WNV Infected, rep1

source_name: 14-day carcass WNV infected

value: 14-day carcass

source_name: 14-day carcass


title: 14-day Gut WNV Infected, rep2


title: 14-day Gut WNV Infected, rep1


title: 7-day Gut WNV Infected, rep4

source_name: 7-day gut WNV infected

value: 7-day gut

source_name: 7-day gut


title: 14-day Carcass WNV Infected, rep4


title: 14-day Carcass WNV Infected, rep3


title: 7-Day Carcass WNV Infected, rep1

source_name: 7-day carcass WNV infected

value: 7-day carcass

source_name: 7-day carcass


title: 14-day Carcass WNV Infected, rep2


title: 7-day Carcass WNV Infected, rep4


title: 7-day Gut WNV Infected, rep2


title: Bean-Flower rep2

city: Notre Dame d’OE - BP 49716-3709 Tours

first: Isabelle

last: Privat

address: 101 Av. Gustave Eiffel

department: Centre de Recherche Nestlé

country: France

institute: NESTLE

hyb_protocol: The two labelled aRNA were mixed, fragmented and hybridized to  the coffe microarray.

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation. ArrayVision software was used for feature extraction. Spots with high local background or contamination fluorescence were flagged manually. A local background was calculated for each spot as the median values of the fluorescence intensities of 4 squares surrounding the spot. This background was subtracting from the foreground fluorescence intensity.

data_processing: Images were quantified using ArrayVision software (version 8.0).

organism: Coffea arabica

source_name: Bean

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according the manufacturer’s instructions.

growth_protocol: Samples were collected from C. arabica L. cv. Caturra T2308 grown in greenhouse conditions in Tours, France

extract_protocol: total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Valencia, Cal. USA), then treated with DNase following the manufacturer’s instructions.  Total RNAs were finally eluted from the columns with RNase-free water (2x30µL).  For each tissue, three independent RNA extractions were performed.  All RNA samples were analyzed by formaldehyde agarose gel electrophoresis to assess their integrity.  To test for contamination by polyphenols, carbohydrates and proteins, a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE, USA) was used.  Only RNA samples with OD 260/280 > 1.8 and OD 260/230 > 2 were used for further analysis.

tag: cultivar

value: Caturra T2308

value: Bean

source_name: Flower

value: Flower


title: Leave-Bean rep6

source_name: Leave

value: Leave


title: Leave-Flower rep5


title: 7-day Gut WNV Infected, rep1


title: Bean-Flower rep5


title: Leave-Flower rep6


title: Leave-Flower rep4


title: 7-day Gut WNV Infected, rep3


title: 7-day Carcass WNV Infected, rep3


title: Bean-Flower rep3


title: Bean-Flower rep4


title: Leave-Bean rep5


title: Leave-Flower rep2


title: Leave-Flower rep3


title: Leave-Flower rep1


title: 7-Day Carcass WNV Infected, rep2


title: Bean-Flower rep1


title: Large_cell_carcinoma_sample_33A

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

institute: Uppsala University

description:
PA026_33A_081021_(Mapping250K_Nsp)
Hybridized to 250K_Nsp

hyb_protocol: Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ). The arrays were then washed using Affymetrix fluidics stations.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G.

data_processing: Copy number normalization, to produce log(2) ratios, was performed using the Copy Number Analysis Tool (CNAT) 4.0.1. The reference set was 82 normal samples of Caucasian origin, analyzed at the Uppsala Array Platform. Subsequent copy number analyses and group comparisons were performed using the software BioDiscovery Nexus Copy Number 3.0 and the built-in Rank Segmentation algorithm, for estimating copy numbers and segmenting each interval.

label: Biotin

source_name: Non-small cell lung cancer tissue, short-term survival, large cell carcinoma

extract_protocol: DNA was extracted from 2-10 frozen tissue sections (10mm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) and the RNeasy Mini Kit (Qiagen), respectively.

value: non-small cell lung cancer

tag: histology

value: large cell carcinoma

tag: survival

value: short

tag: registry year


title: Leave-Bean rep3


title: Leave-Bean rep2


title: mESC_undifferentiated_Alkb1-/-_rep2

city: Oslo

first: Rune

last: Ougland

address: Sognsvannsveien 20

department: Dept. of Microbiology

country: Norway

institute: Oslo University Hospital, Rikshospitalet

description:
C10-2
Whole genome gene expression data from Alkbh1-/- C57BL/6 mouse embryonic stem cells.

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45oC on a GeneChip Mouse Genome Array 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The raw data have been normalized together using the RMA algorithm (developed and described by R. A. Irizarry (2003)) in the statistical package R (http://www.r-project.org/).

source_name: Mouse embryonic stem cells, day 0, Alkb1-/-

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (3_ivt_express_kit_manual, 2009, Affymetrix).

growth_protocol: Embryonic stem cells were cultured at 37oC under standard conditions maintaining the undifferentiated state, i.e., KO-DME supplemented with LIF. 5% CO2/21% O2.

extract_protocol: Total RNA was purified using the Qiagen miRNeasy kit (cat. No. 217004) according to the manufacturer's instructions.

treatment_protocol: No treatment was applied prior to RNA extraction.

tag: genetic background/strain

tag: genotype

value: embryonic stem cells

tag: developmental stage

value: day 0, undifferentiated

tag: passage


title: mESC_undifferentiated_Alkb1-/-_rep1

description:
C10-1
Whole genome gene expression data from Alkbh1-/- C57BL/6 mouse embryonic stem cells.


title: Bean-Flower rep6


title: Liver_Control_rep3

city: Al ain

first: Starling Emerald

last: Bright David

address: Tawam Medical Campus

department: Anatomy

country: United Arab Emirates

institute: United Arab Emirates University

description: Liver_average birth weight_rep3

hyb_protocol: Microarray was hybridized for 17 hours at 65C, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37C.

scan_protocol: Microarray was scanned using Agilent High Resolution Microarray Scanner (C-model). Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1).

data_processing: gProcessed Signal (from Agilen Feature Extraction) was normalized via Percentile shift to the 75th percentile of each array and baseline transformed

organism: Macaca fascicularis

source_name: Liver_average birth weight

label_protocol: 100 ng of total RNA was labeled with  Agilent Quick Amp Labeling Kit, One-Color  following manufacturer instruction. Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA. 600ng of labeled cRNA was hybridized onto Agilent Microarray.

extract_protocol: Toatal RNA was extracted using TRIzol reagent according to the manufacturers instructions (Invitrogen).

treatment_protocol: We compard tissues from neonates at birth in the average birth weight (50-75th centile) to those of lower birth weight (5-25th centile).

tag: age

value: neonate

tag: birth weight

value: average birth weight (50-75th centile)

value: Liver


title: mESC_undifferentiated_Alkb1-/-_rep3

description:
C10-3
Whole genome gene expression data from Alkbh1-/- C57BL/6 mouse embryonic stem cells.


title: Liver_Treated_rep2

description: Liver_lower birth weight_rep2

source_name: Liver_lower birth weight

value: lower birth weight (5-25th centile)


title: Liver_Treated_rep1

description: Liver_lower birth weight_rep1


title: Cells incubated with PBS

city: Rehovot

first: Idit

last: Shachar

address: 2 Hersel st

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Geneschips were scanned ccording to the manufacturer's instructions.

data_processing: The data were analyzed using Affymetrix deafault analysis settins and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: colon epithilial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

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

value: 7 weeks old

tag: agent

value: PBS


title: Leave-Bean rep1


title: Cells incubated with MIF

value: MIF


title: Id1 KO ES cell self-renewing

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: these were Id1KO ES cells grown under standard self-renewing conditions (i.e. in the presence of serum and LIF)

hyb_protocol: 15ug of labeled cRNA were hybridized on the MOE 430A arrays

scan_protocol: according to manufacturer

data_processing: Overall intensity was targetted to 500. Signal intensities were generated using GCOS1.4

source_name: Id1 KO ES cell self-renewing

label_protocol: 1ug total RNA was labeled using the Megascript Ambion kit (cat#AM1334)

extract_protocol: RNeasy

value: ES


title: Normal_tissue_sample_11E

description:
PA026_human_11E_070516
Hybridized to 250K_Nsp

source_name: Normal tissue

label_protocol: Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ).

value: normal lung


title: RGSV infected Rice_rep3

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

country: Japan

institute: NARO/HARC

description: Biological replication 3 of 3, RGSV infected rice

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies
Log 10 based (normalized ch1intensity / normalized ch2 intensity)

organism: Oryza sativa Japonica Group

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (W: 53 cm x D: 35 cm x H: 10 cm)
Growth media :mixed soil (50 % natural soil and 50% commercial soil (Bonsol: Sumitomo Chemical, Osaka,Japan))
No of seedling per pot : 42
Light condition: Natural conditions
Tempareture: 25±3℃
Growth length: 28 days past inoculation

extract_protocol:
separation: trimming
extraction source: frozen
extraction source: shoots pooled from 5 individual plants
kit: Qiagen Rneasy maxi kit
manual: Qiagen

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: Rice grassy stunt virus
virus inoculation: three viruliferous green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours

value: Nipponbare

value: newly two leaves

treatment_protocol:
Growth environment: growth chamber study (w:34cm, D: 26cm, H: 34cm)
growth stage: two leaves visible
Light condition: continuous light
Tempareture: 25±3℃
virus inoculation: mock inoculation
virus inoculation: three virus free green leafhoppers (Nephotettix cincticeps) per 1 seedling
virus inoculation: 24 hours


title: RGSV infected Rice_rep2

description: Biological replication 2 of 3, RGSV infected rice


title: Liver_Treated_rep3

description: Liver_lower birth weight_rep3


title: Liver_Control_rep2

description: Liver_average birth weight_rep2


title: RGSV infected Rice_rep1

description: Biological replication 1 of 3, RGSV infected rice


title: GIST 32

first: Hiromu

last: Suzuki

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description: miRNA expression in clinical GIST

hyb_protocol: Hybridization was performed using a miRNA Labeling Reagent & Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction.

source_name: GIST specimen 32

label_protocol: Total RNA (100 ng) was labeled using a miRNA Labeling Reagent & Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

extract_protocol: Total RNA was extracted using a mirVana miRNA isolation kit (Ambion).

value: GIST

tag: grade

value: intermediate

tag: location

value: small intestine

tag: gender

value: F


title: GIST 30

description: miRNA expression in clinical GIST

source_name: GIST specimen 30

tag: tissue

value: high

value: stomach

value: M


title: GIST 31

description: miRNA expression in clinical GIST

source_name: GIST specimen 31


title: mESC_undifferentiated_wild type_rep1

description:
C3-1
Whole genome gene expression data from wild type C57BL/6 mouse embryonic stem cells.

source_name: Mouse embryonic stem cells, day 0, wild type

value: wild type

tag: cell type

value: embryonic stem cells

value: day 0, undifferentiated


title: Cord_Treated_rep4

description: Umbilical Cord_lower birth weight_rep4

source_name: Umbilical Cord_lower birth weight

value: neonate

value: lower birth weight (5-25th centile)

value: Umbilical Cord


title: GIST 29

description: miRNA expression in clinical GIST

source_name: GIST specimen 29


title: mESC_undifferentiated_wild type_rep2

description:
C3-2
Whole genome gene expression data from wild type C57BL/6 mouse embryonic stem cells.


title: mESC_undifferentiated_wild type_rep3

description:
C3-3
Whole genome gene expression data from wild type C57BL/6 mouse embryonic stem cells.


title: GIST 27

description: miRNA expression in clinical GIST

source_name: GIST specimen 27


title: Adenocarcinoma_sample_19A

description:
PA026_19A_081021_(Mapping250K_Nsp)
Hybridized to 250K_Nsp

source_name: Non-small cell lung cancer tissue, short-term survival, adenocarcinoma

value: non-small cell lung cancer

value: adenocarcinoma

value: short


title: Liver_Control_rep1

description: Liver_average birth weight_rep1

value: average birth weight (50-75th centile)

value: Liver


title: mFoxp1-2

city: La Jolla

first: Elizabeth

middle: A.

last: Thomas

address: 10550 N. Torrey Pines Rd

department: Molecular Biology

institute: The Scripps Research Institute

description: replicate 2

hyb_protocol: Samples were hybridized onto the Illumina Sentrix BeadChip Array MouseRef-8 v2 for 18 hours at 58°C (protocol available at http://www.illumina.com/products/mouseref-8_expression_beadchip_kits_v2.ilmn).

scan_protocol: BeadChip Arrays were scanned using the Illumina BeadArray Reader with default settings.

data_processing: Data normalization was performed using GenomeStudio Gene Expression Module v1.0 with quantile normalization.

source_name: striatal cell

label_protocol: Biotin-labeled

extract_protocol: RNA  from striatal cells was extracted using RNAeasy mini kit (Qiagen) with DNase I treatment to eliminate genomic DNA contamination

value: striatum

tag: cell line

value: STHdh striatal cell line

tag: genotype/variation


title: Cord_Treated_rep2

description: Umbilical Cord_lower birth weight_rep2


title: GIST 28

description: miRNA expression in clinical GIST

source_name: GIST specimen 28

value: GIST

value: low

value: F


title: mFoxp1-3

description: replicate 3


title: GIST 26

description: miRNA expression in clinical GIST

source_name: GIST specimen 26

value: high

value: stomach


title: mFoxp1-1

description: replicate 1


title: Cord_Treated_rep1

description: Umbilical Cord_lower birth weight_rep1


title: Leave-Bean rep4

source_name: Leave

tag: cultivar

value: Caturra T2308

value: Leave

source_name: Bean

value: Bean


title: Patient 6 [CNV]

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

country: Australia

institute: SA Pathology

description: LCL gDNA

hyb_protocol: Performed by Australian Genomic Research Facility (AGRF)

data_processing: Raw data was originally processed by AGRF in Genome Bead Studio then exported to Partek Genomic Suite compatible files: allele intensity, genotype call and Ballele frequency files. Copy number was created from allele intentisity file against control 1 as reference model, then adjusted for GC content to reduce noise. CNV was detected in patients samples using Genomic Segmentation algorithm in Partek with the following settings: minimum markers 10, P value threshold < 0.001, signal to noise > 0.5, expected range = 0.3.

source_name: Lymphoblastoid cell line

growth_protocol: The Epstein-Barr virus (EBV) immortalized B- cell lines (B-LCL) used in this study were established from peripheral blood lymphocytes of patients and controls. Once established the LCL cell lines were cultured in RPMI 1640 (Sigma) supplemented with 10% FCS, 2mM L-Glutamine, 0.017mg/ml benzylpenicillin and grown at 37 0 C with 5% CO2

extract_protocol: The extraction was set up in a 1.5 ml Eppendorf screw cap tube (containing the pellet) with 400 µl of proteinase K buffer, 50 µl of 10% SDS and 50 µl of 10 mg/ml proteinase K (final concentration 1 mg/ml) (ROCHE). The tube was sealed off with paraffin to prevent leakage and spun on rotating wheel over night in 37oC incubator. DNA was separated from the lysate by adding 500 µl Phenol:Water:Chloroform mix and mixed well by rotating on wheel for 15 minutes at room Tm. To separate lysates into layers, the tube was spun at 12000 RPM for 5 minutes. The top aqueous phase, which contained DNA, was transferred into another 1.5 ml Eppendorf screw cap tube. To clean up more cell debris and protein contamination, another lot of 500 µl of Phenol:Water:Chloroform was added. The process was repeated until a cleaner top aqueous phase was collected in a different 1.5 ml Eppendorf screw cap tube. To remove RNA contamination, 2 µl of RNAse A (QIAGEN) was added to the DNA mixture and incubated at for 1 hour at 37oC. DNA was precipitated by adding ice cold absolute ethanol and incubated in -20oC freezer for 30 minutes, then spun at 12000 RPM for 10 minutes. All supernatant was removed and the DNA pellet was dried under vacuum. The dried DNA pellet was resuspended in 100-300 µl 1 x TE depending on the size of the original sample.

treatment_protocol: No treatment

tag: individual

value: Patient 6

value: Lymphoblastoid cell line

tag: disease state

value: UPF3B patient


title: Control 1 [CNV]

description: LCL gDNA

scan_protocol: Performed by Australian Genomic Research Facility (AGRF)

value: Control 1

value: Normal control


title: Patient 2 [CNV]

description: LCL gDNA

label_protocol: Performed by Australian Genomic Research Facility (AGRF)

value: Patient 2


title: GIST 25

description: miRNA expression in clinical GIST

source_name: GIST specimen 25

value: M


title: Cord_Control_rep4

description: Umbilical Cord_average birth weight_rep4

source_name: Umbilical Cord_average birth weight

value: neonate

value: average birth weight (50-75th centile)

value: Umbilical Cord


title: Cord_Treated_rep3

description: Umbilical Cord_lower birth weight_rep3

value: lower birth weight (5-25th centile)


title: GIST 21

description: miRNA expression in clinical GIST

source_name: GIST specimen 21

value: GIST

value: intermediate

value: F


title: GIST 22

description: miRNA expression in clinical GIST

source_name: GIST specimen 22

value: low

value: stomach


title: GIST 23

description: miRNA expression in clinical GIST

source_name: GIST specimen 23


title: Patient 1 [CNV]

description: LCL gDNA

value: Patient 1


title: GIST 24

description: miRNA expression in clinical GIST

source_name: GIST specimen 24

value: high

value: small intestine


title: PcDNA-2

description: replicate 2

value: striatum

value: STHdh striatal cell line

value: wild-type


title: Cord_Control_rep3

description: Umbilical Cord_average birth weight_rep3


title: GIST 20

description: miRNA expression in clinical GIST

source_name: GIST specimen 20


title: PcDNA-3

description: replicate 3


title: Control 2 [CNV]

description: LCL gDNA

value: Control 2

value: Lymphoblastoid cell line

value: Normal control


title: Patient 4 [CNV]

description: LCL gDNA

value: Patient 4

value: UPF3B patient


title: Patient 5 [CNV]

description: LCL gDNA

value: Patient 5


title: Patient 3 [CNV]

description: LCL gDNA

value: Patient 3


title: Bicep_Treated_rep4

description: Skeletal muscle_lower birth weight_rep4

source_name: Skeletal muscle_lower birth weight

value: neonate

value: lower birth weight (5-25th centile)

value: Skeletal muscle


title: PcDNA-1

description: replicate 1


title: Cardiomyocyte control_mRNA content_rep2

city: Umea

first: Urban

last: Hellman

address: Nus 6M

department: Public health and clinical medicine

institute: Umea University

description:
total RNA->cRNA
Chip sample 4613963055_G

hyb_protocol: Performed according to Illumina protocol

scan_protocol: Illumina Beadstation 500GX according to Illumina protocol

data_processing:
Gene expression analysis (not differential) Cubic spline normalization, subtracted background, False Discovery Rate.
Illumina Beadstudio 3.3 was used with gene expression module 3.4.0

source_name: Cardiomyocyte control_mRNA content

label_protocol: Illumina TotalPrep RNA Amplification Kit was used. Terminal deoxynucleotidyl transferase were used to add a poly-T tail to DNA from microvesicles to construct cDNA, possible to label as cRNA and bind to chip.

growth_protocol: Cultured cardiomyocytes in claycomb medium in 37 degrees, 5% CO2

extract_protocol: Cardiomyocytes were put in RNAlater, Qiagen miRNEasy Mini Kit was used to extract total RNA. Sigma GenElute Mammalian Genomic DNA Miniprep Kit were used to extract DNA. Terminal deoxynucleotidyl transferase were used to add a poly_T tail to DNA from microvesicles to construct cDNA, possible to label as cRNA and use on the chip to identify part of the sequence of the original DNA.

value: cardiomyocyte


title: GIST 18

description: miRNA expression in clinical GIST

source_name: GIST specimen 18

value: GIST

value: stomach

value: M


title: Cord_Control_rep2

description: Umbilical Cord_average birth weight_rep2

value: average birth weight (50-75th centile)

value: Umbilical Cord


title: Cord_Control_rep1

description: Umbilical Cord_average birth weight_rep1


title: Bicep_Treated_rep3

description: Skeletal muscle_lower birth weight_rep3


title: Bicep_Treated_rep1

description: Skeletal muscle_lower birth weight_rep1


title: Cardiomyocyte control_mRNA content_rep1

description:
total RNA->cRNA
Chip sample 4613963055_F


title: GIST 17

description: miRNA expression in clinical GIST

source_name: GIST specimen 17

value: low


title: Cardiomyocyte microvesicle_DNA content_only one rep.

type: other

description:
DNA->cRNA
Chip sample 4936640002_A

molecule: other

source_name: Cardiomyocyte microvesicle_DNA content


title: WT ES cell self-renewing

description: these were WT ES cells grown under standard self-renewing conditions (i.e. in the presence of serum and LIF)

source_name: WT ES cell self-renewing

value: ES


title: GIST 19

description: miRNA expression in clinical GIST

source_name: GIST specimen 19


title: Bicep_Treated_rep2

description: Skeletal muscle_lower birth weight_rep2


title: GIST 16

description: miRNA expression in clinical GIST

source_name: GIST specimen 16

value: F


title: Bicep_Control_rep4

description: Skeletal muscle_average birth weight_rep4

source_name: Skeletal muscle_average birth weight


title: Fibroblasts NIH-3T3_microvesicles_rep2

description: Chip sample 4613963056_H

data_processing:
Cubic spline normalization, subtracted background, False Discovery Rate.
Illumina Beadstudio 3.3 was used with gene expression module 3.4.0

label_protocol: Illumina TotalPrep RNA Amplification Kit was used

growth_protocol: Cultured cardiomyocytes and fibroblasts in claycomb medium in 37 degrees, 5% CO2

extract_protocol: Fibroblasts were put in RNAlater, Qiagen miRNEasy Mini Kit was used to extract total RNA.

value: fibroblasts


title: Bicep_Control_rep1

description: Skeletal muscle_average birth weight_rep1


title: Bicep_Control_rep2

description: Skeletal muscle_average birth weight_rep2


title: GIST 14

description: miRNA expression in clinical GIST

source_name: GIST specimen 14

value: intermediate

value: omentum


title: Fibroblasts NIH-3T3_microvesicles_rep1

description: Chip sample 4613963056_G


title: Cardiomyocyte microvesicle_mRNA content_rep1

description:
total RNA->cRNA
Chip sample 4613963055_H

source_name: Cardiomyocyte microvesicle_mRNA content


title: Bicep_Control_rep3

description: Skeletal muscle_average birth weight_rep3


title: Fibroblasts NIH-3T3_control_rep1

description: Chip sample 4613963056_A


title: IT unselected timepoint5

city: Edinburgh

first: Antoine

last: Claessens

address: West Mains Road

department: Institute of Immunology and Infection Research

country: United Kingdom

institute: Edinburgh university

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA)

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA)

data_processing: All arrays were visually inspected using GenePix and any bad quality spots (signal below background or dust on the chip) were flagged out. After gridding, the data were loaded onto the Acuity 4.0 software. Each array was then normalized with Lowess (locally weighted least squares regression).   A dataset with all time points was created using the following parameters: only unflagged spots and spots with median intensities (green or red) greater than the local background plus 2 times the standard deviation of the background were used.

organism: Plasmodium falciparum

source_name: Unselected IT parasites, timepoint 5

label_protocol: Each aminoallyl-cDNA sample was coupled to Cy5 (red dye) while Cy3 (green dye) was added to the pool. Cy5-labelled time point samples were mixed with the same amount of Cy3-labelled pool sample.

growth_protocol: P. falciparum parasites was cultured at 2% haematocrit with group O erythrocytes. The culture medium used was RPMI 1640 medium supplemented with 25 mM Hepes, 2 mM glutamine, 25mM glucose, 25 μg/ml gentamicin, adjusted with 1M NaOH to pH 7.2 to 7.4 with 10% pooled normal human serum.

extract_protocol: The tube with TRIzol solution was thawed on ice. Two volumes chloroform (Sigma) were added per volume packed cells. After mixing, the tube was incubated on ice for 5min then centrifuged at 3600g for 40min at 4°C without brakes. The supernatant (aqueous layer) was carefully transferred into a fresh tube without disturbing the pellet. The same volume of ice-cold isopropanol (Sigma) was added and the tube was incubated at 4°C overnight. The next day, the tube was centrifuged at 3600g for 60 min at 4°C. The supernatant was discarded and the pellet was resuspended and washed with ice-cold 70% ethanol (Sigma). After another centrifugation at 3600g and 4°C for 10min, the supernatant was completely but carefully removed using a fine Pasteur pipette. The tube was left upside down to air dry for 15 to 60min until no liquid was visible. The dried pellet was resuspended with 25μl of warm DEPC-H2O then placed on ice. RNA concentration was measured using a spectrophotometer. For RNA, ten times the culture packed cell volume of room temperature TRIzol reagent (Invitrogen 15596-026) was added, and after thorough mixing, stored at -80°C. 12μg of RNA from the unselected parasites at each of the 6 time points was combined together to form the reference pool. The pool and 12μg of each individual time point sample from both selected and unselected parasites were then used for first-strand cDNA synthesis using an amino-allyl dye coupling protocol

treatment_protocol: HBEC-selected parasites were cultured and synchronized alongside their unselected (non-binding) counterpart. At late schizont stage, HB3-HBEC1 and HB3-Uns1 control cultures (pilot experiment) were Percoll-treated to purify infected erythrocytes, while for all other selections, schizont-infected erythrocytes were purified on a MACS column. 5 to 7 hours later, after most schizonts had ruptured and parasites were mostly at early-ring stage, cultures were sorbitol-treated. Time point 1 of a time-course experiment started 8 hours after the end of the Percoll/MACS treatment (i.e. 1-3 hours after sorbitol treatment).

tag: selection

source_name: Pool of all IT unselected timepoints


title: IT unselected timepoint6

source_name: Unselected IT parasites, timepoint 6


title: Fibroblasts NIH-3T3_control_rep2

description: Chip sample 4613963056_B


title: Cardiomyocyte microvesicle_mRNA content_rep2

description:
total RNA->cRNA
Chip sample 4936640002_B


title: GIST 13

description: miRNA expression in clinical GIST

source_name: GIST specimen 13


title: GIST 15

description: miRNA expression in clinical GIST

source_name: GIST specimen 15


title: IT unselected timepoint4

source_name: Unselected IT parasites, timepoint 4


title: IT unselected timepoint3

source_name: Unselected IT parasites, timepoint 3


title: IT unselected timepoint2

source_name: Unselected IT parasites, timepoint 2


title: GIST 12

description: miRNA expression in clinical GIST

source_name: GIST specimen 12

value: small intestine


title: GIST 11

description: miRNA expression in clinical GIST

source_name: GIST specimen 11


title: Fibroblasts NIH-3T3_ultracentrifuged media from cardiomyocytes_rep1

description: Chip sample 4936640003_D

source_name: Fibroblasts_ultracentrifuged media from cardiomyocytes


title: GIST 9

description: miRNA expression in clinical GIST

source_name: GIST specimen 9


title: GIST 10

description: miRNA expression in clinical GIST

source_name: GIST specimen 10

value: high


title: IT-HBEC timepoint6

source_name: IT parasites selected on HBEC-5i (IT-HBEC), timepoint 6


title: GIST 7

description: miRNA expression in clinical GIST

source_name: GIST specimen 7


title: IT unselected timepoint1

source_name: Unselected IT parasites, timepoint 1


title: GIST 8

description: miRNA expression in clinical GIST

source_name: GIST specimen 8


title: GIST 6

description: miRNA expression in clinical GIST

source_name: GIST specimen 6


title: Fibroblasts NIH-3T3_media from cardiomyocytes_rep2

description: Chip sample 4613963056_C

source_name: Fibroblasts_media from cardiomyocytes


title: Fibroblasts NIH-3T3_ultracentrifuged media from cardiomyocytes_rep2

description: Chip sample 4613963056_E


title: IT-HBEC timepoint5

source_name: IT parasites selected on HBEC-5i (IT-HBEC), timepoint 5

source_name: Pool of all IT unselected timepoints


title: Fibroblasts NIH-3T3_media from cardiomyocytes_rep1

description: Chip sample 4936640003_H


title: GIST 4

description: miRNA expression in clinical GIST

source_name: GIST specimen 4


title: GIST 5

description: miRNA expression in clinical GIST

source_name: GIST specimen 5


title: IT-HBEC timepoint4

source_name: IT parasites selected on HBEC-5i (IT-HBEC), timepoint 4


title: Fibroblasts NIH-3T3_unused cardiomyocyte media_rep2

description: Chip sample 4936640003_B


title: Fibroblasts NIH-3T3_unused cardiomyocyte media_rep3

description: Chip sample 4936640003_C


title: Fibroblasts NIH-3T3_unused cardiomyocyte media_rep1

description: Chip sample 4936640003_A


title: GIST 3

description: miRNA expression in clinical GIST

source_name: GIST specimen 3


title: Fibroblasts NIH-3T3_media from cardiomyocytes_rep3

description: Chip sample 4613963056_D


title: IT-HBEC timepoint1

source_name: IT parasites selected on HBEC-5i (IT-HBEC), timepoint 1


title: IT-HBEC timepoint2

source_name: IT parasites selected on HBEC-5i (IT-HBEC), timepoint 2


title: IT-HBEC timepoint3

source_name: IT parasites selected on HBEC-5i (IT-HBEC), timepoint 3


title: GIST 2

description: miRNA expression in clinical GIST

source_name: GIST specimen 2


title: GIST 1

description: miRNA expression in clinical GIST

source_name: GIST specimen 1


title: Cardiomyocytes HL-1_6-mer oligo hyaluronan_rep2

description: Chip sample 4613963055_D

source_name: Cardiomyocytes_6-mer oligo hyaluronan

extract_protocol: Cardiomyocytes were put in RNAlater, Qiagen miRNEasy Mini Kit was used to extract total RNA.

value: cardiomyocytes


title: Cardiomyocytes HL-1_1000kDA hyaluronan_rep1

description: Chip sample 4613963055_A

source_name: Cardiomyocytes_1000kDA hyaluronan


title: 3D7 unselected timepoint6

source_name: 3D7 unselected parasites, timepoint 6

source_name: Pool of all 3D7 unselected timepoints


title: Cardiomyocytes HL-1_untreated_rep2

description: Chip sample 4613963055_G


title: mouse_nerve

city: Koto

first: Jun

last: Sese

state: Tokyo

institute: National Institute of Advanced Industrial Science and Technology

description: SAMPLE 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 8x60k Oligo Microarrays (030829) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 030829_D_F_20101021) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mouse, nerve cell

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

extract_protocol: All RNAs are provided by Lonza. We extracted them accroding to their manuals.

tag: strain

value: nerve


title: 3D7 unselected timepoint2

source_name: 3D7 unselected parasites, timepoint 2


title: CardiomyocytesHL-1_1000kDA hyaluronan_rep2

description: Chip sample 4613963055_B


title: 3D7 unselected timepoint3

source_name: 3D7 unselected parasites, timepoint 3


title: human_astrocyte

description: SAMPLE 1

source_name: Human, astrocyte cell

value: astrocyte


title: 3D7 unselected timepoint5

source_name: 3D7 unselected parasites, timepoint 5


title: Cardiomyocytes HL-1_6-mer oligo hyaluronan_rep1

description: Chip sample 4613963055_C


title: SPC+3

city: Singapore

first: Frank

middle: Daniel

last: McKeon

address: 60 Biopolis street

department: Stem cell and Developmental Biology 7

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Hybridization was done using standard Affymetrix protocols

scan_protocol: GeneChip® Scanner 3000,Affymetrix

data_processing:
To validate sample quality probe hybridization ratios were calculated using Affymetrix Expression Console software.  The intensity values were log2-transformed and imported into the Partek Genomics Suite 6.5(beta).  Exons were summarized to genes and a 1-way ANOVA was performed to identify differentially expressed genes.  P values and fold-change were calculated for each analysis.  Heatmaps were generated using Pearson’s correlation and Ward’s method and Principal Component Analysis was conducted using all probe sets.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: infected mouse lung

label_protocol: RNA was amplified and labelled using WT Pico RNA Amplification System, WT-Ovation Exon Module and Encore Biotin Module (NuGEN Technologies)

extract_protocol: RNA was extracted using Pico pure RNA isolation kit from Arcturus after Laser Capture Microdissection

treatment_protocol: C57/B6 mice were infected with sublethal dose of H1N1 PR8 mouse adapted virus and sacrificed at 25 dpi to harvest the lungs

value: lung

tag: infection

value: H1N1 PR8 virus

tag: lung cell population

value: SPC+


title: rat_nerve

description: SAMPLE 4

source_name: Rat, nerve cell

value: Sprague-Dawley


title: Texas D7-1 585 RNA Cy3 1

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: Thirty-four cynomolgus macaques (M. fascicularus) (half of each sex), weighing 2.1–2.7 kg, were exported from the Huazheng laboratory animal breeding center, Zuo Village Chengjiao Town, Conghua, Guangzhou, China and received by Covance Research Products. Animals were quarantined for 6 weeks, prescreened, and certified as specific pathogen-free. Husbandry and procedures were approved by the Battelle Institutional Animal Care and Use Committee and by the Battelle Biosafety Committee. Influenza-infected animals were housed in an ABSL-3 enhanced facility

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

source_name: RNA from lung tissue infected with A/Texas/36/91, 7 dpi, animal 585

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol: Tissues were collected at necropsy and immersed immediately in solution D. Tissue was homogenized immediately for 30 seconds with a Kinematica Polytron PT1200 instrument and a model PT-DA1212/2 generator (Kinematica, Lucerne, Switzerland) in 10-ml round-bottom polypropylene test tubes with 5 ml of solution D. In order to reduce the generation of aerosols during this process, the Polytron generator was passed through a hole in the test tube lid, which had been drilled in a manner that ensured a tight fit with the instrument. To further minimize possible contact with aerosols, a barrier shield was used in addition to positive-air-pressure respirators and full-protective personal protection equipment. The homogenized samples were then snap frozen on dry ice and stored at −70°C . Added to this were 650 μl of 2 M sodium acetate, 6.5 ml of water-saturated phenol, and 1.3 ml chloroform-isoamyl alcohol (49:1). Tubes were vortexed and gently rocked for 10 min at room temperature. The mixture was then centrifuged for 30 min at 8,500 rpm and 4°C by using a Beckman L8-80 M ultracentrifuge with a JA18 rotor. The resulting aqueous layer was transferred to a new tube and precipitated with an equal volume of cold isopropanol at −20°C overnight. Centrifugation was performed again as described above. The resulting pellet was rinsed in 75% ethanol and resuspended in 150 μl of RNase-free water. A Beckman Coulter DU 640B spectrophotometer was used to quantify total RNA. One hundred micrograms of total RNA was purified with an RNA-Easy column according to the manufacturer's specifications. A Hewlett-Packard Kayak XM600 bioanalyzer was used to check the purity of the RNA prior to amplification.

treatment_protocol: The H5N1 human influenza isolate A/Vietnam/1203/2004 was obtained from the World Health Organization (WHO) influenza collaborating laboratory at the Centers for Disease Control (CDC), Atlanta, GA. The reassortant A/Texas/36/1991 influenza viruses possessing the A/South Carolina/1/18 HA (GenBank AF117241) and A/Brevig Mission/1/1918 NA (GenBank AF250356) or the A/South Carolina/1/18 HA, A/Brevig Mission/1/1918 NA, and A/Brevig Mission/1/18 NS (GenBank AF333238) were generated as previously described (50, 51). Recombinant viruses were plaque-purified, and the sequences of the virus segments were confirmed by reverse transcription-PCR and sequencing.intratracheal, intranasal, tonsillar, and conjunctival routes with a total of 107 pfu of A/Vietnam/1203/2004 (H5N1) virus, A/Texas/36/91 (H1N1) virus or reassortants of this virus containing either 2 (HA, NA) or 3 (HA, NA, NS) genes from the 1918 virus. Two animals per group were scheduled for sacrifice on days 1, 2, 4, and 7. Two additional animals were used as uninfected control animals and killed on day 7. Blood was collected from all animals 2 weeks before infection and on days 2, 4, and 7 or until sacrifice, for hematology, immunophenotyping, and cytokine analysis. Blood was also collected on day 1 from all animals except those with a day 7 endpoint, due to limitations in the total permissible blood draw. At necropsy, the lungs, tracheobronchial and retropharyngeal lymph nodes, heart, liver, spleen, kidneys, brain, and gastrointestinal tract were examined and sampled either by snap-freezing for viral isolation, cytometric bead array, real-time PCR, or microarray analysis, or by fixation in 10% formalin for histology and immunohistochemistry.

tag: time (post virus infection)

value: Day 7


title: rat_astrocyte

description: SAMPLE 2

source_name: Rat, astrocyte cell


title: Cardiomyocytes HL-1_untreated_rep1

description: Chip sample 4613963055_F


title: Mismatch_6

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 8x15k Oligo Microarrays (027004) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

extract_protocol: All RNAs are provided by Takara Co. Ltd. We extracted them accroding to their manuals.

tag: sample type

value: reference total RNA


title: SPC+2

growth_protocol: C57/B6 mice were infected with sublethal dose of H1N1 PR8 mouse adapted virus


title: Mismatch_5


title: 3D7 unselected timepoint4

source_name: 3D7 unselected parasites, timepoint 4


title: 3D7 unselected timepoint1

source_name: 3D7 unselected parasites, timepoint 1


title: Texas D7-1 509 RNA Cy3 2

source_name: RNA from lung tissue infected with A/Texas/36/91, 7 dpi, animal 509


title: Mismatch_4


title: Mismatch_3


title: Texas D7-1 585 RNA Cy3 2


title: K5+2


title: K5+3


title: Texas D4-1 642 RNA Cy3 2

source_name: RNA from lung tissue infected with A/Texas/36/91, 4 dpi, animal 642

value: Day 4


title: 3D7-HBEC timepoint4

source_name: 3D7 parasites selected on HBEC-5i (3D7-HBEC), timepoint 4


title: 3D7-HBEC timepoint6

source_name: 3D7 parasites selected on HBEC-5i (3D7-HBEC), timepoint 6


title: K5+1


title: Texas D4-1 642 RNA Cy3 1


title: Texas D7-1 509 RNA Cy3 1


title: K5&SPC neg-2

value: K5&SPC neg-


title: 3D7-HBEC timepoint5

source_name: 3D7 parasites selected on HBEC-5i (3D7-HBEC), timepoint 5


title: 3D7-HBEC timepoint3

source_name: 3D7 parasites selected on HBEC-5i (3D7-HBEC), timepoint 3

source_name: Pool of all 3D7 unselected timepoints


title: K5&SPC neg-3


title: Mismatch_2


title: Mismatch_1


title: Texas D4-1 476 RNA Cy3 2

source_name: RNA from lung tissue infected with A/Texas/36/91, 4 dpi, animal 476


title: 3D7-HBEC timepoint2

source_name: 3D7 parasites selected on HBEC-5i (3D7-HBEC), timepoint 2


title: 3D7-HBEC timepoint1

source_name: 3D7 parasites selected on HBEC-5i (3D7-HBEC), timepoint 1


title: K5&SPC neg-1


title: Neural Complex spawning after dark 1 h rep2

city: Onnna, Kunigami

first: Takeshi

last: Kawashima

state: Okinawa

institute: Okinawa Institute of Science and Technology

description: This sample is extracted from a same individual with 469305A12. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: RMA and summalization were executed by NimbleScan.

organism: Ciona intestinalis

source_name: Neural Complex spawning after dark 1 h

label_protocol: 1 color, 24 reaction kit, official instruction

extract_protocol: All samples were saturated in RNAlater. RNA extraction: Trizol Reagent and Rneasy micro. Total RNA samples from Neural complex were amplified by Ovation Pico SL.

value: Neural Complex

tag: light condition

value: spawning after dark

tag: time

value: 1 h


title: Neural Complex dark 15 min rep2

description: This sample is extracted from a same individual with 469305A10. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Neural Complex dark 15 min

value: dark

value: 15 min


title: HB3-HBEC-TNF timepoint6

source_name: HB3 parasites selected on HBEC-5i activated with TNF (HB3-HBEC-TNF), timepoint 6

value: HBEC-5i activated with TNF

source_name: Pool of all HB3 unselected timepoints


title: Texas D4-1 476 RNA Cy3 1


title: Neural Complex dark 15 min rep1

description: This sample is extracted from a same individual with 469305A09. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: Neural Complex spawning after dark 1 h rep1

description: This sample is extracted from a same individual with 469305A11. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: Texas D2-1 605 RNA Cy3 2

source_name: RNA from lung tissue infected with A/Texas/36/91, 2 dpi, animal 605

value: Day 2


title: Texas D2-1 477 RNA Cy3 1

source_name: RNA from lung tissue infected with A/Texas/36/91, 2 dpi, animal 477


title: alveoli-2

source_name: infected mouse lung

value: alveoli


title: alveoli-3


title: alveoli-1


title: HB3-HBEC-TNF timepoint5

source_name: HB3 parasites selected on HBEC-5i activated with TNF (HB3-HBEC-TNF), timepoint 5


title: Neural Complex dark 0 min rep1

description: This sample is extracted from a same individual with 469305A07. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Neural Complex dark 0 min

value: 0 min


title: HB3-HBEC-TNF timepoint4

source_name: HB3 parasites selected on HBEC-5i activated with TNF (HB3-HBEC-TNF), timepoint 4


title: HB3-HBEC-TNF timepoint3

source_name: HB3 parasites selected on HBEC-5i activated with TNF (HB3-HBEC-TNF), timepoint 3


title: Texas D2-1 477 RNA Cy3 2

value: lung


title: Neural Complex dark 0 min rep2

description: This sample is extracted from a same individual with 469305A08. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: HB3-HBEC-TNF timepoint2

source_name: HB3 parasites selected on HBEC-5i activated with TNF (HB3-HBEC-TNF), timepoint 2


title: colony infected-3

source_name: primary cell culture

growth_protocol: mouse lungs were disossciated enzymatically and cultured on irradiated mouse fibroblast feeder layer

extract_protocol: RNA was extracted using Pico pure RNA isolation kit from Arcturus

treatment_protocol: infectedmice were infected with a sublethal dose of H1N1 PR8 virus

value: H1N1 PR8 virus

tag: growth protocol

value: lungs dissociated enzymatically and cultured on irradiated mouse fibroblast feeder layer


title: Texas D1-1 617 RNA Cy3 3

source_name: RNA from lung tissue infected with A/Texas/36/91, 1 dpi, animal 617

value: Day 1


title: Texas D1-1 617 RNA Cy3 4


title: colony infected-2


title: Neural Complex light 24 h rep2

description: This sample is extracted from a same individual with 469305A06. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Neural Complex light 24 h

value: light


title: Neural Complex light 24 h rep1

description: This sample is extracted from a same individual with 469305A05. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: HB3-HBEC-TNF timepoint1

source_name: HB3 parasites selected on HBEC-5i activated with TNF (HB3-HBEC-TNF), timepoint 1


title: HB3 unselected2 timepoint6

source_name: Unselected HB3 parasites, timepoint 6


title: Texas D2-1 605 RNA Cy3 1


title: Texas D1-1 617 RNA Cy3 1


title: colony control-3

value: control


title: colony infected-1


title: HB3 unselected2 timepoint5

source_name: Unselected HB3 parasites, timepoint 5


title: HB3 unselected2 timepoint4

source_name: Unselected HB3 parasites, timepoint 4


title: Neural Complex light 15 min rep2

description: This sample is extracted from a same individual with 469305A04. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Neural Complex light 15 min


title: Neural Complex light 15 min rep1

description: This sample is extracted from a same individual with 469305A03. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: HB3 unselected2 timepoint2

source_name: Unselected HB3 parasites, timepoint 2

source_name: Pool of all HB3 unselected timepoints


title: HB3 unselected2 timepoint3

source_name: Unselected HB3 parasites, timepoint 3


title: Texas D1-1 484 RNA 3 Cy3 1

source_name: RNA from lung tissue infected with A/Texas/36/91, 1 dpi, animal 484


title: colony control-1


title: Neural Complex light 0 min rep2

description: This sample is extracted from a same individual with 469305A02. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Neural Complex light 0 min


title: Texas D1-1 484 RNA 3 Cy3 2


title: colony control-2


title: Texas D1-1 617 RNA Cy3 2


title: Neural Complex light 0 min rep1

description: This sample is extracted from a same individual with 469305A01. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: HB3-HBEC2 timepoint4

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 4


title: NMuMG_Gene_control

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description: gene level data

hyb_protocol: Hybridization was performed according to the protocols provided by Affymetrix, using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: Scanning was performed according to the protocols provided by Affymetrix.

data_processing: CEL files were generated using Affymetrix GeneChip Command Console Software (AGCC).

source_name: normal murine mammary gland epithelial cell line (NMMuMG), untreated

label_protocol: Labeling was performed according to the protocols provided by Affymetrix.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA) supplemented with 4.5 g/l glucose, 10% fetal bovine serum (FBS), 10 ug/ml insulin, 50 U/ml penicillin, and 50 ug/ml streptomycin.

extract_protocol: Total RNA was purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Cells were treated with 1 ng/ml recombinant human TGF-beta1 (R&D Systems, Minneapolis, MN) or left untreated.

value: NMuMG

tag: tissue origin

value: mammary gland


title: HB3-HBEC2 timepoint5

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 5


title: HB3 unselected2 timepoint1

source_name: Unselected HB3 parasites, timepoint 1


title: Ovary spawning after dark 1 h rep2

description: This sample is extracted from a same individual with 469376A12. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ovary spawning after dark 1 h

tag: tissue

value: Ovary


title: Ovary dark 15 min rep2

description: This sample is extracted from a same individual with 469376A10. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ovary dark 15 min


title: H5 D7-1 618 RNA Cy3 1

source_name: RNA from lung tissue infected with VN1203, 7 dpi, animal 618

value: Day 7


title: lox/loxMZ_rep3

city: Madrid

first: Almudena

last: Ramiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

description: US22502553_251911910078_S01_miRNA-v1_95_May07_1_1.txt

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: all the labeled sample. Duration: 40 hours. Volume: 45 uL. Temperature (ºC): 55.

scan_protocol: Scanned on an G2565C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1).

data_processing: Images were quantified  and normalized using default normalization with Agilent Feature Extraction Software (ver. 10.1.1).

label_protocol: Amount of nucleic acid labeled: 120ng. Commercial miRNA Microarray System with miRNA Complete Labeling and Hyb Kit by following manufacturer instructions. Agilent manual G4170-90011 Ver. 2.0 June 2008. Fluorescent Cyanine 3-pCp molecules are ligated with T4 RNA ligase to dephosphorilated 3' ends from the RNA sample.

extract_protocol: RNA of purified populations was extracted with TRIzol (Invitrogen) following manufacturer’s instructions.

value: C57/Bl6, possibly with some contribution of CBA

value: spleen

tag: cell type

value: marginal zone (MZ) B cells


title: lox/loxFO_rep1

description: US22502553_251911910078_S01_miRNA-v1_95_May07_1_3.txt

value: follicular (FO) B cells


title: (+)/loxFO_rep1

description: US22502553_251911910078_S01_miRNA-v1_95_May07_1_2.txt


title: (+)/loxMZ_rep1

description: US22502553_251911910078_S01_miRNA-v1_95_May07_2_2.txt


title: lox/loxMZ_rep1

description: US22502553_251911910078_S01_miRNA-v1_95_May07_2_4.txt


title: Ovary dark 15 min rep1

description: This sample is extracted from a same individual with 469376A09. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

value: dark

value: 15 min


title: NMuMG_Gene_TGF-beta

description: gene level data

source_name: normal murine mammary gland epithelial cell line (NMMuMG), treated with TGF-beta

tag: cell line


title: H5 D7-1 618 RNA Cy3 2

description: Thirty-four cynomolgus macaques (M. fascicularus) (half of each sex), weighing 2.1–2.7 kg, were exported from the Huazheng laboratory animal breeding center, Zuo Village Chengjiao Town, Conghua, Guangzhou, China and received by Covance Research Products. Animals were quarantined for 6 weeks, prescreened, and certified as specific pathogen-free. Husbandry and procedures were approved by the Battelle Institutional Animal Care and Use Committee and by the Battelle Biosafety Committee. Influenza-infected animals were housed in an ABSL-3 enhanced facility


title: H5 D7-1 618L RNA Cy3 1

source_name: RNA from lung tissue infected with VN1203, 7 dpi, animal 618L


title: Ovary spawning after dark 1 h rep1

description: This sample is extracted from a same individual with 469376A11. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

value: spawning after dark

value: 1 h


title: SPC+1

source_name: infected mouse lung

value: lung

value: H1N1 PR8 virus

value: SPC+


title: Ovary dark 0 min rep1

description: This sample is extracted from a same individual with 469376A07. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ovary dark 0 min

value: 0 min


title: H5 D7-1 618L RNA Cy3 2


title: H5 D4-1 562 RNA Cy3 2

source_name: RNA from lung tissue infected with VN1203, 4 dpi, animal 562

value: Day 4


title: lox/loxMZ_rep2

description: US22502553_251911910077_S01_miRNA-v1_95_May07_2_4.txt

tag: genotype/variation


title: H5 D4-1 562 RNA Cy3 1


title: lox/loxFO_rep2

description: US22502553_251911910077_S01_miRNA-v1_95_May07_2_3.txt


title: H5 D4-1 507 RNA Cy3 2

source_name: RNA from lung tissue infected with VN1203, 4 dpi, animal 507


title: HB3-HBEC2 timepoint3

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 3

source_name: Pool of all HB3 unselected timepoints


title: HB3-HBEC2 timepoint2

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 2


title: HB3-HBEC2 timepoint1

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 1


title: H5 D4-1 507 RNA Cy3 1


title: HB3-HBEC1_vs_HB3-Uns_Timepoint6

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 6

source_name: Unselected HB3 parasites (HB3-Uns)


title: (+)/loxMZ_rep2

description: US22502553_251911910077_S01_miRNA-v1_95_May07_2_2.txt


title: Ovary light 24 h rep2

description: This sample is extracted from a same individual with 469376A06. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ovary light 24 h

value: light


title: Ovary dark 0 min rep2

description: This sample is extracted from a same individual with 469376A08. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: (+)/loxFO_rep2

description: US22502553_251911910077_S01_miRNA-v1_95_May07_2_1.txt


title: HB3-HBEC1_vs_HB3-Uns_Timepoint5

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 5


title: (+)/loxMZ_rep3

description: US22502553_251911910077_S01_miRNA-v1_95_May07_1_4.txt


title: (+)/loxFO_rep3

description: US22502553_251911910077_S01_miRNA-v1_95_May07_1_3.txt


title: H5 D2-1 638 RNA Cy3 2

source_name: RNA from lung tissue infected with VN1203, 2 dpi, animal 638

value: Day 2


title: Ovary light 24 h rep1

description: This sample is extracted from a same individual with 469376A05. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

value: Ovary


title: HB3-HBEC1_vs_HB3-Uns_Timepoint4

source_name: HB3 parasites selected on HBEC-5i (HB3-HBEC), timepoint 4


title: Ovary light 15 min rep2

description: This sample is extracted from a same individual with 469376A04. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ovary light 15 min


title: H5 D2-1 534 RNA Cy3 2

source_name: RNA from lung tissue infected with VN1203, 2 dpi, animal 534


title: HB3-HBEC1_vs_HB3-Uns_Timepoint2


title: Ovary light 15 min rep1

description: This sample is extracted from a same individual with 469376A03. This individual is mature adult of wild-type and was kept in fresh-sea water individually.


title: HB3-HBEC1_vs_HB3-Uns_Timepoint3


title: H5 D2-1 638 RNA Cy3 1


title: lox/loxFO_rep3

description: US22502553_251911910077_S01_miRNA-v1_95_May07_1_1.txt


title: H5 D2-1 534 RNA Cy3 1


title: Ovary light 0 min rep2

description: This sample is extracted from a same individual with 469376A02. This individual is mature adult of wild-type and was kept in fresh-sea water individually.

source_name: Ovary light 0 min


title: HB3-HBEC1_vs_HB3-Uns_Timepoint1