title: H4IIE_6h_ExpvsCo

city: Antwerp

first: Tine

last: Hectors

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

description: This GEO Sample represents 8 arrays (see linked supplementary files)

hyb_protocol: 825 ng of both Cy3 and Cy5 labelled cRNA were co-hybridized on a 44K Whole Rat Genome Oligo Microarray (G4131F, Agilent) for 17h at 60°C in a continuous rotation Agilent hybridization oven. Slides were subsequently washed with Agilent wash buffers and acetonitrile and finally submersed in stabilization and drying solution (Agilent Technologies, Diegem, Belgium) to prevent ozone-induced Cy5-degradation. A separate v+2 A-optimal hybridization design was used for each time-point. Using this design each exposure condition is represented by three biological replicates, with each biological replicate analysed in technical duplicate while applying the dye swap principle to correct for dye bias.

scan_protocol: Arrays were scanned at 532 and 635 nm using a Genetix Personal 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 µm. The photomultiplier tube voltage (PMT) was adjusted for each slide for the separate wavelengths to obtain an overall red/green ratio of one.

data_processing: The images were analysed using the Genepix Pro software 4.1 (Axon Instruments) for spot identification and for quantification of the fluorescent signal intensities. Statistical analysis of microarray data was performed with the R package limma. Briefly, spots for which red or green FG < BG + 2SD on all arrays were deleted before analysis (FG: medium foreground intensity; BG: average local background intensity calculated over the full microarray; SD: standard deviation of local background intensities). After background correction (backgroundCorrect, method “normexp”, offset = 50) of the median intensity data, loess normalisation (normalizeWithinArrays) was applied. Between-array normalization like vsn (variance stabilization), was not necessary because of low inter-array variability of the printed arrays. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. Exposure versus control contrasts were fitted to the linear models and considered significant if p<0.05 and ǀlog2FCǀ>0.75 (log2 fold change).

label: Cy3, Cy5

source_name: H4IIE 6h control

label_protocol: RNA was amplified and labeled using the Two-Color Microarrays-Based Gene Expression Analysis (Quick Amp Labeling) protocol from Agilent (Agilent, Diegem, Belgium). Briefly, in a first step 500 ng of total RNA was reverse transcribed using a T7 promoter primer. The resulting cDNA was immediately used for one round of amplification by T7 in vitro transcription reaction in the presence of cyanine 3 (Cy3) or cyanine 5 (Cy5) labeled cytidine triphosphate (CTP). The amplified and labeled RNA probes were purified separately with Qiagen RNeasy purification columns. Probes were verified for amplification yield and incorporation efficiency by measuring the RNA concentration at 280 nm, Cy3 incorporation at 550 nm and Cy5 incorporation at 650 nm using a Nanodrop spectrophotometer (NanoDrop Technologies, Rockland, DE, USA).

growth_protocol: H4IIE rat hepatoma cells (ATCC CRL-1548) were cultured in 25 cm2 Nunc cell culture flasks in standard growth medium (DMEM, Gibco BRL, 31885-023) supplemented with 1% non essential amino acids, 5% heat inactivated foetal bovine serum, 50 IU/mL penicillin, 50 mg/L streptomycin and phenol red as pH indicator. Cells were grown in a 37°C incubator under a 5% CO2 atmosphere and cultures were routinely verified as mycoplasma free with the PCR-based VenorTM GeM Mycoplasma Detection kit (Sigma-Aldrich, Bornem, Belgium). At 90-95% confluence, cells were detached with 0.25% tryspin/EDTA during 1 min (room temperature). Trypsin/EDTA was removed and cells were left for 5 min at 37°C. The remaining trypsin was neutralized with growth medium and cells were split 1/8 once a week, with a maximum of 30 passages. Every 3-4 days, medium was refreshed.

extract_protocol: Total RNA extracted using the Qiagen RNeasy mini kit

treatment_protocol: H4IIE cells were seeded at a density of 3 to 4 x 105 in 25 cm2 Nunc culture flasks in standard growth medium and cultured for 48h. Then, medium was replaced with serum-free growth medium to deprive cells from serum endogenous growth factors (including insulin), to reduce confounding factors and thus increase the cells’ sensitivity for insulin. After 24h, exposure to 100 nM insulin (solved in 1% glacial acetic acid solution) was started in exposure medium which consisted of serum-free high glucose (4.5 g/L) DMEM medium (Gibco, 41965-039) with standard supplements and 1% sodium pyruvate. High glucose medium was chosen to mimic the physiological situation in which insulin concentrations are high. Solvent controls were exposed to a diluted 1% glacial acetic acid solution (final concentration 0.006% glacial acetic acid). After 6h and 24h exposure, medium was removed, cells were washed with PBS (with Ca2+ and Mg2+) and RNA extraction was started

label: Cy5, Cy3

source_name: H4IIE 6h 100 nM insulin


title: snf4-del-1-a

status: Public on Jun 18 2012

type: RNA

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: refpool

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strain

tag: genetic modification

value: refpool


title: H4IIE_24h_ExpvsCo

organism: Rattus norvegicus

source_name: H4IIE 24h control

tag: cell line

source_name: H4IIE 24h 100 nM insulin


title: H596

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

country: USA

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

label: biotin

organism: Homo sapiens

source_name: Lung cancer cell line

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: RPMI 5% BFS

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

tag: cell type

value: lung cancer cell line

tag: atcc alias

tag: histology

value: Adenosquamous

tag: age

tag: race

value: Caucasian

tag: gender

value: M


title: H524

value: SCLC


title: H522

value: Adenocarcinoma


title: H460

value: Large Cell


title: H650

value: Z


title: snf3-del-1-b


title: H520

value: Squamous


title: shr5-del-3-a


title: H510


title: Control_p53-/-NOS2-/-_6

city: Bethesda

first: Ewy

last: Mathe

state: MD

address: 37 Convent Dr.

institute: National Cancer Institute/National Institutes of Health

hyb_protocol: labeled cDNA was ybridized onto the chips, and processed by direct detection of the biotin-containing transcripts by streptavidin-Alexa 647 conujugate.

scan_protocol: Slides were scanned using the Axon 4000B Scanner (Molecular Device, Inc)

data_processing: Spot intensities were quantified with Genepix (version Pro 6.0.1.00). Microarray data was processed as described in Mathe et al., Clin Cancer Res 2009 Oct 1; 15(19):6192-200

organism: Mus musculus

source_name: spleen

label_protocol: 5 ug RNA was converted to biotin-labeled first strand cDNA.

extract_protocol: total RNA was extracted from spleen using Trizol (Invitrogen, cat no. 15596-026) according to manufacturer's procedures.

tag: genotype/variation

tag: treatment

value: Control


title: Control_p53-/-NOS2-/-_5


title: Control_p53-/-NOS2-/-_4


title: Control_p53-/-NOS2-/-_3


title: sfl1-del-3-a

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: AE9a_siPRMT1_rep3

city: La Jolla

first: Dong-Er

last: Zhang

state: CA

address: 3855 Health Sciences Drive, Mail Stop 0815

department: Cancer Center

institute: University of California San Diego

description: Gene expression data from wild type K562-AE9a cells treated with siPRMT1

hyb_protocol: The Illumina hybridization protocol was used. Hybridization in HYB buffer for 18-20 hours at 58°C with gentle rocking followed by standard Illumina washes and streptavidin-Cy3 staining.

scan_protocol: Illumina BeadArray Reader was used. Green Channel with a PMT setting of 100%.

data_processing: Illumina Genome Studio Software produced raw data which was normalized using a modified LOESS.

source_name: K562-AE9a cells treated with siPRMT1

label_protocol: Biotinylated cRNA were prepared using Illumina TotalPrep RNA Amplification Kit from Ambion.

growth_protocol: Wild type or AE9a expressing K562 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum at 37°C.

extract_protocol: Qiagen RNeasy Mini column extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were nucleofected with 3 μg of siRNA (control or siPRMT1) according to manufacturer’s protocol (Lonza) and harvested after 24 hours.

tag: sirna


title: sfl1-del-3-d


title: H441


title: Control_p53-/-NOS2-/-_2


title: H345


title: sdc25-del-1-b


title: C. Parvum_p53-/-NOS2-/-_5

value: C. Parvum


title: AE9a_siPRMT1_rep2


title: H378

value: F


title: C. Parvum_p53-/-NOS2-/-_4


title: H324

value: Black


title: H358


title: Control_p53-/-NOS2-/-_1


title: AE9a_(-)siRNA_rep1

description: Gene expression data from wild type K562-AE9a cells treated with (-) control siRNA

value: (-) Control siRNA


title: C. Parvum_p53-/-NOS2-/-_6


title: AE9a_(-)siRNA_rep2

source_name: K562-AE9a cells treated with (-) control siRNA


title: sch9-del-3-b-q


title: AE9a_siPRMT1_rep1


title: AE9a_(-)siRNA_rep3


title: H290

value: Mesothelioma


title: H322


title: C. Parvum_p53-/-NOS2-/-_3


title: sch9-del-3-a-q


title: rgt2-del-1-b


title: H292

value: Muco-epidermoid carcinoma


title: sdc25-del-1-a

value: refpool


title: C. Parvum_p53-/-NOS2-/-_2


title: WT_siPRMT1_rep3

description: Gene expression data from wild type K562 cells treated with siPRMT1

value: wild type


title: C. Parvum_p53-/-NOS2-/-_1


title: rgt2-del-1-a


title: WT_siPRMT1_rep2

source_name: wild type K562 cells treated with siPRMT1


title: H289

value: lung cancer cell line


title: H226

value: Squamous Mesothelioma


title: Control_p53-/-NOS2+/+_5


title: H211


title: WT_(-)siRNA_rep3

description: Gene expression data from wild type K562 cells treated with (-) control siRNA


title: WT_siPRMT1_rep1


title: rgt1-del-1-b


title: rgt1-del-1-a


title: H209

value: Caucasian

value: M


title: Control_p53-/-NOS2+/+_4


title: Control_p53-/-NOS2+/+_1


title: Control_p53-/-NOS2+/+_2


title: WT_(-)siRNA_rep1

source_name: wild type K562 cells treated with (-) control siRNA


title: C. Parvum_p53-/-NOS2+/+_5


title: rgs2-del-1-b


title: H187

value: SCLC


title: rgs2-del-1-a


title: reg1-del-1-b


title: C. Parvum_p53-/-NOS2+/+_3


title: reg1-del-1-a


title: rce1-del-2-b


title: H157


title: C. Parvum_p53-/-NOS2+/+_2


title: H128


title: H146


title: H125

value: Adenosquamous


title: C. Parvum_p53-/-NOS2+/+_1


title: C. Parvum_p53-/-NOS2+/+_4


title: ras2-del-1-a


title: H82


title: Control_p53+/+NOS2-/-_5


title: Control_p53+/+NOS2-/-_4


title: rce1-del-2-a


title: ras2-del-1-b


title: H69


title: Control_p53+/+NOS2-/-_3


title: Control_p53+/+NOS2-/-_2


title: ras1-del-1-b

label_protocol: aminoallyl labeling v2.1.1


title: ras1-del-1-a


title: Control_p53+/+NOS2-/-_1


title: H28


title: ram1-del-3-b


title: yeast_0.4mM_H2O2_msn2/4∆∆_30min_rep4

city: Madison

first: Dana

middle: J

last: Huebert

state: WI

address: 425G Henry Mall

department: Genetics

institute: University of Wisconsin-Madison

hyb_protocol: cDNA from stressed and unstressed samples were mixed in equal mass with 2X Nimblegen Hybridization Buffer, Nimblegen Solution A and pre-labeled CPK6 alignment oligo and applied to arrays according to standard Nimblegen protocols.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to standard Nimblegen protocols.

data_processing: Data were extracted using NimbleScan. Background was calculated based on empty regions throughout the array and data probes were removed if they had signal <2X std. dev. from the average of the empty spots. The remaining probes were assigned to genes if they were fully-enclosed within the transcript boundaries and median centered at the gene level.

label: Oyster 650 cyanine dye

organism: Saccharomyces cerevisiae S288C

source_name: total RNA from S. cerevisiae

label_protocol: Indirect labelling using amino-allyl-dUTP as described in Gasch AP, Methods in Enzymology 350: 393-414

growth_protocol: yeast were grown at least 10 generations to log phase (OD600 ~0.6) in YPD at 30C

extract_protocol: Yeast were grown at least 10 generations to OD(600) ~0.6.  Total RNA was isolated from unstressed and cells treated with 0.4mM H2O2. Cell lysis and RNA extraction were performed as in Gasch AP, Methods in Enzymology 350: 393-414. cDNA synthesis was performed using both random hexamers and oligo-dT to obtain cDNA from total RNA.

value: BY4741, msn2∆msn4∆

tag: time

value: 30 min

label: Oyster 550 cyanine dye

value: 0 min (no treatment)


title: C. Parvum_p53+/+NOS2-/-_5

value: C. Parvum


title: EKVX

value: EKVX

value: Adenocarcinoma


title: yeast_0.4mM_H2O2_msn2/4∆∆_30min_rep2


title: DFCI032

value: F


title: H23

value: Black


title: DFCI024


title: C. Parvum_p53+/+NOS2-/-_4


title: ram1-del-3-a


title: pgm1-del-1-a


title: yeast_0.4mM_H2O2_msn2/4∆∆_8min

value: 8 min


title: yeast_0.4mM_H2O2_msn2/4∆∆_4min

value: 4 min


title: C. Parvum_p53+/+NOS2-/-_3


title: pgm1-del-1-b

value: refpool


title: pgm2-del-2-b


title: yeast_0.4mM_H2O2_msn2/4∆∆_30min_rep3


title: yeast_0.4mM_H2O2_msn2/4∆∆_60min

value: 60 min


title: Calu-3

value: lung cancer cell line


title: Calu-1

value: Muco-epidermoid carcinoma

value: Caucasian


title: C. Parvum_p53+/+NOS2-/-_2


title: Calu-6


title: yeast_0.4mM_H2O2_msn2/4∆∆_12min

value: 12 min


title: pfk27-del-1-b


title: Control_p53+/+NOS2+/+_5

value: Control


title: pgm2-del-2-a


title: A549

value: M


title: pfk27-del-1-a


title: yeast_0.4mM_H2O2_msn2/4∆∆_30min

value: BY4741, msn2∆msn4∆

value: 30 min


title: Control_p53+/+NOS2+/+_4


title: yeast_0.4mM_H2O2_msn2/4∆∆_16min

value: 0 min (no treatment)

value: 16 min


title: Control_p53+/+NOS2+/+_3


title: pfk2-del-3-b


title: yeast_0.4mM_H2O2_msn2/4∆∆_40min

value: 40 min


title: pfk26-del-2-a


title: pfk2-del-3-a


title: C. Parvum_p53+/+NOS2-/-_1

value: C. Parvum


title: pfk1-del-2-c1


title: yeast_0.4mM_H2O2_msn2/4∆∆_20min

value: 20 min


title: Control_p53+/+NOS2+/+_2


title: yeast_0.4mM_H2O2_wildtype_8min

value: 8 min


title: Control_p53+/+NOS2+/+_1


title: WT_(-)siRNA_rep2

value: wild type

value: (-) Control siRNA


title: yeast_0.4mM_H2O2_wildtype_4min

value: 4 min


title: mouse 3 Control shRNA

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

country: Germany

institute: Technische Universität Dresden

description: mouse strain Runx1 Δ/Δ

hyb_protocol: RNA was hybridized using the Gene Expression Hybridization Kit (Agilent) in an Agilent hybridization oven and subsequently washed with the Gene expression wash buffer kit according to the Quick Amp v5.5 protocol.

scan_protocol: Agilent Microarray Scanner

data_processing: Data was extracted using Feature Extraction v10.1 (Agilent) and analyzed with the GeneSpring Software (Agilent)

source_name: HSPCs, control shRNA, replicate 3

label_protocol: 400 ng of total RNA sample was amplified and labeled with the Agilent One-Color Microarray-Based Gene Expression Analysis v5.5 protocol (Quick Amp) (Agilent).

growth_protocol: Cells were isolated from the bone marrow (femur + tibia) of Runx1 Δ/Δ mice. Bone marrow was lineage depleted (mouse lineage depletion Kit/Miltenyi) and cultivated for 2 days in StemSpan® SFEM (STEMCELL Technologies) supplemented with 50 ng/ml mSCF, 100ng/ml hFlt3 Ligand, 100ng/ml hIL-11, and 10ng/ml mIL-3 (Peprotech).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA quantity and quality was assessed with a NanoDrop 2000 Spectrophotometer (Thermo Scientific) and by capillary gel electrophoresis using the Bioanalyzer (Agilent) and the RNA 6000 Nano Kit.

treatment_protocol: Viral supernatant was produced in Phoenix-GP packaging cells as described online (http://www.stanford.edu/-group/nolan/protocols/pro_helper_dep.html). Envelope and packaging plasmids p522 and pR690 were a kind gift from Carol Stocking. 1x10^7 cells were transfected with 18 µg pRS, 5 µg p522, and 10 µg pR690 using Lipofectamine 2000 (Invitrogen). Viral supernatant was harvested 24 h post transfection every 12 hours. For transduction, plates were coated with 50 µg/ml retronectin (TaKaRa) according to the manufacturer’s instructions. 3 ml viral supernatant was spin-occulated in the presence of 100 mM HEPES and 0.4 µg/ml polybrene (Sigma-Aldrich) onto a 6-well plate at 2000 rpm for 20 minutes. After repeating this procedure 2 or 3 times, 7.5x105 HSPCs in 1.5 ml SFEM and 1.5 ml viral supernatant with 100 mM HEPES were spin-occulated onto the virus-coated plate. Supernatant was removed after 4 hours. 24 hours post transduction, cells were selected with 5 µg/ml puromycin for 36 hours.

value: mixed C57Bl/6 and 129SvJ

value: Runx1 Δ/Δ

value: HSPCs


title: mouse 4 Pcgf1 shRNA

description: mouse strain Runx1 Δ/Δ

source_name: HSPCs, Pcgf1 shRNA, replicate 4


title: yeast_0.4mM_H2O2_wildtype_30min_rep4


title: yeast_0.4mM_H2O2_wildtype_40min


title: C. Parvum_p53+/+NOS2+/+_4


title: C. Parvum_p53+/+NOS2+/+_5


title: pfk1-del-2-c2

value: refpool


title: yeast_0.4mM_H2O2_wildtype_30min


title: mouse 4 Control shRNA

description: mouse strain Runx1 Δ/Δ

source_name: HSPCs, control shRNA, replicate 4


title: mouse 3 Pcgf1 shRNA

description: mouse strain Runx1 Δ/Δ

source_name: HSPCs, Pcgf1 shRNA, replicate 3


title: C. Parvum_p53+/+NOS2+/+_3


title: pde2-del-1-b


title: yeast_0.4mM_H2O2_wildtype_20min


title: C. Parvum_p53+/+NOS2+/+_2


title: pde2-del-1-a


title: Root Phosphate recovery, biological rep3 [At35b_MR]

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

description:
Root Phosphate recovery, biological rep3
13PR3

hyb_protocol: Hybridization and scanning of all arrays were done at the Genomics Resource Center in the Rockefeller University following the manufacturer’s instructions (Affymetrix).

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.

data_processing: Raw Signal intensity were normalized by quantile method using CisGenome software.

organism: Arabidopsis thaliana

label_protocol: The efficiency of biotin labeling was confirmed by Gel-shift assay with NeutrAvidin (Pierce) as described in Genechip Whole transcript (WT) double-stranded target assay manual (Affymetrix).

growth_protocol: Non-sterile WT (Col-0) seeds were sowed on rock wool (Grodan Inc.) pre-soaked in basal MGRL hydroponic media24 and cold-treated at 4C for 3 days. Plants were grown at 22°C under 150 μmol m-2 S-1 fluence rate and a 12hr:12hr light:dark cycle. To minimize environmental variation, plants were rotated in growth chambers once a day.

extract_protocol: Total RNAs extracted by RNA easy extraction kit (Qiagen) were used for Arabidopsis Genechip ATH1

treatment_protocol: In phosphate depleted media, 1.75 mM MES (pH 5.8) was used instead of 1.75 mM sodium phosphate (pH 5.8). All hydroponic media were aerated to maximize air supply during hydroponic culture. All plants were grown in basal MGRL hydroponic media for 20 days before being transferred to a phosphate-deficient medium. During the 10-day treatment, the phosphate-deficient medium was replaced every three days. For recovery experiments, plants previously grown in phosphate-deficient medium for 10 days were transferred to full-strength MGRL medium for an additional 3 days. Samples were collected on the 10th and 13th (10+3) day. Phosphate-starved shoot and root samples were collected separately at the indicated time point. Furthermore, all experiment procedures such as media replacement and sample collection were performed in the middle of day in order to minimize possible circadian effect. In parallel, control plants were grown in a full-strength MGRL media before sample collection on the 10th day after the initial 20-day growth period.

tag: ecotype

tag: organ

value: root

value: Recovery, 10-day Phosphate starvation then transferred to full-strength MGRL medium for 3 days

value: 33 days


title: mouse 2 Pcgf1 shRNA

description: mouse strain Runx1 Δ/Δ

source_name: HSPCs, Pcgf1 shRNA, replicate 2


title: pde1-del-1-b


title: Root Phosphate recovery, biological rep1 [At35b_MR]

description:
Root Phosphate recovery, biological rep1
13PR1


title: C. Parvum_p53+/+NOS2+/+_1


title: mouse 2 Control shRNA

description: mouse strain Runx1 Δ/Δ

source_name: HSPCs, control shRNA, replicate 2


title: Root Phosphate starvation, biological rep3 [At35b_MR]

description:
Root Phosphate starvation, biological rep3
10PR3

value: P_starvation, 10-day Phosphate starvation

value: 30 days


title: mouse 1 Pcgf1 shRNA

description: mouse strain Runx1 Δ/Δ

source_name: HSPCs, Pcgf1 shRNA, replicate 1


title: mouse 1 Control shRNA

description: mouse strain Runx1 Δ/Δ

source_name: HSPCs, control shRNA, replicate 1


title: nth2-del-1-a

source_name: refpool


title: yeast_0.4mM_H2O2_wildtype_16min

value: 16 min

value: 0 min (no treatment)


title: nth1-del-2-a


title: pde1-del-1-a


title: yeast_0.4mM_H2O2_wildtype_30min_rep3

value: 30 min


title: muc1-del-1-b


title: nth2-del-1-b


title: Root Phosphate starvation, biological rep1 [At35b_MR]

description:
Root Phosphate starvation, biological rep1
10PR1


title: nth1-del-2-b


title: yeast_0.4mM_H2O2_wildtype_60min

value: 60 min


title: yeast_0.4mM_H2O2_wildtype_12min

value: 12 min


title: muc1-del-1-a


title: Root Mock, biological rep3 [At35b_MR]

description:
Root Mock, biological rep3
10MR3

source_name: Root Mock, biological rep3

value: Mock, 10-day full-strength MGRL medium


title: Root Mock, biological rep2 [At35b_MR]

description:
Root Mock, biological rep2
10MR2

source_name: Root Mock, biological rep2


title: Root Phosphate starvation, biological rep2 [At35b_MR]

description:
Root Phosphate starvation, biological rep2
10PR2


title: mth1-del-2-b


title: mth1-del-2-a


title: yeast_0.4mM_H2O2_wildtype_30min_rep2


title: Shoot Phosphate recovery, biological rep2 [At35b_MR]

description:
Shoot Phosphate recovery, biological rep2
13PL2

value: shoot


title: Msn2p_yeast_0.4mM_H2O2_40min

type: genomic

hyb_protocol: DNA from ChIP and Whole Cell Extract samples were mixed in equal mass with 2X Nimblegen Hybridization Buffer, Nimblegen Solution A and pre-labeled CPK6 alignment oligo and applied to arrays according to standard Nimblegen protocols.

data_processing: Data were extracted using NimbleScan. Background was calculated based on empty regions throughout the array and data probes were removed if they had signal <2X std. dev. from the average of the empty spots.  The remaining data were normalized by median centering at the probe level.

molecule: genomic DNA

source_name: Msn2Myc ChIP from S. cerevisiae

label_protocol: Indirect labelling using amino-allyl-dUTP as described in Gasch AP, Methods in Enzymology 350:393-415.

extract_protocol: Yeast were grown at least 10 generations to OD(600) ~0.6.  Unstressed and cells treated with 0.4mM H2O2 were cross-lined with 1% formaldehyde for 30 minutes at 25C and quenched with 125mM glycine for 5 minutes at 25C. Lysate was sonicated to produce chromatin fragments ~250-300bp in length. An aliquot was retained as Whole Cell Extract and an additional 1-2.5mg of protein was incubated with 5ul anti-c-Myc antibody (9E11, Abcam) overnight at 4C. Samples were amplified by the Ligation-mediated PCR method.

value: integrated Msn2-Myc construct

value: 40 min

tag: antibody

value: anti-c-Myc

source_name: Input DNA from S. cerevisiae

value: none, input DNA


title: Msn2p_yeast_0.4mM_H2O2_60min


title: Msn2p_yeast_0.4mM_H2O2_12min


title: Shoot Phosphate recovery, biological rep3 [At35b_MR]

description:
Shoot Phosphate recovery, biological rep3
13PL3


title: mig2-del-3-b

value: refpool


title: mig2-del-3-a


title: Shoot Phosphate recovery, biological rep1 [At35b_MR]

description:
Shoot Phosphate recovery, biological rep1
13PL1


title: Msn2p_yeast_0.4mM_H2O2_20min

value: 20 min


title: maf1-del-1-b-a


title: Melanoma primary lesion

city: Vienna

first: Mario

last: Mikula

address: Waehringergürtel 18-20

department: General Dermatology

country: Austria

institute: Medical University Vienna

description:
Hybridized to SNP6.0
Patient_prim.chp
Patient_prim.CEL

hyb_protocol: According to manufacturer protocol

scan_protocol: According to manufacturer protocol

data_processing: CEL files were processed via the genotyping console 3.0.1 using default parameters. CHP files were generated via the genotyping console 3.0.1 using default parameters. Normalization was performed using the birdseed v2 algorithm.

label: Biotin

source_name: Melanoma lesion

label_protocol: According to manufacturer protocol Affymetrix dsDNA terminal label

extract_protocol: DNA was isolated by using the All Prep DNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

tag: tumor

value: patient-derived melanoma lesion


title: Root Phosphate recovery, biological rep2 [At35b_MR]

description:
Root Phosphate recovery, biological rep2
13PR2

value: root

value: Recovery, 10-day Phosphate starvation then transferred to full-strength MGRL medium for 3 days

value: 33 days


title: OPNM_0407_9-Organpipe-Rep1

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_9, replicate 1.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila mojavensis

source_name: OPNM_0407_9, organpipe

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

extract_protocol: Total RNA extraction was performed using Invitrogen’s PureLink Micro-to-Midi Total Purification System. The suggested manufacturer’s instructions were followed, which included a DNase I digestion to remove any possible genomic DNA contamination. The quality and concentration of the RNA was determined using a NanoDrop spectrophotometer (NanoDrop Technologies).

treatment_protocol: The nine D. mojavensis lines were reared in either necrotic organpipe or agria cactus. The cactus necroses were created using natural microflora. The procedure for creating the lab necroses followed that of Matzkin et al. 2006 (PMID 17107489).

tag: host race

value: mainland Sonoran

tag: line

tag: tissue

value: larvae

tag: developmental stage

value: third instar

tag: cactus host treatment

value: organpipe


title: mig1-del-2-b

tag: strain

tag: genetic modification


title: Msn2p_yeast_0.4mM_H2O2_4min

value: 4 min


title: OPNM_0407_9-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_9, replicate 2.


title: OPNM_0407_9-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_9, replicate 1.

source_name: OPNM_0407_9, agria

value: agria


title: OPNM_0407_9-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_9, replicate 2.


title: mig1-del-2-a


title: Msn2p_yeast_0.4mM_H2O2_0min

value: 0 min


title: Shoot Phosphate starvation, biological rep2 [At35b_MR]

description:
Shoot Phosphate starvation, biological rep2
10PL2

value: shoot

value: P_starvation, 10-day Phosphate starvation

tag: age

value: 30 days


title: Shoot Phosphate starvation, biological rep1 [At35b_MR]

description:
Shoot Phosphate starvation, biological rep1
10PL1


title: MNase_yeast_0.4mM_H2O2_wildtype_20min-rep2

hyb_protocol: DNA from Nucleosomal and gDNA samples were mixed in equal mass with 2X Nimblegen Hybridization Buffer, Nimblegen Solution A and pre-labeled CPK6 alignment oligo and applied to arrays according to standard Nimblegen protocols.

data_processing: Data were extracted using NimbleScan. Background was calculated based on empty regions throughout the array and data probes were removed if they had signal <2X std. dev. from the average of the empty spots. The remaining data was quantile normalized using Bioconductor.

source_name: Nucleosomes from S. cerevisiae

extract_protocol: Yeast were grown at least 10 generations to OD(600) ~0.6.  Unstressed and cells treated with 0.4mM H2O2 were treated with formaldehyde (1%) for 15 minutes at 25C and quenched with 125mM glycine. Cells were digested to spheroplasts with Zymolyase and treated with micrococcal nuclease for 20 minutes at 37C. DNA was purified and amplified using the In vitro transcription method as described in Liu et al (PLoS Biol, 2005).

source_name: Sheared genomic DNA from S. cerevisiae


title: krh2-del-1-b


title: maf1-del-1-b


title: OPNM_0407_8-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_8, replicate 1.

source_name: OPNM_0407_8, organpipe


title: OPNM_0407_8-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_8, replicate 2.


title: rice seedling exposed to Pi-deficient solution for 72 hours, biological rep2

city: Beijing

first: xiaoyan

last: dai

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, the Chinese Academy of Sciences

description: All the processes for cDNA and cRNA synthesis, cRNA fragmentation, hybridization, washing and staining, and scanning, were conducted according to the GeneChip Standard Protocol (Eukaryotic Target Preparation, Affymetrix).

hyb_protocol: According to the GeneChip Standard Protocol (Eukaryotic Target Preparation, Affymetrix).

data_processing: GCOS software (Affymetrix GeneChip Operating Software) was used for data collection and MAS5 normalization. The overall intensity of all arrays was equivalent, each probe set is assigned with “P”,“A”,“M”and p-value from algorithm in GCOS.

organism: Oryza sativa Japonica Group

label_protocol: For Affymetrix GeneChip analysis, 8 μg of total RNA was used for making biotin-labeled cRNA target.

extract_protocol: Total RNA was isolated from two independent treated plants and nontreated plants with the RNA extraction kit (TRizol reagent; Invitrogen).

treatment_protocol: Rice seedlings were exposed to low phosphate for 6h, 24h, 48h and 72 h, respectively.

tag: cultivar

value: Zhonghua 10

value: seedlings


title: MNase_yeast_0.4mM_H2O2_msn24_20min

value: BY4741 msn2∆msn4∆

value: 20 min


title: Shoot Mock, biological rep3 [At35b_MR]

description:
Shoot Mock, biological rep3
10ML3

source_name: Shoot Mock, biological rep3

value: Mock, 10-day full-strength MGRL medium


title: Shoot Phosphate starvation, biological rep3 [At35b_MR]

description:
Shoot Phosphate starvation, biological rep3
10PL3


title: Shoot Mock, biological rep2 [At35b_MR]

description:
Shoot Mock, biological rep2
10ML2

source_name: Shoot Mock, biological rep2


title: Root Mock, biological rep1 [At35b_MR]

description:
Root Mock, biological rep1
10MR1

source_name: Root Mock, biological rep1

value: root


title: Shoot Mock, biological rep1 [At35b_MR]

description:
Shoot Mock, biological rep1
10ML1

source_name: Shoot Mock, biological rep1


title: MNase_yeast_0.4mM_H2O2_wildtype_20min


title: MNase_yeast_0.4mM_H2O2_wildtype_0min-rep2


title: MNase_yeast_0.4mM_H2O2_msn24_0min


title: OPNM_0407_8-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_8, replicate 2.

source_name: OPNM_0407_8, agria


title: OPNM_0407_30-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_30, replicate 1.

source_name: OPNM_0407_30, agria


title: krh1-del-1-a

source_name: refpool

value: refpool


title: rice seedling exposed to Pi-deficient solution for 48 hours, biological rep1

scan_protocol: According to the GeneChip Standard Protocol (Eukaryotic Target Preparation, Affymetrix).


title: krh2-del-1-a


title: rice seedling exposed to Pi-deficient solution for 72 hours, biological rep1


title: rice seedling exposed to Pi-deficient solution for 24 hours, biological rep2


title: hxk2-del-1-b


title: OPNM_0407_8-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_8, replicate 1.

value: mainland Sonoran


title: rice seedling exposed to Pi-deficient solution for 48 hours, biological rep2


title: rice seedling exposed to Pi-deficient solution for 6 hours, biological rep2


title: ira1-del-1-b


title: ira2-del-4-b


title: OPNM_0407_2-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_2, replicate 1.

source_name: OPNM_0407_2, organpipe

value: larvae


title: Biofilm_Chronic stress_rep3

city: Heverle

first: Tekle Tafese

last: Fida

address: Kastelpark Arenberg 220

department: Earth and environmental Science

institute: KU Leuven

description: gene expression in Chronic stressed biofilm

hyb_protocol: Sixty nanograms of labeled cDNA with an incorporation efficiency of cyanine-3-labeled dCTP between 3-5.9% were used for microarray analysis. The cDNA was hybridized with the array for 17 h at 65oC, washed, and scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

scan_protocol: The Agilent Feature Extraction software package (version 9.5.3; Agilent Technologies) was used to extract the hybridization signal intensities from the images scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

data_processing: Normalization of the signal intensities (Quantile normalization) and analysis of the data were done using the Genespring GX software package (version 11, Agilent technologies). Normalized signals of the probe names are combined/averaged signals based on raw data from duplicate probes, a and b (Note: some probes are also not present in duplicate). To test for significantly differentially expressed genes, Welch’s t- test with unequal variances was first used to calculate p-values. The Benjamini and Hochberg procedure was then used to correct the p-vales for multiple hypothesis testing and convert the p-vales into false discovery rates (FDRs)

organism: Sphingomonas sp. LH128

source_name: chronic  solute stress_3 day _replicate3

label_protocol: The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript II reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 42oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer

growth_protocol: Cells were grown as biofilm in flow chambers

extract_protocol: Biofilm cells together with the phenanthrene crystals were scraped off from the glass slides using a sterile scalpel blade while flushing with 2 ml of MM containing 1 ml of RNAprotect Bacteria Reagent (Qiagen, Benelux BV). RNA was immediately extracted using the Promega SV total RNA extraction kit (Promega, Benelux BV) with minor modifications of the protocol (centrifugation was performed at 17,000 x g instead of 14,000 x g and 200 µl of Tris-EDTA containing Lysozyme was used instead of 100 µl). The RNA was eluted with 80 µl of RNase free water and precipitated to the required concentration after adding 0.1 volume of 3 M sodium acetate and 2 volumes of 100% ethanol. Traces of remaining DNA were removed by using the TURBO DNA-free kit (Ambion).

treatment_protocol: LH128 biofilms were grown in customized glass flow chambers equipped with one inlet and three outlets.  Biofilms were grown at 25oC for a total of 11 days. Solute stress was imposed by irrigating the flow chambers with MM containing 450 mM NaCl at a rate of 15 ml/h from day 8 for a period of 3 days (chronic stress) or at day 11 for 4 h (acute stress). Simultaneously, control biofilms without stress were operated continuously

tag: mode of growth

value: Biofilm

tag: stress

value: Chronic solute stress


title: Biofilm_Chronic stress_rep1

source_name: chronic  solute stress_3 day _replicate1


title: rice seedling exposed to Pi-deficient solution for 6 hours, biological rep1


title: Biofilm_Chronic stress_rep2

source_name: chronic  solute stress_3 day _replicate2


title: Biofilm_Acute stress_rep2

description: gene expression in acute stressed biofilm

source_name: acute solute stress_4h _replicate2

value: Acute solute stress


title: ira1-del-1-a


title: krh1-del-1-b


title: OPNM_0407_30-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_30, replicate 2.

value: third instar

value: agria


title: hxk2-del-1-a


title: Biofilm_Acute stress_rep3

source_name: acute solute stress_4h _replicate3


title: rice seedling exposed to Pi-deficient solution for 24 hours, biological rep1


title: Biofilm_Acute stress_rep1

source_name: acute solute stress_4h _replicate1


title: ira2-del-4-a


title: OPNM_0407_30-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_30, replicate 2.

source_name: OPNM_0407_30, organpipe

value: organpipe


title: rice seedling grown under Pi-sufficient condition, biological rep1


title: Biofilm_none stressed_rep3

description: gene expression in none stressed biofilm

source_name: control_Biofilm_ replicate3

value: Control


title: OPNM_0407_2-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_2, replicate 1.

source_name: OPNM_0407_2, agria


title: hxk1-del-1-b


title: OPNM_0407_2-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_2, replicate 2.


title: E. coli strain 86-24 grown with ethanolamine

first: Melissa

middle: M

last: Kendall

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: U.T. Southwestern Medical Center at Dallas

hyb_protocol: All protocols were done according to manufacturer's specifications (http://www.affymetrix.com/support/index.affx)

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli

source_name: Wild type + ethanolamine

extract_protocol: Ambion RiboPure RNA Isolation

value: EHEC 8624 wild-type


title: OPNM_0407_29-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_29, replicate 2.

source_name: OPNM_0407_29, organpipe


title: OPNM_0407_2-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_2, replicate 2.


title: rice seedling grown under Pi-sufficient condition, biological rep2

value: Zhonghua 10


title: OPNM_0407_30-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_30, replicate 1.


title: E. coli strain 86-24

scan_protocol: All protocols were done according to manufacturer's specifications

source_name: Wild type


title: hxk1-del-1-a


title: Biofilm_none stressed_rep2

source_name: control_Biofilm_ replicate2


title: Biofilm_none stressed_rep1

source_name: control_Biofilm_ replicate1


title: hsp12-del-1-b


title: hap4-del-1-b


title: hsp12-del-1-a


title: GLBRCE1_ACSH_anaerobic_Sta_72hr_biorep2

first: Michael

middle: S

last: Schwalbach

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

description: Gene Expression Data

hyb_protocol: Hybridization was performed following manufacturer's instructions.

scan_protocol: Array scanning was performed following manufacturer's instructions using a NimbleGen MS 200 Microarray Scanner. Probe intensities were determined using software package NimbleScan v2.6 (Roche Nimblegen).

data_processing:
Probe signal intensities were pre-processed using robust multichip averaging (RMA) in the program ArrayStar (DNASTAR) and the resulting summarized gene expression signals were quantile-normalized across all samples using the software package R.  Bioreplicates in the normalized dataset were screened for a high degree of similarity (Pearson Coefficient > 0.95) and dissimilar arrays were omitted from subsequent analyses.  Average gene expression values were then determined within identified growth phases (i.e. exponential, transition and stationary phase) in each media. Significant expression changes were assigned to genes exhibiting a ≥ 2-fold change in signal intensity and a Benjamini-Hochberg adjusted Student’s t-test p-value < 0.05 between selected pairwise comparisons of the means.
Arrays were processed using the following software packages: NimbleScan v2.6, ArrayStar (DNASTAR), Microsoft Office-Excel and the statistical package R.

source_name: E.coli GLBRCE1, ACSH, anaerobic, stationary phase_late

label_protocol: cDNA was generated using SuperScript Double Stranded cDNA Synthesis reagents (Invitrogen).  Labeling was performed following manufacturer's instructions.

growth_protocol: GLBRCE1 cells were cultivated in Applikon fermentors using the following conditions: sparge rate with 95% N2, 5% CO2: 150cc/min, Temperature: 37 Celsius, Stir Speed: constant 300 rpm, pH: media pH was maintained at pH7 using automated addition of 10M NaOH.

extract_protocol: Total RNA was extracted using the hot SDS:phenol:ethanol extraction protocol described by Rhodius, V.A. and C.A. Gross. 2011. Using DNA microarrays to assay part function. Methods Enzymol 497: 75-113.

treatment_protocol: Cells (10ml) were collected for transcriptomic samples as follows:  RNA was stabilized using Ethanol:Phenol (95:5% v/v) (E:P) stop solution, Cell pellets were collected via centrifugation (10,000 x g, 3 min), washed twice with GMM media containing E:P stop solution, flash frozen in a dry ice: ethanol bath then stored at -80 Celsius prior to extraction.

tag: time point

tag: genotype/variation

value: E.coli K-12 MG1655 background ldhA-, ackA-, pflB::PET, pJGG2


title: OPNM_0407_29-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_29, replicate 1.


title: GLBRCE1_ACSH_anaerobic_Sta_22hr_biorep2

description: Gene Expression Data

source_name: E.coli GLBRCE1, ACSH, anaerobic, stationary phase


title: GLBRCE1_ACSH_anaerobic_Sta_28hr_biorep2

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Sta_52hr_biorep2

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Tran_16hr_biorep2

description: Gene Expression Data

source_name: E.coli GLBRCE1, ACSH, anaerobic, transition phase


title: OPNM_0407_29-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_29, replicate 1.

source_name: OPNM_0407_29, agria


title: MNase_yeast_0.4mM_H2O2_wildtype_0min

source_name: Nucleosomes from S. cerevisiae

tag: time

value: 0 min

source_name: Sheared genomic DNA from S. cerevisiae


title: OPNM_0407_29-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_29, replicate 2.


title: GLBRCE1_ACSH_anaerobic_Tran_12hr_biorep2

description: Gene Expression Data


title: hap3-del-1-a

source_name: refpool


title: hap3-del-1-b


title: OPNM_0407_26-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_26, replicate 2.

source_name: OPNM_0407_26, organpipe


title: hap4-del-1-a


title: hap2-del-3-a


title: hap2-del-3-b


title: OPNM_0407_26-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_26, replicate 1.


title: OPNM_0407_26-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_26, replicate 1.

source_name: OPNM_0407_26, agria


title: OPNM_0407_26-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_26, replicate 2.


title: OPNM_0407_25-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_25, replicate 1.

source_name: OPNM_0407_25, organpipe


title: OPNM_0407_25-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_25, replicate 2.


title: GLBRCE1_ACSH_anaerobic_Tran_14hr_biorep2

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Tran_8hr_biorep2

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Exp_6hr_biorep2

description: Gene Expression Data

source_name: E.coli GLBRCE1, ACSH, anaerobic, exponential phase


title: GLBRCE1_ACSH_anaerobic_Exp_3hr_biorep2

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Sta_72hr_biorep1

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Exp_5hr_biorep2

description: Gene Expression Data


title: gsy2-del-1-a


title: OPNM_0407_25-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_25, replicate 2.

source_name: OPNM_0407_25, agria


title: gsy2-del-1-b


title: grr1-del-3-b


title: gsy1-del-1-b


title: Melanoma cell line

description:
Hybridized to SNP6.0
MCM1_cellline.chp
MCM1_cellline.CEL

source_name: Melanoma cell line MCM1

value: Melanoma cell line MCM1 derived from melanoma lesion


title: OPNM_0407_25-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_25, replicate 1.


title: OPNM_0407_21-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_21, replicate 2.

source_name: OPNM_0407_21, agria


title: gsy1-del-1-a


title: T-REx293-NPAP1-induced-3

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description: Gene expression data from cell line T-REx293-NPAP1, 24 h after induced expression of the integrated NPAP1 gene, technical replicate 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Human Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 wit G7 update

data_processing: The data were analyzed with RMA default setting in Partek GS

source_name: Flp-In™ T-REx™ 293

label_protocol: Amplified cDNA was prepared according to the Ambion WT Expression Kit protocol starting from 200 ng total RNA. Amplified cDNA was fragmented with UDG and APE1 and finally labelled using the Affymetrix WT terminal labelling kit

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% FCS, 1% penstrep and appropriate concentration of selective antibiotics

extract_protocol: RNA was extracted using the RNeasy mini kit (QIAGEN), treated with DNase I, followed by cleaning-up on spin columns (RNeasy mini kit. Qiagen)

treatment_protocol: 1 µg/ml doxycycline was used to induce expression of the integrated NPAP1 copy.

tag: cell line

value: HEK293 cells

tag: transgene

tag: treatment

value: induced


title: grr1-del-3-a

extract_protocol: yeast RNA isolation for robotic amplification v1.0

value: refpool


title: GLBRCE1_ACSH_anaerobic_Sta_52hr_biorep1

description: Gene Expression Data


title: T-REx293-NPAP1-uninduced-3

description: Gene expression data from cell line T-REx293-NPAP1, not induced, technical replicate 3

treatment_protocol: Cells were mock treated (H2O)

value: uninduced


title: gpr1-del-1-a


title: T-REx293-NPAP1-uninduced-1

description: Gene expression data from cell line T-REx293-NPAP1, not induced, technical replicate 1


title: OPNM_0407_21-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_21, replicate 1.

source_name: OPNM_0407_21, organpipe

tag: host race

value: mainland Sonoran

value: larvae


title: gpr1-del-1-b


title: T-REx293-NPAP1-uninduced-2

description: Gene expression data from cell line T-REx293-NPAP1, not induced, technical replicate 2


title: T-REx293-NPAP1-induced-2

description: Gene expression data from cell line T-REx293-NPAP1, 24 h after induced expression of the integrated NPAP1 gene, technical replicate 2


title: gph1-del-1-b


title: T-REx293-NPAP1-induced-1

description: Gene expression data from cell line T-REx293-NPAP1, 24 h after induced expression of the integrated NPAP1 gene, technical replicate 1

treatment_protocol: 1 µg/ml doxycycline or mock (H2O) was used to induce expression of the integrated NPAP1 copy.


title: OPNM_0407_10-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_10, replicate 2.

source_name: OPNM_0407_10, organpipe

tag: line


title: OPNM_0407_21-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_21, replicate 1.

tag: tissue


title: GLBRCE1_ACSH_anaerobic_Sta_22hr_biorep1

description: Gene Expression Data


title: OPNM_0407_10-Organpipe-Rep1

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_10, replicate 1.

tag: developmental stage


title: GLBRCE1_ACSH_anaerobic_Sta_28hr_biorep1

description: Gene Expression Data


title: MCM1DLN rep4

description: MCM1 clone D lymph node metastatic

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturer instructions

scan_protocol: Affymetrix protocol

data_processing: RMA

source_name: MCM1 clone D lymph node metastatic

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: primary tumor tissue was resected from SCID mice

extract_protocol: The RNeasy Mini Kit (Qiagen) was used for the isolation of total RNA from primary tumors, which were intradermally grafted to C.B. 17 SCID mice and reached 300 mg of weight.

treatment_protocol: not applicable

tag: group

value: lymphangiogenic and very metastatic MCM1DLN


title: OPNM_0407_21-Organpipe-Rep2

description: Expression of third instar larvae reared in necrotic organpipe. Isofemale line OPNM_0407_21, replicate 2.

tag: cactus host treatment


title: OPNM_0407_10-Agria-Rep2

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_10, replicate 2.

source_name: OPNM_0407_10, agria


title: GLBRCE1_ACSH_anaerobic_Tran_16hr_biorep1

description: Gene Expression Data

source_name: E.coli GLBRCE1, ACSH, anaerobic, transition phase

tag: strain


title: gph1-del-1-a

hyb_protocol: Tecan HS4800 hybridization

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.

tag: genetic modification


title: GLBRCE1_ACSH_anaerobic_Tran_14hr_biorep1

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Tran_10hr_biorep1

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Tran_12hr_biorep1

description: Gene Expression Data


title: MCM1DLN rep3

description: MCM1 clone D lymph node metastatic


title: gpg1-del-1-b


title: gpg1-del-1-a


title: OPNM_0407_10-Agria-Rep1

description: Expression of third instar larvae reared in necrotic agria. Isofemale line OPNM_0407_10, replicate 1.


title: gpa2-del-1-a


title: GLBRCE1_ACSH_anaerobic_Tran_8hr_biorep1

description: Gene Expression Data


title: MCM1DLN rep2

description: MCM1 clone D lymph node metastatic


title: YFP-pos GMP Dicer wt rep1

city: Rotterdam

first: Stefan

last: Erkeland

address: Dr. Molewaterplein 50

department: Hematology

institute: ErasmusMC

description:
C57BL/6, Female, bonemarrow, GMPs
Dicer wild type

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol, Affymetrix 7G

data_processing: Microarray data were normalized with Affymetrix Microarray Suite (MAS 5.0)

source_name: YFP-pos GMPs

label_protocol: standard Affymetrix protocol, eukaryotic Target Labeling Assay

extract_protocol: EYFP positive GMPs were sorted into RLT buffer (Qiagen, Venlo, the Netherlands). RNA was extracted with the RNeasy Micro Kit (Qiagen).

tag: genetic background

value: Cebpa-Cre;R26-LSL-Eyfp;Dicer1wt/fl/Dicer1fl/fl (donror), C57BL/6 (recipient)

tag: genotype

value: Dicer wild type

tag: cell type

value: YFP-positive  granulocyte-macrophage progenitor


title: MCM1D rep2

description: MCM1 clone D

source_name: MCM1 clone D

value: lymphangiogenic MCM1D


title: gpa2-del-1-b

label_protocol: robot amplification and labeling v1.0


title: GLBRCE1_ACSH_anaerobic_Exp_6hr_biorep1

description: Gene Expression Data

tag: time point


title: GLBRCE1_ACSH_anaerobic_Exp_5hr_biorep1

description: Gene Expression Data

tag: genotype/variation


title: glg2-del-1-b


title: YFP-pos GMP Dicer het rep2

description:
C57BL/6, Female, bonemarrow, GMPs
Dicer heterozygous deletion

value: Dicer heterozygous deletion


title: GLBRCE1_ACSH_anaerobic_Tran_10hr_biorep2

description: Gene Expression Data


title: YFP-pos GMP Dicer wt rep2


title: YFP-pos GMP Dicer wt rep3


title: MCM1DLN rep1

description: MCM1 clone D lymph node metastatic


title: glg2-del-1-a


title: GLBRCE1_SynH_anaerobic_Sta_biorep2

description: Gene Expression Data

source_name: E.coli GLBRCE1, SynH, anaerobic, stationary phase


title: GLBRCE1_SynH_anaerobic_Sta_biorep1

description: Gene Expression Data


title: GLBRCE1_ACSH_anaerobic_Exp_3hr_biorep1

description: Gene Expression Data


title: glg1-del-1-a

source_name: refpool


title: GLBRCE1_SynH_anaerobic_Tran_biorep3

description: Gene Expression Data

source_name: E.coli GLBRCE1, SynH, anaerobic, transition phase


title: YFP-pos GMP Dicer het rep3


title: MCM1G rep2

description: MCM1 clone G

source_name: MCM1 clone G

value: nonlymphangiogenic MCM1G


title: GLBRCE1_SynH_anaerobic_Tran_biorep2

description: Gene Expression Data


title: glg1-del-1-b


title: glk1-del-1-b


title: MCM1 rep4

description: MCM1 pool

source_name: MCM1 pool

value: parental pool MCM1


title: MCM1G rep4

description: MCM1 clone G


title: MCM1G rep1

description: MCM1 clone G


title: MCM1D rep1

description: MCM1 clone D


title: SI3, 2 wks on a HF-OO diet

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
Pooled total RNA sample of 6 mice.
SI3_wk2_HF-OO

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

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data analysis was performed in Bioconductor using the MAS5 algorithm. The mean target intensity of each array was set to 100.

source_name: SI3 after 2 wks on a HF-OO diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (described in the eukaryotic section in the GeneChip Expression Analysis Technical Manual Rev. 3 from Affymetrix).

growth_protocol: Male C57BL/6J mice were purchased from Harlan (Horst, The Netherlands) and were housed in the light- and temperature-controlled animal facility of Wageningen University. They had free access to water and prior to the diet intervention they received standard laboratory chow.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer’s instructions. The isolated RNA was further column-purified using the SV total RNA isolation system (Promega, Leiden, The Netherlands). RNA concentration was measured on a NanoDrop ND-1000 UV-Vis spectrophotometer (Isogen, Maarssen, The Netherlands) and analyzed on a bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. For each part of small intestine, total RNA was pooled per diet group (n=6).

treatment_protocol: Nine-week-old C57Bl/6J mice were fed a low-fat diet (LF-PO) and three different types of high-fat diet, based on palm oil (HF-PO; P/S1.0), olive oil (HF-OO; P/S4.6) and safflower oil (HF-SO; P/S10.1) for 8 weeks.

tag: gender

value: male

value: small intestine, SI 3

tag: dietary fat type

value: olive oil

tag: age

value: 9wks old at start of diet intervention

tag: diet intervention time


title: gcr2-del-1-a

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction


title: YFP-pos GMP Dicer null rep2

description:
C57BL/6, Female, bonemarrow, GMPs
Dicer null

value: Dicer null


title: YFP-pos GMP Dicer null rep3


title: MCM1 rep2

description: MCM1 pool


title: MCM1G rep3

description: MCM1 clone G


title: gal83-del-1-b

value: refpool


title: SI3, 2 wks on a HF-SO diet

description:
Pooled total RNA sample of 6 mice.
SI3_wk2_HF-SO

source_name: SI3 after 2 wks on a HF-SO diet

value: safflower oil


title: MCM1 rep1

description: MCM1 pool


title: YFP-pos GMP Dicer het rep1


title: YFP-pos GMP Dicer null rep1


title: glk1-del-1-a


title: SI3, 2 wks on a HF-PO diet

description:
Pooled total RNA sample of 6 mice.
SI3_wk2_HF-PO

source_name: SI3 after 2 wks on a HF-PO diet

value: palm oil


title: gal83-del-1-a


title: GLBRCE1_GMM_anaerobic_Exp_biorep2

description: Gene Expression Data

source_name: E.coli GLBRCE1, GMM, anaerobic, exponential phase

value: E.coli K-12 MG1655 background ldhA-, ackA-, pflB::PET, pJGG2


title: fbp1-del-2-b


title: GLBRCE1_GMM_anaerobic_Exp_biorep1

description: Gene Expression Data


title: 2C::tomato+, WT-1

first: Todd

last: Macfarlan

address: 10010 North Torrey Pines

institute: The Salk Institute

description: Replicate 1

hyb_protocol: 25ng/ul sense DNA was hybed at 45 degrees C, washed with Affy fluidics station 4500

scan_protocol: Affymetrix 300 7G scanner

data_processing: RMA using Expression Console

source_name: 2C::tomato+, WT-1

label_protocol: Labeling was perfomred with 100ng total RNA using Whole Transcript Sense target labeling kit (Affymetrix)

growth_protocol: ES cells were passaged on gelatin in ES-KOSR media

extract_protocol: RNA was prepared using Qiagen Rneasy kit with on-column DNAse digestion

treatment_protocol: Cells were treated with vehicle or 4OHT to delete Kdm1a, and 2C::tomato+ and - cells were collected using FACS.

tag: cell line

value: ES cells


title: fbp1-del-2-a

first: Patrick

last: Kemmeren

address: Universiteitsweg 100


title: MCM1D rep4

description: MCM1 clone D


title: MCM1D rep3

description: MCM1 clone D


title: SI2, 2 wks on a HF-PO diet

description:
Pooled total RNA sample of 6 mice.
SI2_wk2_HF-PO

source_name: SI2 after 2 wks on a HF-PO diet

value: small intestine, SI 2


title: erf2-del-1-b


title: GLBRCE1_GMM_anaerobic_Exp_biorep3

description: Gene Expression Data


title: GLBRCE1_GMM_anaerobic_Sta_biorep2

description: Gene Expression Data

source_name: E.coli GLBRCE1, GMM, anaerobic, stationary phase


title: GLBRCE1_GMM_anaerobic_Sta_biorep1

description: Gene Expression Data


title: 2C::tomato+, WT-3

description: Replicate 3

source_name: 2C::tomato+, WT-3


title: GLBRCE1_SynH_anaerobic_Exp_biorep1

description: Gene Expression Data

source_name: E.coli GLBRCE1, SynH, anaerobic, exponential phase


title: GLBRCE1_SynH_anaerobic_Exp_biorep2

description: Gene Expression Data


title: erf2-del-1-a


title: GLBRCE1_SynH_anaerobic_Tran_biorep1

description: Gene Expression Data


title: MCM1 rep3

description: MCM1 pool


title: gdb1-del-1-a


title: 2C::tomato-, WT-3

description: Replicate 3

source_name: 2C::tomato-, WT-3


title: Interdigital Tissue Tbr2Prx1KO mutants

city: Chapel Hill

first: Anna

last: Spagnoli

state: NC

address: 103 Mason Farm Road

department: Pediatrics

institute: University of North Carolina at Chapel Hill

description: Gene expression after 12hr  in 8Gy-irradiated human blood

hyb_protocol: Samples were hybridized to an Agilent Whole Mouse Genome Oligo Microarrays 4X44K for 17 hours at 65° according to Miltenyi Biotec’s undisclosed protocol

scan_protocol: Scanning of the microarrays were performed using the Agilent Technologies equipment.

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the image files

source_name: E14.5 limb

label_protocol: The purified PCR products (250 ng) were labeled with Cy3-dCTP

extract_protocol: We obtained E14.5 autopods from two normal controls and two Tgfbr2Prx1KO littermate embryos. Samples were frozen in OTC and cryosectioned, then processed with ethanol and xylene, and subjected to laser-capture microdissection for RNA sampling . To minimize RNA degradation, the process from sectioning to shipment was performed in less than 20 minutes. We sequentially laser-captured cells in the interzone,  the adjacent growth plates and interdigital tissue from controls and Tgfbr2Prx1KO mutants .  Captured specimens were frozen in SuperAmp Lysis Buffer (Miltenyi Biotec) and shipped to Miltenyi Biotec. mRNA was extracted and transcribed into cDNA according to Miltenyi Biotec’s undisclosed procedure (SuperAmp Miltenyi Biotec).

value: limb autopod interdigital tissue


title: gcr2-del-1-b

institute: UMC Utrecht


title: 2C::tomato-, WT-1

description: Replicate 1

source_name: 2C::tomato-, WT-1


title: MG1655_GMM_aerobic_Exp_biorep2

description: Gene Expression Data

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

source_name: E.coli K-12 MG1655, GMM, aerobic, exponential phase

value: Wildtype


title: cap-del-3-b

source_name: cap-del

value: cap-del

source_name: refpool


title: SI1, 2 wks on a HF-PO diet

description:
Pooled total RNA sample of 6 mice.
SI1_wk2_HF-PO

source_name: SI1 after 2 wks on a HF-PO diet

value: small intestine, SI 1


title: Embryos_EtOH1.5%_24hpf_R2

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

hyb_protocol: PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS. 2. Heat the prehybridization solution to 50 ºC in a 100 ml Coplin Jar. 3. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible. 4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water. 5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization. HYBRIDIZATION: Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine labeled RNA with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature. Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.

scan_protocol: Scanning of slides using the Agilent G2565AA DNA microarray scanner: Resolution: 10, Red laser PMT= 0, Green laser PMT= 100

data_processing: Microarray images were analyzed using Quantarray v3.0 software (PerkinElmer). Manually flagged bad spots were eliminated and the Cy3 median pixel intensity values were  background subtracted, followed by the averaging of quadruplicate features on the array. Data points were removed when intensity values were below 100. A global median normalization of zebrafish 24hpf larvae microarray data was applied using BRB-ArrayTools v3.4.0 software. Cy3 intensities were obtained. Data was normalized for each miRNA with the correspondent NCode™ Positive Control probe intensity. Log-transformed (base 2) of the ratio between miRNA and NCode™ Positive Control intensities of each sample was calculated.

organism: Danio rerio

source_name: 24 hours post fertilization tissues: embryos in EtOH 1.5% solution

label_protocol: Total RNA from control and test samples were labeled using the ULS microRNA labeling kit (Kreatech) according to the manufacturer’s instructions. Briefly, 2 ug of total RNA from control and test samples were incubated with Cy3-ULS for 15 min at 85ºC. The labeled RNAs were purified to remove non-reacted Cy-ULS to produce a fluorescently-labeled RNA sample for microarray analysis. Dye incorporation was monitored by UV-visible spectroscopy.

growth_protocol: Zebrafish embryos were collected and Petri dishes with approximately 250 eggs each were incubated at 28ºC to allow normal zebrafish development until 4hpf, when blastula is reached. At this stage, embryos were examined under a dissecting microscope and those that had developed normally were selected for EtOH exposure (approximately 200 eggs). Briefly, 200 embryos were randomly distributed into plastic Petri dishes containing 20 mL of EtOH test solutions (1% EtOH, 1.5% EtOH) or system water for control conditions. All solutions were made by dilution of absolute EtOH in system water. Exposure was from 4hpf to 24hpf.

extract_protocol: Total RNA was extracted from 24hpf samples using TRIzol® (Invitrogen) according to the manufacturer's instructions and treated with DNaseI (Invitrogen). RNA quantity and quality was assessed using the Nanodrop and Agilent 2100 bioanalyzer systems, respectively. Samples with a RIN number above 7 were used.

treatment_protocol: Zebrafish embryos were allowed to grow in system water or in 1% or 1.5% ethanol solutions from 4hpf until 24hpf.

tag: tissues

value: embryos

tag: treatment

value: 1.5% EtOH


title: Embryos_EtOH1.5%_24hpf_R1


title: liver_EHL_newborn_male_rep2_miRNA

city: Nanjing

first: Runsheng

last: Li

state: Jiangsu

department: Nanjing Agricultural University

institute: Nanjing Agricultural University

description: This sample is of Erhualian liver. It is a pooled total RNA sample of two littermate piglets.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). Hybridization used 100 µL 6×SSPE buffer containing 25% formamide at 34 °C.

scan_protocol: Axon GenePix 4000B Microarray Scanner

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

organism: Sus scrofa

source_name: porcine liver ,newborn,male,Erhualian breed

label_protocol: An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. Concentration of the extracted RNA was measured using NanoDrop ND-1000 Spectrophotometer. RNA integrity was confirmed by denaturing agarose electrophoresis, and DNA contamination was evaluated by PCR using isolated RNA as template with the primer of GAPDH. High quality RNA samples were then stored at -70°C till further use. The assay started from 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.

tag: breed

value: Erhualian

value: male

value: newborn

tag: tissue

value: liver

tag: rna subset

value: small RNAs (< 300 nt)


title: SI2, 2 wks on a HF-OO diet

description:
Pooled total RNA sample of 6 mice.
SI2_wk2_HF-OO

source_name: SI2 after 2 wks on a HF-OO diet

tag: strain

value: olive oil

value: 9wks old at start of diet intervention


title: Embryos_EtOH1%_24hpf_R2

source_name: 24 hours post fertilization tissues: embryos in EtOH 1% solution

value: 1% EtOH


title: liver_EHL_newborn_male_rep1_miRNA


title: MG1655_GMM_aerobic_Exp_biorep1

description: Gene Expression Data


title: SI2, 2 wks on a HF-SO diet

description:
Pooled total RNA sample of 6 mice.
SI2_wk2_HF-SO

source_name: SI2 after 2 wks on a HF-SO diet

value: safflower oil


title: liver_LW_newborn_male_rep3_miRNA

description: This sample is of Large White liver. It is a pooled total RNA sample of two littermate piglets.

source_name: porcine liver ,newborn,male,Large White breed

value: Large White


title: 2C::tomato-, WT-2

description: Replicate 2

source_name: 2C::tomato-, WT-2

value: ES cells


title: SI1, 2 wks on a HF-OO diet

description:
Pooled total RNA sample of 6 mice.
SI1_wk2_HF-OO

source_name: SI1 after 2 wks on a HF-OO diet


title: liver_EHL_newborn_male_rep3_miRNA


title: Embryos_EtOH1%_24hpf_R1


title: asc1-del-3-a

city: Utrecht

department: Department of Molecular Cancer Research

tag: genetic modification

value: refpool


title: Embryos_Ctrl_24hpf_R2

source_name: 24 hours post fertilization tissues: embryos in system water


title: Growth Plate Chondrocyte Tgfbr2Prx1KO  mutants

description: Gene expression after 6hr in 8Gy-irradiated human blood

source_name: E14.5 Limb

value: growth plate chondrocyte

tag: genetic background


title: 2C::tomato+, WT-2

description: Replicate 2

source_name: 2C::tomato+, WT-2


title: liver_LW_newborn_male_rep2_miRNA


title: cap-del-3-a

value: cap-del


title: SI1, 2 wks on a HF-SO diet

description:
Pooled total RNA sample of 6 mice.
SI1_wk2_HF-SO

source_name: SI1 after 2 wks on a HF-SO diet

value: small intestine, SI 1


title: liver_LW_newborn_male_rep1_miRNA


title: Embryos_Ctrl_24hpf_R1

value: embryos


title: Growth Plate Chondrocyte Controls

description: Gene expression after 6hr in 0.5Gy-irradiated human blood

source_name: E14.5 limb

tag: genotype

value: wild type


title: bcy1-del-1-a


title: Interzone Tgfbr2Prx1KO mutants

description: Gene expression after 6hr in 5Gy-irradiated human blood

value: limb autopod interzone tissue


title: Interdigital Tissue Controls

description: Gene expression after 6hr in 2Gy-irradiated human blood

value: limb autopod interdigital tissue


title: bcy1-del-1-b


title: adr1-del-1-b


title: pmr1∆ rep3

city: Seville

first: Nestor

last: Garcia-Rodriguez

state: Seville

address: Av Americo Vespucio

country: Spain

institute: CABIMER

hyb_protocol: Hybridization,washing and staining was performed using the GeneChip Hybridization Wash and Stain kit (Affymetrix)

scan_protocol: Data adquisition was performed using GeneChip Scanner 3000 7G and AGCC software (Affymetrix)

data_processing: Data were normalized using Robust Multy-Array Average(RMA). Fold change values (log2) and their p-values were calculated with the LIMMA analysis using the affylmGUI interface. All the statistical analysis was performed using R language and the packages freely available from Bioconductor Project, affylmGUI.

source_name: pmr1∆ mutant

label_protocol: Labelling was performed using the GeneChip 3' IVT Express Kit (Affymetrix)

growth_protocol: Yeast cells were grown on YPD at 30ºC to mid-log-phase

extract_protocol: Total RNA was isolated using the Rneasy Midi kit (Quiagen)


title: pmr1∆ rep1


title: adr1-del-1-a


title: asc1-del-2-b


title: pmr1∆ rep2


title: Interzone Controls

description: Gene Expression Interzone Control E14.5


title: RIL118_flo_2

status: Public on Jun 17 2012

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). Expression studies will be investigated in ear internode at two stages (emerging tassel and early silking).

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Zea mays

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: ear internode - Crop field Irrigation was applied during a dry and hot summer to prevent water stress

treatment_protocol: no treatment

tag: developmental stage (boyes et al. plant cell 2001)

value: early silking


title: RIL118_pan_2

value: emerging tassel


title: RIL118_flo_1


title: RIL54_flo_2


title: RIL54_flo_1


title: RIL99_flo_2


title: RIL71_pan_2


title: RIL71_flo_2


title: RIL99_flo_1


title: RIL71_flo_1


title: RIL39_pan_2


title: RIL39_flo_1


title: RIL39_flo_2


title: Normalized control sample 3 of 3 (0.05mg/L SNC)

city: Itakura-machi

first: Shosaku

last: Kashiwada

state: Ora-gun, Gunma

address: 1-1-1 Izumino

department: Department of Life Sciences

country: Japan

institute: Toyo University

description:
Nano_raw.txt
Nano-3-n

hyb_protocol: 5μg of the purified Cy5-aRNA sample was dissolved in 100μl of hybridization solution (CombiMatrix CustomArray Hybridization and Imaging Protocol), and hybridization reaction was carried out at 45ºC for 16hours.

scan_protocol: The microarrays went through post-hybridization washes according to CombiMatrix CustomArray Hybridization and Imaging Protocol, and they were scaned by Axon Instruments' GenePix 4000B scanner (5μm resolution, PMT gain at 450-550, Laser power at 100%).

data_processing: The raw data (CTL_raw.txt and Nano_raw.txt) were obtained from the scanned images using MicroarrayImager ver.6.0.1(CombiMatrix Corp.), and were background-subtracted and median-normalized by Microsoft Office Excel 2003 within each of the microarray.  We employed statistical analysis by arraySTAT z-test (Imaging Research Inc., St. Catharines, ON, Canada) with significance determination at p < 0.05 to obtain differentiated transcriptional expression ratio (also called “fold difference” or “FD”) for each of the gene probes on the microarray.

organism: Oryzias latipes

source_name: whole embryo

label_protocol: 1μg from each of the extracted total RNA was reverse-transcribed with T7-oligo dT primer to synthesize single-stranded cDNA (ss-cDNA).  Subsequently, double-stranded cDNA was synthesized from the ss-cDNA, and in vitro transcription with T7 RNA polymerase and amino-allyl UTP to generate amino-allyl labeled aRNA target samples was performed.  The aRNA samples were purified and coupled with amine reactive Cy5 fluorescent dye, then Cy5-coupled aRNA samples were spin column-purified for microarray hybridization.  All of the processes from reverse-transcription of the total RNA to Cy5-aRNA purification were carried out with Amino Allyl MessageAmp II aRNA amplification kit (Ambion Inc., Austin, TX, USA).

growth_protocol: 3 embryos at stage 21 were exposed in triplicate to 0mg/L and 0.05mg/L of SNC for 48 hours at 28±0.1ºC in 6-well polystyrene plates protected from light. Test solutions were renewed every 24 hours.

extract_protocol: After the exposure test three medaka embryos were homogenized in RLT lysis buffer (QIAGEN), and total RNA was extracted by RNeasy Mini Kit according to the manufacturer's protocol provided in the kit (QIAGEN, cat#74903).

treatment_protocol: Purified silver nanocolloids (SNC, 10mg/L, 99.99% purity, nominal size = 3.6nm diameter, dissolved in distilled water) were purchased from Synergenesis, Inc. (Pengilly, MN, USA).  SNC solutions for exposures were prepared with ultrapure water.  Then, three embryos at stage 21 were exposed in triplicate to 0mg/L and 0.05mg/L of SNC for 48 hours at 28±0.1ºC with no light.

tag: organ/tissue

value: whole embryo

tag: developmental stage

tag: stress

value: 0.05mg/L SNC


title: RIL99_pan_2


title: RIL54_pan_2


title: Normalized control sample 2 of 3 (0.05mg/L SNC)

description:
Nano_raw.txt
Nano-2-n


title: RIL71_pan_1


title: Normalized control sample 2 of 3 (0mg/L SNC)

description:
CTL_raw.txt
CTL-2-n

value: control


title: Low estrogen, fish number 314

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Targets were combined and purified using Microcon YM-30 filter (Millipore, Billerica, USA). The microarray slides were pretreated with blocking solution (1% BSA fraction V, 20x SSC and 5% SDS) at 50°C for 30 min, then washed with 2x SSC (3 min) and 0.2xSSC (3 min). For hybridization, Lifter Slips (Erie Scientific, Portsmouth, USA) were placed on the slides. Labels were adjusted to 80 µl volumes and contained 1.3x Denhardt’s, 3x SSC, 0.3% SDS, 0.67 μg/μl polyadenylate and 1.4 μg/μl yeast tRNA. Hybridization was carried out overnight at 60°C in a water bath; the ArrayIt® Hybridization Chamber was used. Next, slides were washed in 0.5x SSC/0.1% SDS (15 min), 0.5x SSC/0.01% SDS (15 min) and twice in 0.06x SSC (3 min each) at room temperature in dim lighting with gentle agitation. Slides were dried using ArrayIt® Microarray High-Speed Centrifuge.

scan_protocol: Scanning was performed on a GenePix Personal 4100A microarray scanner (Molecular Devices, California, USA)

data_processing: The raw data file provided only contains the raw data spots that passed quality control. Images were processed using the standard procedures of GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed

organism: Oncorhynchus mykiss

source_name: Liver of infected fish, low dose of E2

label_protocol: 10 μg RNA in each were labeled with Cy3-dUTP (pooled sample of untreated fish used as reference) and Cy5-dUTP (fish from the exposed groups) (Amersham Biosciences, UK); labels were introduced during cDNA synthesis using SuperScript III RT (Invitrogen, Basel, Switzerland). The cDNA synthesis was performed at 46°C for 3 hours in 25 μl reaction volumes. RNA was degraded by adding 2.5M NaOH at 37°C for 15 min and alkaline was neutralized with 2M HEPES buffer.

growth_protocol: Juvenile rainbow trout (1.15 g) was kept in aerated glass tanks with a flow-through of 1 liter/sec of normal tap water at temperature 13.8C. Fish was fed with dry feeds at 3% body weight / day.

extract_protocol: Total RNA was extracted and purified using Trizol Plus/PureLink RNA Mini Kit (Invitrogen, Basel, Switzerland)

treatment_protocol: Feed was spiked with E2 using alcohol evaporation method. For infection, the fish (n = 75 / treatment group) were transferred and kept in aerated 30 liter tanks/replicate filled with 5 liter of normal tap water with bacteria for 1 hour  and then re-transferred to their original tanks. Three concentrations were applied: 10exp2 (low), 10exp4 (intermediate) and 10exp6 (high) colony forming units. Liver from fish exposed to high concentration was used for microarray analyses. Samples were collected after 10 days.

tag: treated with

value: low dose (2 mg/kg feed) of E2 (17β-estradiol)

tag: infected with

value: 10^6 cfu of Yersinia ruckeri

value: liver

source_name: Liver of control fish (no pathogen, no E2), pooled sample

tag: sample type

value: pooled control smaple


title: Normalized control sample 1 of 3 (0mg/L SNC)

description:
CTL_raw.txt
CTL-1-n


title: High estrogen, fish number 324

source_name: Liver of infected fish, high dose of E2

value: high dose (20 mg/kg feed) of E2 (17β-estradiol)


title: Low estrogen, fish number 324


title: RIL118_pan_1


title: Low estrogen, fish number 315


title: Low estrogen, fish number 325


title: RIL54_pan_1


title: Normalized control sample 3 of 3 (0mg/L SNC)

description:
CTL_raw.txt
CTL-3-n


title: RIL99_pan_1


title: Normalized control sample 1 of 3 (0.05mg/L SNC)

description:
Nano_raw.txt
Nano-1-n


title: RIL39_pan_1


title: VE-RANKL treatment for 4 day No.3

city: Yokohama

first: Takashi

last: Kanaya

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN

description: Intestinal epithelial cells from mice RANKL-treated (for 4 days) mice

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99º for 5 minutes, then 45º for 5 minutes centrifuge at max speed for 1 minute. Transfer 200 µl of hyb solution to each array, then tape holes and parafilm. Hybridize 17 hours at 45º at 60 rpm. Fluidics washing is FS450_0001.

scan_protocol: Hewlett-Packard Gene Array Scanner

data_processing:
Data were processed by GeneSpring GX software.
probe group file: MoGene-1_1-st-v1
meta-probeset file: MoGene-1_1-st-v1_na31_1_mm9

source_name: Intestinal epithelial cells

growth_protocol: Mouse intestinal epithelial cells isolated from small intestine of 10 weeks-old BALB/c mice.

extract_protocol: Intestinal epithelial cells were treated with 30 mM EDTA/HBSS for 10 min, and peeled off with needles.

treatment_protocol: The GST-RANKL fusion protein was intraperitoneally administered to mice twice a day for up to 4 days.

tag: age

value: 10 weeks-old

value: Small intestine

value: BALB/c

value: Wild-type

tag: time point

value: 4 day

tag: agent

value: GST-RANKL fusion protein


title: High estrogen, fish number 325


title: High estrogen, fish number 315


title: Control No.2

description: Intestinal epithelial cells from normal mice


title: High estrogen, fish number 323


title: Control No.3


title: High estrogen, fish number 314


title: Low estrogen, fish number 323


title: VE-RANKL treatment for 4 day No.1


title: Control No.1


title: VE-RANKL treatment for 3 day No.2

description: Intestinal epithelial cells from mice RANKL-treated (for 3 days) mice

value: 3 day


title: VE-RANKL treatment for 4 day No.2


title: VE-RANKL treatment for 2 day No.2

description: Intestinal epithelial cells from mice RANKL-treated (for 2 days) mice

value: 2 day


title: No estrogen, fish number 324

source_name: Liver of infected fish, no E2 treatment


title: VE-RANKL treatment for 3 day No.3


title: No estrogen, fish number 325


title: VE-RANKL treatment for 2 day No.3


title: No estrogen, fish number 315


title: VE-RANKL treatment for 3 day No.1


title: No estrogen, fish number 323


title: VE-RANKL treatment for 1 day No.1

description: Intestinal epithelial cells from mice RANKL-treated (for 1 day) mice

value: 1 day


title: VE-RANKL treatment for 2 day No.1


title: VE-RANKL treatment for 1 day No.3


title: No estrogen, fish number 314


title: VE-RANKL treatment for 1 day No.2


title: 8wk Lung 5

status: Public on Jun 16 2012

city: Bethesda

first: Julian

middle: CK

last: Lui

address: 10 Center Drive

institute: NICHD, NIH

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

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

data_processing: RMA nomanization method of Partek Genomics Suite Version 6.6

source_name: 8 wks_Lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: gender

value: male

value: 8 weeks

tag: growth rate

value: very slowly proliferating

value: Lung


title: 8wk Kidney 2

source_name: 8 wks_Kidney

tag: tissue

value: Kidney


title: 8wk Lung 4

tag: strain


title: 8wk Lung 1


title: 8wk Kidney 4


title: 4wk Lung 5

source_name: 4 wks_Lung

value: 4 weeks

value: slowly proliferating


title: 8wk Lung 3


title: 8wk Kidney 1


title: 8wk Kidney 5


title: A/CAL/07_animal no.139_Euthanized@3DPI

city: Birmingham

first: Carl

middle: E

last: Bruder

state: AL

address: 2000 9th Ave South

department: Viral Biochemistry

institute: Southern Research Institute

scan_protocol: One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit from Agilent according to the manufacturers protocol. A GenePix 4000B scanner was used.

data_processing:
The raw image files were then processed by the Agilent feature extraction software and raw data files were obtained. The raw data files were then normalized and filtered using the Agi4x44 R-plugin available at the bioconductor website. Deaflut settings for Agi4x44 was used. These scripts performed inter microarray normalization and filtered out spots below the low signal threshold. The data was then log2 transformed and imported into Multi experiment viewer (MEV) v4.6 for statistical analysis
Agi4x44 performed inter microarray normalization (quantile) and filtered out spots below the low signal threshold. The data was then log2 transformed [log2(intensity value+50)].

organism: Mustela putorius furo

label_protocol: 200 mg of total RNA was labelled using One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit from Agilent according to the manufacturers protocol.

extract_protocol: 2 ml Blood was isolated in PaxGene tubes and frozen at -80 C. Isolation of RNA was carried out according to the supplied protocol (www.qiagen.com/literature/render.aspx?id=104458). The quality of the RNA was analyzed using a BioRad Experion capillary electrophoresis system.

treatment_protocol: The ferrets were assigned to their respective infection groups using a computer-generated randomization procedure. The animals had ad libitum access to water and food and a maximum of two animals were caged together at any time. Control animals were caged in a separate room. On Day 0, each ferret was anesthetized using a ketamine/xylazine/atropine mixture, formulated to provide doses of 25 mg/kg ketamine, 1.7 mg/kg xylazine, and 0.05 mg/kg of atropine to each animal, and challenged intranasally with one milliliter of virus diluted in PBS. The mock infected animals were challenged with PBS only.

value: male (castrated, descented)

value: whole blood

tag: infection dose

value: low (10E4 TCID50/ml)


title: A/CAL/07_animal no.174_Euthanized@7DPI

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit from Agilent according to the manufacturers protocol.


title: 4wk Lung 2


title: A/CAL/07_animal no.157_Euthanized@5DPI


title: A/CAL/07_animal no.171_Euthanized@7DPI


title: A/CAL/07_animal no.160_Euthanized@5DPI


title: A/CAL/07_animal no.177_Euthanized@7DPI


title: 8wk Kidney 3


title: 4wk Lung 4


title: A/CAL/07_animal no.101_Euthanized@2DPI


title: A/CAL/07_animal no.163_Euthanized@5DPI


title: A/CAL/07_animal no.110_Euthanized@3DPI


title: 8wk Lung 2


title: A/CAL/07_animal no.111_Euthanized@3DPI


title: A/CAL/07_animal no.105_Euthanized@2DPI


title: 4wk Heart 3

source_name: 4 wks_Heart

value: Heart


title: A/CAL/07_animal no.100_Euthanized@2DPI


title: 4wk Lung 3


title: 4wk Heart 5


title: 4wk Lung 1


title: 4wk Heart 4


title: A/CAL/07_animal no.093_Euthanized@1DPI


title: A/BN/59_animal no. 169_Euthanized@7DPI


title: A/CAL/07_animal no.096_Euthanized@1DPI


title: 4wk Heart 1


title: A/BN/59_animal no. 140_Euthanized@3DPI


title: A/CAL/07_animal no.095_Euthanized@1DPI


title: A/BN/59_animal no. 168_Euthanized@7DPI


title: A/BN/59_animal no. 156_Euthanized@7DPI


title: 4wk Heart 2


title: A/BN/59_animal no. 138_Euthanized@3DPI


title: A/BN/59_animal no. 128_Euthanized@2DPI


title: A/BN/59_animal no. 131_Euthanized@2DPI


title: 4wk Kidney 5

source_name: 4 wks_Kidney


title: A/BN/59_animal no. 135_Euthanized@3DPI


title: A/BN/59_animal no. 107_Euthanized@1DPI


title: A/BN/59_animal no. 123_Euthanized@2DPI


title: A/BN/59_animal no. 113_Euthanized@1DPI


title: 4wk Kidney 1


title: A/BN/59_animal no. 103_Euthanized@1DPI


title: 4wk Kidney 3


title: A/MEX/4482_animal no. 170_Euthanized@5DPI


title: A/MEX/4482_animal no. 175_Euthanized@7DPI


title: A/MEX/4482_animal no. 173_Euthanized@7DPI


title: A/MEX/4482_animal no. 180_Euthanized@7DPI


title: A/MEX/4482_animal no. 155_Euthanized@5DPI


title: A/MEX/4482_animal no. 166_Euthanized@5DPI


title: A/MEX/4482_animal no. 136_Euthanized@3DPI


title: 4wk Kidney 2


title: A/MEX/4482_animal no. 137_Euthanized@3DPI


title: A/MEX/4482_animal no. 134_Euthanized@2DPI


title: A/MEX/4482_animal no. 124_Euthanized@2DPI


title: 1wk Heart 4

source_name: 1 wk_Heart

value: 1 week

value: rapidly proliferating


title: A/MEX/4482_animal no. 120_Euthanized@2DPI


title: 1wk Heart 2


title: 1wk Heart 1


title: 1wk Heart 3


title: 1wk Lung 4

source_name: 1 wk_Lung


title: 1wk Kidney 5

source_name: 1 wk_Kidney


title: 1wk Lung 5


title: 4wk Kidney 4


title: A/MEX/4482_animal no. 150_Euthanized@3DPI


title: 1wk Heart 5


title: 1wk Kidney 3


title: 1wk Lung 3


title: 1wk Kidney 4


title: 1wk Lung 1


title: 1wk Kidney 2


title: 1wk Kidney 1


title: A/CAL/07_animal no. 117_Euthanized@2DPI

value: high (10E6 TCID50/ml)


title: A/CAL/07_animal no. 145_Euthanized@3DPI


title: A/CAL/07_animal no. 162_Euthanized@7DPI


title: CTRL_animal no. 184_Euthanized@7DPI

source_name: mock (PBS)_infected_CTRL_ferret


title: A/MEX/4482_animal no. 94_Euthanized@1DPI


title: A/CAL/07_animal no. 132_Euthanized@2DPI


title: A/CAL/07_animal no. 98_Euthanized@1DPI


title: A/MEX/4482_animal no. 116_Euthanized@1DPI


title: A/CAL/07_animal no. 176_Euthanized@7DPI


title: A/MEX/4482_animal no. 106_Euthanized@1DPI


title: A/CAL/07_animal no. 146_Euthanized@3DPI


title: A/CAL/07_animal no. 147_Euthanized@5DPI


title: 1wk Lung 2


title: A/CAL/07_animal no. 142_Euthanized@3DPI


title: A/CAL/07_animal no. 159_Euthanized@5DPI


title: A/CAL/07_animal no. 108_Euthanized@1DPI


title: A/CAL/07_animal no. 109_Euthanized@1DPI


title: A/CAL/07_animal no. 178_Euthanized@7DPI


title: A/CAL/07_animal no. 161_Euthanized@5DPI


title: A/CAL/07_animal no. 126_Euthanized@2DPI


title: CTRL_animal no. 182_Euthanized@7DPI


title: CTRL_animal no. 122_Euthanized@3DPI


title: CTRL_animal no. 121_Euthanized@3DPI


title: CTRL_animal no. 114_Euthanized@1DPI


title: CTRL_animal no. 112_Euthanized@1DPI


title: Mouse_colon_LEC_rep3

city: Zurich

first: Giorgia

last: Jurisic

address: Wolfgang-Pauli Strasse 10

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

LEC_3

hyb_protocol: Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.

source_name: Mouse, colon, normal, lymphatic endothelial cells

label_protocol: Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.

growth_protocol: Mice were maintained under conventional conditions.

extract_protocol: Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).

treatment_protocol: Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).

value: female

value: colon

tag: cell type

value: lymphatic endothelial cells

tag: condition

value: normal, healthy

tag: cell isolation method

value: FACS


title: Mouse_colon_BEC_rep3

description:
Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA.

BEC_3

source_name: Mouse, colon, normal, blood endothelial cells

value: 8 weeks

value: blood vascular endothelial cells