title: 4351 24h_post-infection

city: Tjele

first: A.J. (Bart)

last: Buitenhuis

address: Blichers allé 20

department: Faculty of Agricultural Sciences, Dept. of Genetics and Biotechnology

country: Denmark

institute: Aarhus University

hyb_protocol: Fifteen micrograms of cRNA was fragmented at 94 C for 35 min in a final volume of 40 ul in a buffer containing 40mM Tris-acetate pH 8.1, 100mM KOAc, and 30 mM MgOAc. Next, 260 ul of 6x SSPE-T hybridization buffer (1 M NaCl, 10 mM Tris pH 7.6, 0.005% Triton) was added and the cRNA was denatured by heating to 95 C for 5 min. The hybridization mixture was loaded onto the Affymetrix probe array cartridge (Affymetrix Bovine Genome Array) and incubated for 16 hr at 45 C at constant rotation (60 rpm). The washing and staining procedure was performed in the Affymetrix Fluidics Station. The probe array was exposed to 10 washes in 6x SSPE-T at 25 C followed by 4 washes in 0.5x SSPE-T at 50 C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C followed by 10 washes in 6x SSPE-T at 25 C. An antibody amplification step followed, using normal goat IgG as blocking reagent, final concentration 0.1 mg/ml (Sigma, St. Louis), and biotinylated anti-streptavidin antibody (goat), final concentration 3 ug/ml (Vector Laboratories, Burlingame, CA). This was followed by a staining step with a streptavidinphycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C and10 washes in 6x SSPE-T at 25 C (Kristensen et al. 2005: Genetics 171: 157–167).

scan_protocol: The arrays were scanned at 560 nm using a confocal microscope (Hewlett Packard GeneArray Scanner G2500A)

data_processing: The data was analyzed using R (version 2.10.0) (http://www.r-project.org/). The Bovine genome array annotation is available from the NetAffx Analysis Center (Bovine.na29.annot.csv). Additional and updated annotation was obtained from the Ensemble database, using the biomaRt package (version 2.0.0) in R. Normalization of the expression values for the udder samples were performed using the Robust Multi-array Average (RMA) algorithm as implemented in the Affy package (version 1.24.2).Differential expression of each gene was assessed using linear modeling and empirical Bayes methods, which were implemented using the R package Limma (version 3.2.1). The linear models allowed for changes for time points. Each transcript targeted by a probe was tested for its expression change using a modified t-test. In the modified t-test, the residual standard deviations are moderated across the probe sets to ensure that there is a more stable inference for each transcript. The moderated standard deviations are a compromise between the individual transcript-wise standard deviations and the pooled standard deviation. Multiple testing was accounted for using the bonferroni correction. Probes were considered differentially expressed (DE) if the corrected P-value was below 0.05 and had a minimum log2-fold change of 1. A 2-D-cluster analysis was performed based on the transcripts defined as significantly differentially transcribed using the heatmap.2 option (gplots, version 2.7.4). A hierarchical clustering used Pearson’s correlation coefficients as distance measures. The number of clusters was based on two criteria: 1) it should result in a distinctly lower within:between cluster ratio in transcription variance than one less cluster and 2) no cluster should contain less than ten genes. Finally, we tested for over-representation of gene ontology categories in the defined clusters using a hyper geometric gene-set enrichment test (GOstats version 2.12.0). Each cluster (edited to contain only one copy of each transcript) was tested against a background of all transcripts on the microarray using functional annotation clustering in DAVID.

organism: Bos taurus

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cows were housed in a traditional straw-bedded tie stall barn, where they were fed individually, and with free access to water. A total mixed ration (TMR) diet including vitamins and minerals was fed ad libitum twice a day in equal portions at 8.00 a.m. and 15.30 p.m. The cows were milked at 6.00 a.m. and again at 17.00 p.m. [Buitenhuis et al, submitted]

extract_protocol: Liver biopsies were obtained at 144h pre infection, 12h, 24h, 192h post infection from an incision on the right side of the cow at the 10th intercostal where it was crossed by a line from mid-humerus to tuber coxae. Before taking the biopsies, a 5 cm x 5 cm area was shaved and disinfected and a 5 ml local anaesthesia (Hostacain Vet, 2%; Intervet, Skovlunde, Denmark) was given. After 10–15 min, a 0.5 cm incision in the skin was made. Liver biopsies were taken from this incision using a MANAN Automatic Biopsy System (14 gauge x 17 mm notch) (MARMON/MDTECH, Gainesville,FL, USA). Biopsies taken for in vitro measurements were directly stored in ice-cold phosphate-buffered saline (PBS) and transported to the laboratory where the incubation procedure was initiated within 35 min of removal. Biopsies taken for chemical analyses were immediately frozen in liquid nitrogen and transported to the laboratory where the biopsies were stored at –80 °C until analysed [Andersen et al, 2002: J. Vet. Med. A 49, 65–71].  Liver biopsies were homogenized with a bead beater and extracted with 1.5 ml Trizol and 150µl chloroform [Kristensen et al, 2005: Genetics 171: 157–167]. cDNA was prepared using the SuperScript Choise System (Life Technologies), and biotin-labeled cRNA was prepared using the BioArray High Yield RNA Transcript Labelling kit (Enzo) [Dyrskjøt et al, 2003]. Fifteen µg of labeled cRNA was loaded onto each microarray.

treatment_protocol: The E. coli was a Danish field isolate (k2bh2) from a cow with severe, acute mastitis, donated by Dr. Helle Daugaard Larsen. Prior to inoculation, E. coli was grown at 37oC in brain heart infusion medium (BHI) overnight. The bacteria suspension was tested for purity, re-suspended, grown on agar and the number of colony-forming units (CFU)/ml was counted. Each dairy cow was inoculated with 10ml of 0.9% pyrogen-free NaCl solution containing live E. coli in one front quarter directly after evening milking at time 0. The E. coli–NaCl solution was infused into the mammary gland with a sterile teat cannula and the quarter was thoroughly massaged. [Buitenhuis et al, submitted. See this reference for further details]

tag: cow id

tag: breed

value: Danish Holstein Friesian

value: liver

tag: infection

value: post-infection

tag: time point


title: 14119481 - mock1 vs wt1

status: Public on Jan 01 2012

type: RNA

city: evry

first: edu

last: bueso

address: gaston cremieux

country: France

institute: INRA

description: Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system.

hyb_protocol: wt1 Cy5 / mock1 Cy3 : 30pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - MS Infection with 10mM MgCl2 22°C Long day

tag: ecotype

tag: age

value: 2 week

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


title: Wild-type plants _ drought conditions_rep1

city: Changsha

first: Joseph

last: Ning

state: Hunan

address: No.1 Nongda Road，Furong District

country: China

institute: Hunan Agricultural Univrsity

description:
D_CK_Log2NormSignal
251524111878_S01_GE1_105_Dec08_1_3.txt
Gene expression in wild-type plants under drought conditions

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer's instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

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

organism: Oryza sativa

source_name: wild-type rice leaves,drought conditions, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer's instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer's instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The OsDIS1 overexpression 9-4-2 plants and the wild-type plants were cultured on 1/2 MS medium plus 3% sucrose for seven days. About half of the plants were sampled as the untreated control for RNA isolation, and the rest were transferred with 1/2 MS medium onto filter papers to induce drought stress. When the leaves of the OsDIS1 overexpression plants began to show drought stress phenotypes, we collected leaves for RNA isolation

tag: genotype/variation

value: Wild-type

tag: stress

value: drought

tag: tissue

value: Leaves

value: Seven-day-old


title: 4351 12h_post-infection

label: biotin

tag: gender

value: female


title: 14119475 - prgH2 vs mock2

hyb_protocol: mock2 Cy5 / prgH2 Cy3 : 30pmol.

growth_protocol: seedling - MS 22°C Long day


title: 3341 192h_post-infection


title: 3341 24h_post-infection


title: OsDIS1 Ovexpression plants _ normal conditions_rep1

description:
N_OX 9-4-2_Log2NormSignal
251524111878_S01_GE1_105_Dec08_1_2.txt
Gene expression in OsDIS1 overexpression plants under normal conditions

source_name: OsDIS1 overexpression rice leaves,normal conditions, replicate 1

value: OsDIS1 overexpression

value: control


title: 3341 12h_post-infection


title: 4351 144h_pre-infection

value: pre-infection


title: 14119480 - wt1 vs mock1

hyb_protocol: mock1 Cy5 / wt1 Cy3 : 30pmol.


title: Wild-type plants _normal conditions_rep1

description:
N_CK_Log2NormSignal
251524111878_S01_GE1_105_Dec08_1_1.txt
Gene expression in wild-type plants under normal conditions

source_name: wild-type rice leaves,normal conditions, replicate 1


title: 3341 144h_pre-infection


title: 3141 24h_post-infection


title: eid3_45 min after red-light pulse_2

city: Freiburg

first: Cornelia

last: Klose

address: Schänzlestr. 1

department: Institute for Biology 2/ Botany

country: Germany

institute: Albert-Ludwigs-University Freiburg

description: Gene expression 45 min after a red-light pulse in eid3 mutant seedlings.

hyb_protocol: Hybridization was performed with 1.5 µg of labeled cDNA per array at a temperature of 65°C overnight, according to the Agilent protocol.

scan_protocol: scanned on Agilent Technologies Scanner G2505C at a resolution of 5 μm.

data_processing: Agilent Feature Extraction Software 10.5.1.1 was used to process and analyze array images. The software returns a series of spot quality measures to evaluate the quality and reliability of spot intensity estimates. The raw data were analyzed using GeneSpring GX 10.0 (normalization: shift to 75.0 percentile, baseline transformation: median of all samples). The normalized data were filtered to exclude probes flagged “absent” in all samples.

source_name: eid3 mutant seedlings 45 min after red light pulse 2

label_protocol: 0.5 µg of total RNA was reverse transcribed into cDNA and labeled with Cy3 using the one-color Quick Amp Labeling Kit (Agilent) following Agilent´s instructions.

growth_protocol: Arabidopsis thaliana seeds were sterilized with ethanol and sown on 1/2 MS Agar plates covered with filter paper. After stratification for 3 days at 6°C imbibed seeds were treated with red light (30 µmol/m2s) for 2 h at 21°C to induce germination. Seedlings were grown for 4 days at 21°C in darkness.

extract_protocol: Harvested seedlings were immediately frozen in liquid nitrogen. The material was homogenized in eppendorf-tubes together with 7 glass beads (2 mm size) in frozen condition in a silamat homogenizer (vivadent ivoclar) for 2x 10 s. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturer´s recommendations. The protocol includes an on-column DNase (Quiagen) digestion step.  RNA was quantified using a NanoDrop-1000 spectrophotometer (peqlab Biotechnology GmbH) and quality was estimated on an Agilent 2100 Bioanalyzer. The RNA integrity number index was calculated for each sample using Agilent 2100 Expert software. Only RNAs with integrity number >8.0 were further processed.

treatment_protocol: 4-days-old dark-grown seedlings were either kept in darkness or irradiated for 2 min with red-light (30 µmol/m2s) and harvested after further 45 min in darkness.

tag: genotype

value: eid3 mutant

tag: light treatment

value: 2 min red-light pulse + 45 min darkness


title: 3141 192h_post-infection


title: eid3_45 min after red-light pulse_1

source_name: eid3 mutant seedlings 45 min after red light pulse 1


title: WT_45 min after red-light pulse_3

description: Gene expression 45 min after a red-light pulse in Ler wildtype seedlings.

source_name: Ler wildtype seedlings 45 min after red light pulse 3

value: Ler wildtype


title: 3141 12h_post-infection


title: eid3_45 min after red-light pulse_3

source_name: eid3 mutant seedlings 45 min after red light pulse 3


title: 14054267 - wt2 vs mock2

hyb_protocol: mock2 Cy5 / wt2 Cy3 : 30pmol.


title: 14162849 - mpk6_flg1 vs mpk6_1

description: Investigate flagellin mpk dependent genes.

hyb_protocol: mpk6_1 Cy5 / mpk6_flg1 Cy3 : 30pmol.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

growth_protocol: seedling - Plates, MS agar, long day, Percival.


title: eid3_dark control_3

description: Gene expression in dark-grown eid3 mutant seedlings.

source_name: eid3 mutant seedlings dark control 3

value: no


title: 14054266 - mock2 vs wt2

hyb_protocol: wt2 Cy5 / mock2 Cy3 : 30pmol.


title: 14162851 - mpk6_flg2 vs mpk6_2

hyb_protocol: mpk6_2 Cy5 / mpk6_flg2 Cy3 : 30pmol.


title: 14162850 - mpk6_2 vs mpk6_flg2

hyb_protocol: mpk6_flg2 Cy5 / mpk6_2 Cy3 : 30pmol.


title: 14162848 - mpk6_1 vs mpk6_flg1

hyb_protocol: mpk6_flg1 Cy5 / mpk6_1 Cy3 : 30pmol.


title: 3141 144h_pre-infection


title: WT_45 min after red-light pulse_2

source_name: Ler wildtype seedlings 45 min after red light pulse 2


title: 2428 12h_post-infection


title: eid3_dark control_2

source_name: eid3 mutant seedlings dark control 2


title: WT_45 min after red-light pulse_1

source_name: Ler wildtype seedlings 45 min after red light pulse 1


title: WT_dark control_3

description: Gene expression in dark-grown Ler wildtype seedlings.

source_name: Ler wildtype seedlings dark control 3


title: 2428 24h_post-infection


title: 2428 144h_pre-infection


title: eid3_dark control_1

source_name: eid3 mutant seedlings dark control 1


title: 14178273 - mpk6-2 vs wt-2

hyb_protocol: wt-2 Cy5 / mpk6-2 Cy3 : 30pmol.

growth_protocol: seedling - 2 weeks seedlings were grown under 22°c and 70% RH and long day.


title: 2105 24h_post-infection


title: 1981 192h_post-infection


title: WT_dark control_2

source_name: Ler wildtype seedlings dark control 2


title: 14178272 - wt-2 vs mpk6-2

hyb_protocol: mpk6-2 Cy5 / wt-2 Cy3 : 30pmol.


title: 14178271 - mpk6-1 vs wt-1

hyb_protocol: wt-1 Cy5 / mpk6-1 Cy3 : 30pmol.


title: 14178270 - wt-1 vs mpk6-1

hyb_protocol: mpk6-1 Cy5 / wt-1 Cy3 : 30pmol.


title: 1981 24h_post-infection


title: 13969313 - mpk4_flg2 vs mpk4_2

hyb_protocol: mpk4_2 Cy5 / mpk4_flg2 Cy3 : 30pmol.


title: 13969312 - mpk4_2 vs mpk4_flg2

hyb_protocol: mpk4_flg2 Cy5 / mpk4_2 Cy3 : 30pmol.


title: 13968880 - mpk4_flg1 vs mpk4_1

hyb_protocol: mpk4_1 Cy5 / mpk4_flg1 Cy3 : 30pmol.


title: WT_dark control_1

source_name: Ler wildtype seedlings dark control 1


title: 1981 12h_post-infection

hyb_protocol: Fifteen micrograms of cRNA was fragmented at 94 C for 35 min in a final volume of 40 ul in a buffer containing 40mM Tris-acetate pH 8.1, 100mM KOAc, and 30 mM MgOAc. Next, 260 ul of 6x SSPE-T hybridization buffer (1 M NaCl, 10 mM Tris pH 7.6, 0.005% Triton) was added and the cRNA was denatured by heating to 95 C for 5 min. The hybridization mixture was loaded onto the Affymetrix probe array cartridge (Affymetrix Bovine Genome Array) and incubated for 16 hr at 45 C at constant rotation (60 rpm). The washing and staining procedure was performed in the Affymetrix Fluidics Station. The probe array was exposed to 10 washes in 6x SSPE-T at 25 C followed by 4 washes in 0.5x SSPE-T at 50 C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C followed by 10 washes in 6x SSPE-T at 25 C. An antibody amplification step followed, using normal goat IgG as blocking reagent, final concentration 0.1 mg/ml (Sigma, St. Louis), and biotinylated anti-streptavidin antibody (goat), final concentration 3 ug/ml (Vector Laboratories, Burlingame, CA). This was followed by a staining step with a streptavidinphycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C and10 washes in 6x SSPE-T at 25 C (Kristensen et al. 2005: Genetics 171: 157–167).


title: replica2 MM2d RPM1g control vs MM2d RPM mg*

city: Madrid

first: Raúl

last: Herranz

state: Madrid

address: Ramiro de Maeztu 9

department: Plant Cell Nucleolus, proliferation and microgravity

country: Spain

institute: Centro Investigaciones Biológicas

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 2 of 3. Transcriptional status MM2d RPM1g control vs MM2d RPM simulated mg

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

scan_protocol: Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).

data_processing: Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization).

source_name: Arabidopsis thaliana MM2D callus culture

label_protocol: 5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5  and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop

growth_protocol: Callus cultures of Arabidopsis thaliana were prepared one week in advance of the 200 min exposure to altered environments in the simulators from MM2d suspension cultures as described (Menges and Murray 2006). Samples were prepared in a 40.8mm height 25mm diameter tube for the Magnet (3 identical runs performed) and in two regular 90mm diameter Petri dishes for the LDC/RPM experiments (a single run performed). For all devices and conditions, the callus cultures were prepared one week before the expected experiment start and samples were preserved after treatment by quick freezing in liquid nitrogen and dry ice storage.

extract_protocol: The frozen plant tissue (~100 mg) was ground in tiny mortars dipped in liquid nitrogen. The frozen powder was carefully transfered into 1.5 ml microcentrifuge tubes using small funnels and rubber spatulas also cooled with liquid nitrogen. Total RNA was extracted using TRIzol reagent (Invitrogen, 15596-026) according to manufacturer's instructions and purified with an RNeasy mini kit (Qiagen, 74104).1 ug of total RNA was amplified via the aRNA MessageAmp II kit (Ambion, 1751)

treatment_protocol: Callus cultures were exposed to altered gravity/magnetic-inertial forces for 200 minutes. 7 conditions were used: 1 - mg*/10.1T, 2 -0.1g*/14.7T, 3 - 1g*/16.5T, 4 - 1.9g*/14.7T, 5 - 2g*/10.1T, 6 - mg/RPM inertial forces, 7 - 2g/LDC inertial forces

tag: sample type

value: MM2D (Wild type culture) 1g control

tag: cell line

tag: treatment

value: 1g control

value: RPM (random positioning) simulated mg

value: MM2D (Wild type culture) RPM simulated mg


title: replica3 MM2d Mag1g control vs MM2d Mag 2g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 3 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 2g*

value: MAG (magnetic) 2g*

value: MM2D (Wild type culture) MAG 2g*


title: 1922 12h_post-infection

source_name: Liver

value: Danish Holstein Friesian

value: liver

value: post-infection


title: 1922 192h_post-infection

value: female


title: 14-day pkl seedlings, biological replicate 3

city: Shanghai

first: Heng

last: Zhang

state: Shanghai

address: 300 Fenglin Rd, Room 705

institute: Shanghai Center for Plant Stress Biology

description: Gene expression data from 14-day-old pkl seedlings, biological replicate 3

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data were processed using the gcrma package from Bioconductor.

label: Biotin

source_name: 14-day-old seedlings

label_protocol: Standard Affymetrix protocol

growth_protocol: Surface sterilized seeds were individually plated on 1/2 MS plates with 0.9% agar. Seedlings were grown in a CU36L5 incubator under 24-hour illumination.

extract_protocol: RNA extracted using Ambion RNAqueous kit as described in the product manual.

treatment_protocol: None other than surface sterilization (33% bleach, 0.1% Triton X-100)

value: whole seedling


title: 1922 144h_pre-infection


title: replica1 MM2d RPM1g control vs MM2d RPM mg*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 1 of 3. Transcriptional status MM2d RPM1g control vs MM2d RPM simulated mg


title: 14-day pkl seedlings, biological replicate 2

description: Gene expression data from 14-day-old pkl seedlings, biological replicate 2


title: 1920 24h_post-infection


title: 14-day pkl seedlings, biological replicate 1

description: Gene expression data from 14-day-old pkl seedlings, biological replicate 1


title: 14162845 - mpk3_flg1 vs mpk3_1

hyb_protocol: mpk3_1 Cy5 / mpk3_flg1 Cy3 : 30pmol.

growth_protocol: seedling - Plates, MS agar, long day, Percival

value: 2 week


title: 14162846 - mpk3_2 vs mpk3_flg2

hyb_protocol: mpk3_flg2 Cy5 / mpk3_2 Cy3 : 30pmol.


title: 14-day wild-type seedlings, biological replicate 1

description: Gene expression data from 14-day-old WT seedlings, biological replicate 1

value: WT


title: 14162847 - mpk3_flg2 vs mpk3_2

hyb_protocol: mpk3_2 Cy5 / mpk3_flg2 Cy3 : 30pmol.


title: 14-day wild-type seedlings, biological replicate 2

description: Gene expression data from 14-day-old WT seedlings, biological replicate 2


title: 1981 144h_pre-infection

value: pre-infection


title: replica2 MM2d Mag1g control vs MM2d Mag 2g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 2 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 2g*


title: 1920 192h_post-infection


title: 1920 12h_post-infection


title: 14178269 - mpk3-2 vs wt-2

hyb_protocol: wt-2 Cy5 / mpk3-2 Cy3 : 30pmol.

growth_protocol: seedling - 2 weeks seedling grew in MS medium with 22° C and 70% HR


title: 14162844 - mpk3_1 vs mpk3_flg1

hyb_protocol: mpk3_flg1 Cy5 / mpk3_1 Cy3 : 30pmol.


title: replica1 MM2d Mag1g control vs MM2d Mag 1.9g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 1 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 1.9g*

value: MAG (magnetic) 1.9g*

value: MM2D (Wild type culture) MAG 1.9g*


title: replica3 MM2d RPM1g control vs MM2d RPM mg*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 3 of 3. Transcriptional status MM2d RPM1g control vs MM2d RPM simulated mg


title: 1920 144h_pre-infection


title: replica2 MM2d Mag1g control vs MM2d Mag 1.9g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 2 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 1.9g*


title: 14-day wild-type seedlings, biological replicate 3

description: Gene expression data from 14-day-old WT seedlings, biological replicate 3


title: replica3 MM2d Mag1g control vs MM2d Mag 1g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 3 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 1g*

value: MAG (magnetic) 1g*

value: MM2D (Wild type culture) MAG 1g*


title: arabidopsis nhx5-1/nhx6-1 3

city: davis

first: elias

last: bassil

state: CA

address: 1 shields ave

department: plant sciences

country: USA

institute: university of california

description: Gene expression data from Arabidopsis rosette leaf RNA hybridized to Affymetrix Arabidopsis Genome Array

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis 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: The data were normalized using JMPGenomics (ver 3.0) with STD normalization and background correction feature.

source_name: double knockout of AtNHX5-1 (WiscDsLox345-348M8/ AtNHX6-1 (SALK_113129), biological rep3

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

growth_protocol: Plants were grown in Metromix300 soil in 18-pot trays in a growth chamber with 8h L/16h D and fertilized weekly beginning week 2.

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

value: Rosette leaf

tag: strain/ecotype

value: colombia


title: 14178265 - wt-1 vs mpk3-1

description: Investigate flagellin mpk dependent genes.

hyb_protocol: mpk3-1 Cy5 / wt-1 Cy3 : 30pmol.


title: 1867 192h_post-infection

tag: cow id


title: replica1 MM2d Mag1g control vs MM2d Mag 2g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 1 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 2g*

value: MM2D (Wild type culture) 1g control

value: 1g control


title: 14178267 - wt-2 vs mpk3-2

hyb_protocol: mpk3-2 Cy5 / wt-2 Cy3 : 30pmol.


title: 14178266 - mpk3-1 vs wt-1

hyb_protocol: wt-1 Cy5 / mpk3-1 Cy3 : 30pmol.


title: 1867 12h_post-infection

tag: breed


title: 1586 192h_post-infection

tag: infection


title: 13968883 - wt2 vs wtflg2

hyb_protocol: wtflg2 Cy5 / wt2 Cy3 : 30pmol.


title: replica2 MM2d Mag1g control vs MM2d Mag 1g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 2 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 1g*


title: replica1 MM2d Mag1g control vs MM2d Mag 1g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 1 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 1g*


title: 1867 24h_post-infection

tag: time point


title: 13968882 - wtflg1 vs wt1

hyb_protocol: wt1 Cy5 / wtflg1 Cy3 : 30pmol.

tag: ecotype


title: replica1 MM2d Mag1g control vs MM2d Mag 0.1g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 1 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 0.1g*

value: MAG (magnetic) 0.1g*

value: MM2D (Wild type culture) MAG 0.1g*


title: 13968879 - mpk4_1 vs mpk4_flg1

hyb_protocol: mpk4_flg1 Cy5 / mpk4_1 Cy3 : 30pmol.

tag: age


title: replica3 MM2d Mag1g control vs MM2d Mag 0.1g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 3 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 0.1g*


title: 1586 24h_post-infection

value: Danish Holstein Friesian

value: liver


title: 1867 144h_pre-infection

value: female


title: 13968881 - wt1 vs wtflg1

hyb_protocol: wtflg1 Cy5 / wt1 Cy3 : 30pmol.

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


title: 13968884 - wtflg2 vs wt2

hyb_protocol: wt2 Cy5 / wtflg2 Cy3 : 30pmol.


title: replica2 MM2d Mag1g control vs MM2d Mag 0.1g*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 2 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag 0.1g*


title: 1586 12h_post-infection

hyb_protocol: Fifteen micrograms of cRNA was fragmented at 94 C for 35 min in a final volume of 40 ul in a buffer containing 40mM Tris-acetate pH 8.1, 100mM KOAc, and 30 mM MgOAc. Next, 260 ul of 6x SSPE-T hybridization buffer (1 M NaCl, 10 mM Tris pH 7.6, 0.005% Triton) was added and the cRNA was denatured by heating to 95 C for 5 min. The hybridization mixture was loaded onto the Affymetrix probe array cartridge (Affymetrix Bovine Genome Array) and incubated for 16 hr at 45 C at constant rotation (60 rpm). The washing and staining procedure was performed in the Affymetrix Fluidics Station. The probe array was exposed to 10 washes in 6x SSPE-T at 25 C followed by 4 washes in 0.5x SSPE-T at 50 C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C followed by 10 washes in 6x SSPE-T at 25 C. An antibody amplification step followed, using normal goat IgG as blocking reagent, final concentration 0.1 mg/ml (Sigma, St. Louis), and biotinylated anti-streptavidin antibody (goat), final concentration 3 ug/ml (Vector Laboratories, Burlingame, CA). This was followed by a staining step with a streptavidinphycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C and10 washes in 6x SSPE-T at 25 C (Kristensen et al. 2005: Genetics 171: 157–167).

value: post-infection


title: replica1 MM2d Mag1g control vs MM2d Mag mg*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 1 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag mg*

hyb_protocol: The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)

value: MAG (magnetic) mg*

value: MM2D (Wild type culture) MAG mg*


title: 14178261 - bak1bkk1-1 vs wt-1

hyb_protocol: wt-1 Cy5 / bak1bkk1-1 Cy3 : 30pmol.

growth_protocol: seedling - 2 weeks seedlings were grown under 22°c and 70 RH. Long day.

value: 2 week

growth_protocol: seedling - 2 weeks seedlings were grown in MS under 22°c and 70% RH. Long day.


title: replica3 MM2d Mag1g control vs MM2d Mag mg*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 3 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag mg*


title: replica2 MM2d LDC1g control vs MM2d LDC 2g

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 2 of 3. Transcriptional status MM2d LDC1g control vs MM2d LDC 2g

value: LDC (levitation) 2g

value: MM2D (Wild type culture) LDC 2g


title: 1415 24h_post-infection


title: 1415 12h_post-infection


title: 14178264 - bak1bkk1-2 vs wt-2

hyb_protocol: wt-2 Cy5 / bak1bkk1-2 Cy3 : 30pmol.


title: SSc fibroblasts

city: Kumamoto

first: Taiji

last: Naashima

address: 1-1-1 Honjo

department: Department of Dermatology and Plastic Surgery

country: Japan

institute: Faculty of Life Sciences, Kumamoto University

data_processing:
The raw threshold cycle (Ct) was normalized using the value of housekeeping gene ; deltaCt = (Ct_Target − Ct_HKG)]
For the normalization, it uses the average of five housekeeping genes ;SNORD48,SNORD47,SNORD44,U6 . Fold Change worksheet reports 1/2^ΔΔCt (ND or null : not detected data)

label: SYBR Green

organism: Homo sapiens

source_name: Human dermal fibroblasts obtained by skin biopsy from patients with diffuse cutaneous SSc

label_protocol: For RT2 Profiler PCR Array (SABioscience), microRNAs were reverse-transcribed into first strand cDNA using RT2 miRNA First Strand Kit (SABiosciences). A mixture of equal amounts of cDNAs from 5 normal fibroblasts or 5 SSc fibroblasts was prepared. The cDNA was mixed with RT2 SYBR Green/ROX qPCR Master Mix and the mixture was added into a 96-well RT2 miRNA PCR Array (SABiosciences) that included primer pairs for 88 human microRNAs.

extract_protocol: Total RNA was extracted from culture cells with ISOGEN (Nippon Gene, Tokyo, Japan). MicroRNA isolation from total RNA was performed using RT2 qPCR-Grade miRNA Isolation Kit (SA Bioscience).

tag: cell type

value: SSs fibroblasts

tag: activation agent

value: no activation

value: Test


title: 1415 192h_post-infection

tag: tissue


title: replica2 MM2d Mag1g control vs MM2d Mag mg*

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 2 of 3. Transcriptional status MM2d Mag1g control vs MM2d Mag mg*


title: 14178262 - wt-2 vs bak1bkk1-2

hyb_protocol: bak1bkk1-2 Cy5 / wt-2 Cy3 : 30pmol.


title: 1385 24h_post-infection

tag: gender


title: replica1 MM2d LDC1g control vs MM2d LDC 2g

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 1 of 3. Transcriptional status MM2d LDC1g control vs MM2d LDC 2g


title: Normal fibroblasts

source_name: Human dermal fibroblasts obtained by skin biopsy from healthy donors

value: normal fibroblasts

value: control


title: 13912837 - bak1bkk1_2 vs bak1bkk1flg2

hyb_protocol: bak1bkk1flg2 Cy5 / bak1bkk1_2 Cy3 : 30pmol.


title: 13912838 - bak1bkk1flg2 vs bak1bkk1_2

hyb_protocol: bak1bkk1_2 Cy5 / bak1bkk1flg2 Cy3 : 30pmol.


title: arabidopsis nhx5-2 1

source_name: single knockout of AtNHX5, T-DNA line GABI-09H405, biological rep1

value: Rosette leaf

value: colombia

tag: genotype


title: 14178260 - wt-1 vs bak1bkk1-1

hyb_protocol: bak1bkk1-1 Cy5 / wt-1 Cy3 : 30pmol.


title: 1385 192h_post-infection


title: 13912832 - bak1bkk1_1 vs bak1bkk1flg1

hyb_protocol: bak1bkk1flg1 Cy5 / bak1bkk1_1 Cy3 : 30pmol.


title: 1385 12h_post-infection


title: 1415 144h_pre-infection

value: pre-infection


title: ASC 72hr rep2

city: Palo Alto

first: Thomas

middle: A

last: Rando

address: 3801 miranda ave.

department: Department of Neurology and Neurological Sciences

institute: Stanford University School of Medicine

description: Total RNAs were isolated using Trizol (Invitrogen). Reverse transcription and amplification was performed as described by the manufacturer (Applied Biosystems). Diluted cDNAs were loaded onto the Taqman Array Rodent MicroRNA A or B Cards v2.0 and real-time PCR was performed using ABI 7900HT Fast Real-Time PCR System using recommended cycling condition (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing: Raw CT value was extracted using ABI Taqman SDS v2.3 software. miRNA gene expressions were normalized to U6 snRNA: delta CT = Ct_miRNA - Ct_U6snRNA. Relative quantitation of miRNA gene expressions was performed using delta delta CT method (see Supplementary files on Series record).

label: FAM

organism: Mus musculus

source_name: Muscle stem cells

label_protocol: Not applicable

tag: protocol

value: activated stem cells (ASC)

tag: time

value: male

value: 8 weeks

tag: strain


title: ASC 72hr rep1

extract_protocol: Total RNAs were isolated using Trizol (Invitrogen).


title: replica3 MM2d LDC1g control vs MM2d LDC 2g

description:
A.thaliana MM2d callus 1g vs altered gravity/magnet forces
Biological replicate 3 of 3. Transcriptional status MM2d LDC1g control vs MM2d LDC 2g

tag: sample type

value: MM2D (Wild type culture) 1g control

tag: cell line

tag: treatment

value: 1g control


title: ASC 60hr rep3


title: ASC 72hr rep3


title: ASC 60hr rep2


title: 1385 144h_pre-infection

tag: cow id

tag: breed

value: Danish Holstein Friesian

value: female

value: liver


title: CSL7191

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

description: DAT

hyb_protocol: 17 hrs, 60 degrees C according to Agilent protocol in Agilent recommended hyb oven

scan_protocol: Agilent B Scanner

data_processing: Agilent Feature Extraction, Rosetta Resolver

organism: Zalophus californianus

label_protocol: Agilent Quick Amp Labeling Kit, one-color, 500 ng RNA input  Quick Amp Labeling Kit, one-color   500ng input

extract_protocol: Total RNA extracted with PAXgene Blood RNA kit

treatment_protocol: Blood was collected from the caudal gluteal vein into PAXgene tubes from California sea lions (Zalophus californianus) in rehabilitation at the Marine Mammal Center, Sausalito, CA.

value: Blood

value: Male

tag: developmental stage

value: Subadult

tag: preliminary diagnosis

value: DAT


title: ASC 60hr rep1

tag: age


title: HSF-6

city: Taipei

first: Men-Luh

last: Yen

address: No.1, Sect. 1, Jen-Ai Road

country: Taiwan

institute: National Taiwan University

description: Gene expression profiling

hyb_protocol: 0.6 ug of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA was then hybridized to the custom stem cell 8 x 15K oligo microarray (Agilent Technologies, USA) at 60°C for 17 hours.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: The scanned images were analyzed by Feature extraction 9.5.3 software (Agilent Technologies, USA), an image analysis and normalization software for quantification of signal and background intensity. Normalized signal was generated from gProcessedSignal after normalization by 75th percentile. Data was generated by subtracting the mean background light intensity from the mean signal intensity then corrected for multiplicative surface.

source_name: human embryonic stem cell HSF-6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted by Trizol® Reagent (Gibco-Invitrogen, USA), and followed by processing with the RNeasy Mini Kit (Qiagen, Germany).  The extracted RNA was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA), with  purity assessed by using a Bioanalyzer 2100 (Agilent Technology, USA) using the RNA 6000 nano labchip kit (Agilent Technologies, USA).

treatment_protocol: Stem cells were cultured in undifferentiated conditions.

value: embryonic stem cells


title: 1586 144h_pre-infection

tag: infection

tag: time point


title: 1289 24h_post-infection

value: post-infection


title: 1289 192h_post-infection


title: BMMSC 2

description: Gene expression profiling

source_name: bone marrow mesenchymal stem cell donor 2

extract_protocol: Total RNA was extracted by Trizol® Reagent (Gibco-Invitrogen, USA), and followed by processing with the RNeasy Mini Kit (Qiagen, Germany).  The extracted RNA was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA), with purity assessed by using a Bioanalyzer 2100 (Agilent Technology, USA) using the RNA 6000 nano labchip kit (Agilent Technologies, USA).

tag: cell type

value: bone marrow mesenchymal stem cells


title: BMMSC 1

description: Gene expression profiling

source_name: bone marrow mesenchymal stem cell donor 1


title: CSL7203

description: DAT

tag: tissue


title: 13912836 - bak1bkk1flg1 vs bak1bkk1_1

hyb_protocol: bak1bkk1_1 Cy5 / bak1bkk1flg1 Cy3 : 30pmol.

tag: ecotype

value: 2 week

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


title: EMPs

description: Gene expression profiling

source_name: human ESC derived mesenchymal progenitors

value: embryonic mesenchymal progenitors


title: CSL7179

description: DAT

tag: gender

value: Adult


title: 1112 192h_post-infection


title: CSL7178

description: DAT


title: ASC 36hr rep3

tag: protocol

value: activated stem cells (ASC)

tag: time

value: male


title: 1289 12h_post-infection


title: ASC 36hr rep2

value: 8 weeks

tag: strain


title: 1289 144h_pre-infection

value: pre-infection


title: CSL7264

description: DAT

value: Unknown


title: ASC 36hr rep1


title: CSL7177

description: DAT


title: F 16wk vs F 1dph Replicate 1

city: St. Paul

first: Kent

last: Reed

state: MN

address: 295 ASVM, 1988 Fitch Ave

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

description: F line 1dph versus 16wk poult comparison

hyb_protocol: Fragmented, Cy3-coupled aRNA was mixed with its Cy5-coupled partner, and the mixtures were brought to 110 μL with 68°C SlideHyb 1 (Ambion, Inc.) and incubated at 68°C for 5 min.  These dye-coupled mixtures were then hybridized to oligonucleotide microarrays (described previously) for 18 h in a GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI) using the following conditions: 54°C for 18 h, followed by a medium-stringency wash at 42°C (2X SSC, 0.1% SDS), a high-stringency wash (0.2X SSC, 0.1% SDS) at 22°C, and a wash with postwash buffer (0.2X SSC) at 22°C.  Arrays were then rinsed in 2X SSC and Nanopure H2O, dried by centrifugation at 500 × g for 5 min.

scan_protocol: Scanned with a GenePix 4000B (Molecular Devices, Sunnyvale, CA) scanner. Image analysis was performed using GenePix Pro 6.0 with spot intensities exported as GPR files for statistical analysis.

data_processing: Fluorescence intensity data were normalized for dye intensity bias using the LOESS procedure of the normalize WithinArray function of the Bioconductor R software LIMMA(Smyth 2004). [Smyth G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology]. Doubly spotted probes were averaged, and three replicates with dye swap were combined. Label of the raw data files corresponds to the listed order in the 'label' field above. logFC is in the VALUE column of the data table below.

organism: Meleagris gallopavo

source_name: Total RNA from turkey cardiac muscle

label_protocol: Total RNA for use in microarrays was amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Inc.) per manufacturer instructions.  Briefly, 2 μg total RNA was incubated with T7 Oligo(dT) primer for 10 min at 70°C then reverse transcribed into cDNA at 42°C for 2 h.  Second strand synthesis was performed at 16°C for 2 h.  Double-stranded cDNA was then purified, and in vitro transcription was performed at 37°C for 4 h.  Amplified RNA (aRNA) was purified and quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).  For the dye coupling procedure, 10 μg aRNA was coupled to either Cy3 or Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) in the dark at room temperature for 1 hour until the reaction was quenched by the addition of 4M hydroxylamine.  Dye-coupled aRNA was purified and quantified, then 5 μg was fragmented to 60-200 nucleotide segments using RNA Fragmentation Reagents (Ambion, Inc.) at 70°C for 15 min in preparation for microarray hybridization.

extract_protocol: Total RNA extracted using TRIReagent (Molecular Research Center, Cincinnati, OH) following manufacturer's instructions.  RNA integrity and concentration was determined using an Agilent 2100 Bioanlyzer (Santa Clara, CA).

tag: genetic line

value: F

value: 1 dph

value: 16 wk


title: QSC 0hr rep3

value: quiescent  stem cells (QSC)


title: RBC2 1dph vs F 1dph

description: RBC2 line 1dph poult versus F 1dph poult comparison


title: CSL7175

description: DAT

value: Blood

value: Male


title: RBC2 1dph vs RBC2 16wk Replicate 4

description: RBC2 line 1dph poult versus 16wk comparison


title: 1112 24h_post-infection

value: Danish Holstein Friesian

value: female

value: liver


title: CSL7182

description: DAT

value: DAT


title: QSC 0hr rep2

source_name: Muscle Stem cells


title: 1112 12h_post-infection

value: post-infection


title: QSC 0hr rep1


title: CSL6658

description: DAT

value: Female

value: Adult


title: Wild type TFF2 rep4

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood from Tff2 KO as well as WT mice was collected in RNAprotect® Animal Blood Tubes (Qiagen GmbH, Hilden). About 400-500µl of peripheral blood were obtained from each animal. Following centrifugation of the blood samples at 5000 g for 10 min at room temperature (RT), the supernatant was discarded while the pellet was resuspended in 5ml RNase free water. After a second centrifugation step at 5000 g for 10 min and RT, isolation of total RNA including miRNA was performed using the miRNeasy kit (Qiagen GmbH, Hilden).

treatment_protocol: stored at -20 degree

tag: genotype

value: wild type


title: Wild type TFF2 rep6


title: IL-10-/- with Pathology = 1

city: Houston

first: Jeremy

middle: S

last: Schaefer

state: TX

address: 1941 East Rd

department: Diagnostic Sciences

institute: The University of Texas Health Science Center at Houston School of Dentistry

description: Mild Pathology. Pooled total RNA from 3 mice.

hyb_protocol: Samples were hybridized using a Tecan HS4800™ Pro automated hybridization station

scan_protocol: Agilent G2505B Microarray Scanners

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

source_name: IL-10-/- Colon

label_protocol: Samples were labeled using the miRCURY Hy3/Hy5 Power labeling kit following the manufacturer's instructions

extract_protocol: Total RNA extracted using miRNeasy following the manufacturer's instructions

tag: strain background

value: BALB/c

tag: genotype/variation

value: colon

tag: pathology

value: mild pathology

source_name: Common Reference (Samples 1, 2, and 3)


title: IL-10-/- with Pathology > 3

description: Severe Pathology. Pooled total RNA from 3 mice.

value: severe pathology


title: No Pathology Control

description: Control. Pooled total RNA from 3 mice.

source_name: BALB/c Colon

value: No pathology (control)


title: RBC2 16wk vs F 16wk

description: RBC2 16wk versus F 16wk comparison

tag: developmental stage

value: 16 wk

value: F


title: 993 192h_post-infection

source_name: Liver

tag: cow id

tag: breed


title: 1112 144h_pre-infection

tag: infection

value: pre-infection

tag: time point


title: CSL7407 [3]

description: Lepto

tag: tissue

value: Blood

value: Male

value: Subadult

tag: preliminary diagnosis

value: Lepto


title: CSL6652

description: DAT

value: DAT


title: Wild type TFF2 rep3

value: male


title: CSL7423

description: Outgroup

value: Outgroup


title: Wild type TFF2 rep2


title: Wild type TFF2 rep5

value: female


title: 993 24h_post-infection

value: Danish Holstein Friesian

value: liver

value: post-infection


title: CSL7295

description: Outgroup

value: Female

value: Adult


title: Wild type TFF2 rep1

value: wild type


title: CSL7398

description: Lepto


title: tff2 KO rep6

value: tff2 KO


title: tff2 KO rep5


title: developing mouse cochlear sensory epithelia P3_3

city: Montpellier

first: Said

last: Assou

address: 80, Av. Augustin Flich

institute: INSERM

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45°C on the GeneChip mouse U430 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100

source_name: Inner ear

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.

extract_protocol: Total RNA was isolated using RNeasy micro kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

value: Cochlear sensory epithelia


title: R272

type: genomic

city: Ames

first: Dorian

last: Garrick

state: IA

address: 2255 Kildee

institute: Iowa State University

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The genotyping was performed using the Ovine SNP50 BeadChip (Illumina, San Diego, CA, USA) with standard procedures at GeneSeek Inc. Lincoln, NE, USA.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Ovis aries

source_name: blood

label_protocol: standard Illumina protocol

extract_protocol: DNA was extracted from blood using a Roche MagNA Pure automated analyser. DNA samples were randomized on genotyping plates according to disease status.

tag: sample type

value: Female, affected

tag: disease state

value: rickets affected

value: Corriedale


title: 993 12h_post-infection

hyb_protocol: Fifteen micrograms of cRNA was fragmented at 94 C for 35 min in a final volume of 40 ul in a buffer containing 40mM Tris-acetate pH 8.1, 100mM KOAc, and 30 mM MgOAc. Next, 260 ul of 6x SSPE-T hybridization buffer (1 M NaCl, 10 mM Tris pH 7.6, 0.005% Triton) was added and the cRNA was denatured by heating to 95 C for 5 min. The hybridization mixture was loaded onto the Affymetrix probe array cartridge (Affymetrix Bovine Genome Array) and incubated for 16 hr at 45 C at constant rotation (60 rpm). The washing and staining procedure was performed in the Affymetrix Fluidics Station. The probe array was exposed to 10 washes in 6x SSPE-T at 25 C followed by 4 washes in 0.5x SSPE-T at 50 C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C followed by 10 washes in 6x SSPE-T at 25 C. An antibody amplification step followed, using normal goat IgG as blocking reagent, final concentration 0.1 mg/ml (Sigma, St. Louis), and biotinylated anti-streptavidin antibody (goat), final concentration 3 ug/ml (Vector Laboratories, Burlingame, CA). This was followed by a staining step with a streptavidinphycoerythrin conjugate, final concentration 2 ug/ul (Molecular Probes, Eugene, OR) in 6x SSPE-T for 30 min at 25 C and10 washes in 6x SSPE-T at 25 C (Kristensen et al. 2005: Genetics 171: 157–167).

tag: gender


title: developing mouse cochlear sensory epithelia P3_1


title: R61

value: Male, affected

value: Male


title: tff2 KO rep4


title: 993 144h_pre-infection

value: pre-infection


title: CSL7403

description: Lepto

value: Blood

value: Subadult

value: Lepto


title: R271


title: R62


title: CSL7461

description: Lepto


title: CSL7442

description: Outgroup

value: Outgroup


title: CSL7353 [2]

description: DAT

value: DAT


title: developing mouse cochlear sensory epithelia P3_2


title: tff2 KO rep3

value: male


title: R262

value: Female


title: tff2 KO rep2


title: CSL7323

description: Outgroup

value: Adult


title: CSL7443

description: DAT


title: R261


title: adult mouse cochlear sensory epithelia 3


title: adult mouse cochlear sensory epithelia 2


title: CSL7479

description: Lepto


title: R59


title: tff2 KO rep1


title: R58


title: bulge

city: Lausanne

first: Joerg

last: Huelsken

address: Station 19

country: Switzerland

institute: EPFL

hyb_protocol: cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays

scan_protocol: Affymetrix M10 version 1.0

data_processing: R, Bioconductor, GCRMA package

source_name: bulge

label_protocol: 30 ng of total RNA were amplified using the MessageAmpTM II aRNA kit (Ambion)

growth_protocol: 21d old mice were used

extract_protocol: tissue samples were dissected with a mCut Laser Microdissection System, RNA was isolated using the PicoPureTM Isolation Kit (Arcturus)

treatment_protocol: skin was embedded in OCT, frozen in liquid nitrogen, cutted on a cryostat and stained with eosin

tag: age

tag: cell type

value: bulge


title: hairshaft

source_name: hairshaft

tag: strain

value: hairshaft


title: Adult mouse cochlear sensory epithelia 1

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45°C on the  GeneChip mouse U430 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

value: Cochlear sensory epithelia


title: C2C12 5AC treated day3 rep3

city: Nijmegen

first: Marlinda

last: Hupkes

address: Heyendaalseweg 135

department: Cell and Applied Biology

country: Netherlands

institute: Radboud University Nijmegen

description: gene expression from 5AC treated C2C12 myotblasts (day 3)

hyb_protocol: 10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).

scan_protocol: GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).

data_processing: Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1.  To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.

source_name: RNA from 5AC treated, subconfluent C2C12 myoblasts, day 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs

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

treatment_protocol: Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted

tag: cell line

tag: treatment

value: 10 uM 5-azacytidine


title: CSL7477

description: Lepto

value: Juvenile


title: CSL7353

description: DAT


title: R211

value: Female, affected

value: rickets affected

value: Corriedale


title: R101lamb

value: Male, affected

value: Male


title: R172


title: C2C12 5AC treated day3 rep2


title: CSL7473

description: Lepto

value: Blood


title: R57


title: CSL7486

description: DAT


title: CSL7455

description: Lepto

value: Subadult

value: Lepto


title: C2C12 untreated day3 rep2

description: gene expression from untreated C2C12 myoblasts (day 3)

source_name: RNA from untreated, subconfluent C2C12 myoblasts, day 3

value: untreated


title: C2C12 untreated day3 rep3


title: Glioblastoma Case 2

city: Boston

first: Matija

last: Snuderl

state: MA

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

description: comparison between GBM and normal genomic DNA

hyb_protocol: The labeled DNA were purified with the Millipore Amicon 30 kDa centrifugal filter device (Billerica, MA) and mixed in equal proportion for hybridization to the array in the presence of Cot-1 DNA (Invitrogen, Carlsbad, CA) using the Agilent Oligo aCGH Hybridization Kit.

scan_protocol: Washed slides were scanned using the Agilent G2565CA Microarray Scanner.  Microarray TIFF (.tif)

data_processing: Images were processed and analyzed with Agilent CytoGenomics v1.5 software. Copy number aberration calls were made with a minimum regional absolute average log base 2 ratio of 0.25 and minimum contiguous probe count of 5.  All array data were also manually reviewed for subtle copy number changes not detected by the software.

source_name: Brain Tumor

label_protocol: Control and tumor DNA were labeled by random priming with CY3- and CY5-dUTP dyes, respectively using the Agilent Genomic DNA Enzymatic Labeling Kit.

extract_protocol: Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissue using the QIAamp Blood Mini Kit using a modified protocol incorporating deparaffinization and protease digestion (QIAGEN, Valencia, CA).

value: Glioblastoma

value: Brain tumor

source_name: Control

value: male

value: blood

value: control


title: CSL7421

description: Lepto


title: CSL7463

description: Outgroup

value: Female

value: Outgroup


title: CSL7451

description: DAT

value: Adult

value: DAT


title: Glioblastoma Case 5


title: Day 18 - Sample 1 - Liter 8

city: Charleston

first: Frances

middle: M

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

hyb_protocol: 480 ng of Cy3 labeled targets were hybridized to the array for 17 hours at 60°C. After hybridization, arrays were washed according to the manufacturer’s protocol (Agilent, Santa Clara, CA).

scan_protocol: Microarrays were imaged using an Agilent microarray scanner using extended dynamic range scanning

data_processing: Images were extracted with Agilent Feature Extraction version 9.5.3.1

organism: Karenia brevis

source_name: Karenia brevis, day 18

label_protocol: Total RNA (600 ng) was amplified and labeled with Cy3 dye using a low input linear amplification kit (Agilent, Santa Clara, CA). The amplified, labeled RNA was quantified using a NanoDrop ND-1000.

growth_protocol: Karenia brevis (Wilson isolate) was maintained in batch cultures in 1-L glass bottles with autoclaved, 20 µm filtered seawater at 36 psu obtained from the Vero Beach Field Station seawater system at the Florida Institute of Technology. Seawater was enriched with modified f/2 medium with 0.01 mM selenous acid (final concentration) and ferric sequestrene used in place of EDTA.Na2 and FeCl3∙6H2O. Cultures were maintained on a 16:8 light-dark cycle, with illumination from cool white lights at a photon flux density of 50-65 µE.m-2.-1 measured with a LiCor 2pi meter.

extract_protocol: Three replicate cultures at each timepoint were independently harvested by centrifugation. Total RNA from each sample was prepared using TriReagent. Following precipitation in isopropanol, the RNA was resuspended and purified using a Qiagen RNeasy column. Total RNA was quantified using a NanoDrop ND-1000 and qualified on an Agilent 2100.

treatment_protocol: RNA was extracted at days 4, 6, 10, 14, and 18 (3 biological replicates at each timepoint).

tag: isolate

value: Wilson

tag: day sample was collected

tag: growth phase

value: stationary phase


title: C2C12 5AC treated day3 rep1

value: 10 uM 5-azacytidine


title: Day 18 - Sample 3 - Liter 21


title: Day 14 - Sample 3 - Liter 22

source_name: Karenia brevis, day 14


title: R171

value: Female, affected

value: rickets affected

value: Corriedale


title: Day 18 - Sample 2 - Liter 17


title: R55

value: Male, affected

value: Male


title: R90

value: Female, F1 known heterozygote

value: F1 known heterozygote


title: Glioblastoma Case 1

value: Glioblastoma

value: Brain tumor

value: male


title: C2C12 untreated day3 rep1

value: untreated


title: R92

value: Female


title: R53


title: CSL7436

description: DAT

value: Blood

tag: developmental stage

value: Adult


title: Day 14 - Sample 2 - Liter 14

value: Wilson


title: P16 control OC base, biological rep 1

city: Omaha

first: Garrett

last: Soukup

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

description: Gene expression data from mouse organ of Corti base, littermate control

hyb_protocol: 15 ug of biotinylated target was hybridized and stained per standard protocols per manufacturer's suggestions in the Affymetrix hybridization oven model 640 and fluidics station model 450.

scan_protocol: The arrays were scanned using an Affymetrix High Resolution scanner 3000 7G.

data_processing: The data were analyzed using Bioconductor (R) version 2.6.1 and the affy package version 1.26 using the mas5 function to obtain probe set expression values that correspond to those from MAS 5.0 Affymetrix default analysis settings and global scaling normalization method.

source_name: Mouse organ of Corti from cochlea, basal half, littermate control

label_protocol: 75 to 125 ng of total RNA was amplified and labeled using the Affymetrix 2-cycle labeling kit per the manufacturer's suggestions.

growth_protocol: Genotyped mice were aged to postnatal day 16 and euthanized according to IACUC approved protocol.

extract_protocol: mirVana kit isolation of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Organ of Corti was immediately dissected from inner ear in phosphate-buffered saline, parted into apical and basal sections, and placed in lysis buffer on ice for immediate RNA extraction.

tag: mouse genome informatics (mgi) strains

value: Dicer1tm1Bdh (MGI:3589208) X Tg(Atoh1-cre)1Bfri (MGI:3775845)

tag: genotype

value: organ of Corti from cochlea, basal half

value: postnatal day 16


title: P16 control OC base, biological rep 2


title: Day 14 - Sample 1 - Liter 11

value: stationary phase


title: R101

value: Female, rickets affected

value: rickets affected

tag: breed

value: Corriedale


title: CSL7362 [2]

description: DAT

tag: tissue

value: Subadult

value: DAT


title: R24

value: Female, F1 known heterozygote

value: F1 known heterozygote


title: CSL7422 [2]

description: DAT

tag: preliminary diagnosis


title: CSL7471

description: Lepto

value: Male

value: Juvenile

value: Lepto


title: Day 10 - Sample 1 - Liter 5

source_name: Karenia brevis, day 10


title: Day 10 - Sample 2 - Liter 19


title: Day 10 - Sample 3 - Liter 4


title: P16 control OC apex, biological rep 1

description: Gene expression data from mouse organ of Corti apex, littermate control

source_name: Mouse organ of Corti from cochlea, apical half, littermate control


title: Day 6 - Sample 3 - Liter 7

source_name: Karenia brevis, day 6

value: logarithmic phase


title: P16 mutant OC base, biological rep 2

description: Gene expression data from mouse organ of Corti base, Dicer1 conditional knockout

source_name: Mouse organ of Corti from cochlea, basal half, Dicer1 conditional knockout

value: Dicer1 conditional knockout, Atoh1-Cre;Dicer1(flox/flox)


title: R52

tag: sample type

value: Male, rickets affected


title: Day 6 - Sample 2 - Liter 6

value: Wilson


title: CSL7448

description: DAT

value: Blood

value: Female

value: Adult


title: CSL7487

description: Lepto


title: P16 mutant OC base, biological rep 1

value: Dicer1tm1Bdh (MGI:3589208) X Tg(Atoh1-cre)1Bfri (MGI:3775845)

value: organ of Corti from cochlea, basal half

value: postnatal day 16


title: P16 control OC apex, biological rep 2

value: organ of Corti from cochlea, apical half


title: CSL7470

description: Lepto

value: Subadult


title: P16 mutant OC apex, biological rep 2

description: Gene expression data from mouse organ of Corti apex, Dicer1 conditional knockout

source_name: Mouse organ of Corti from cochlea, apical half, Dicer1 conditional knockout


title: Day 6 - Sample 1 - Liter 9


title: CSL7395

description: Lepto


title: BAP-Treated at 500 µg/L for 96 Hour, Replicate 2

city: Singapore

first: Choong Yong

last: UNG

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: Biological replicate 2 of 5: BAP-treated at 500 µg/L for 95 Hr

hyb_protocol: Reference RNA (labelled with Cy3) is co-hybridized with RNA samples extracted either from treated or control fish (labelled with Cy5) on a glass array spotted with Zf_23K_oligo_COMP_v4Apx zebrafish oligo probes.

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized. Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: Male zebrafish liver tissue

label_protocol: For fluorescence labeling of cDNAs, 10 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish. Labeled cDNA were concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were maintained at room temperature (26°C + 1°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

treatment_protocol: Male zebrafish were exposed to 5, 50, 500 µg/L BAP for 24 and 96 hours at room temperature.

value: male

value: BAP-treated liver tissue

value: liver

value: BAP-Treated at 500 ug/L

tag: time

source_name: Male and female zebrafish liver tissue

value: male and female

value: untreated


title: BAP-Treated at 500 µg/L for 96 Hour, Replicate 3

description: Biological replicate 3 of 5: BAP-treated at 500 µg/L for 95 Hr

tag: gender

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Day 4 - Sample 3 - Liter 24

source_name: Karenia brevis, day 4

value: logarithmic phase


title: BAP-Treated at 500 µg/L for 96 Hour, Replicate 4

description: Biological replicate 4 of 5: BAP-treated at 500 µg/L for 95 Hr


title: BAP-Treated at 500 µg/L for 96 Hour, Replicate 5

description: Biological replicate 5 of 5: BAP-treated at 500 µg/L for 95 Hr


title: P16 mutant OC apex, biological rep 1

value: Dicer1 conditional knockout, Atoh1-Cre;Dicer1(flox/flox)

tag: age


title: CSL7489

description: DAT

value: Blood

value: Male

value: Juvenile

value: DAT


title: CSL7362

description: DAT

value: Female


title: Day 4 - Sample 2 - Liter 16

value: Wilson


title: kidney sham--B

city: Salt Lake City

first: Jason

last: Schwartz

state: UT

address: 30 North 1900 East

department: Surgery

institute: University of Utah

description: partial kidney homogenate

hyb_protocol: Hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 Array was carried out according to Affymetrix directions.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 laser confocal slide scanner

data_processing: Data were processed using the affy and gcrma libraries in R.

source_name: kidney sham

label_protocol: cDNA was generated from  RNA and was labeled with the One-Cycle Target labeling kit (Affymetrix)

extract_protocol: Kidneys and liver were harvested after in situ perfusion with 10 ml of RNAse-free PBS and 10 ml of RNA Later reagent (Qiagen). Total cellular RNA was isolated from morcellated whole kidneys and liver using a commercial kit (RNA Easy, Qiagen). To extract RNA, 30 mg of tissue was processed according to the manufacturer’s instructions. RNA integrity was monitored using an Agilent Bioanalyzer (Agilent Technologies).

value: kidney

tag: time point

value: 24 hour post-sham saline injection


title: CSL7407 [2]

description: Lepto

hyb_protocol: 17 hrs, 60 degrees C according to Agilent protocol in Agilent recommended hyb oven

value: Subadult

value: Lepto


title: BAP-Treated at 500 µg/L for 24 Hour, Replicate 5

description: Biological replicate 5 of 5: BAP-treated at 500 µg/L for 24 Hr

value: male

value: BAP-treated liver tissue

value: liver


title: CSL7371

description: Outgroup

value: Adult

value: Outgroup


title: liver sham--C

description: partial liver homogenate

source_name: liver sham


title: CSL7526

description: Outgroup


title: kidney sham--C

description: partial kidney homogenate


title: BAP-Treated at 500 µg/L for 96 Hour, Replicate 1

description: Biological replicate 1 of 5: BAP-treated at 500 µg/L for 95 Hr

value: BAP-Treated at 500 ug/L

value: male and female

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Day 4 - Sample 1 - Liter 28

value: logarithmic phase


title: BAP-Treated at 500 µg/L for 24 Hour, Replicate 2

description: Biological replicate 2 of 5: BAP-treated at 500 µg/L for 24 Hr


title: kidney sham--A

description: partial kidney homogenate


title: BAP-Treated at 500 µg/L for 24 Hour, Replicate 3

description: Biological replicate 3 of 5: BAP-treated at 500 µg/L for 24 Hr


title: BAP-Treated at 500 µg/L for 24 Hour, Replicate 4

description: Biological replicate 4 of 5: BAP-treated at 500 µg/L for 24 Hr


title: liver sham--B

description: partial liver homogenate


title: CSL7523

description: Lepto

value: Blood

value: Male


title: Patient 2 : 253278210006_1_3_Processed

city: Gosselies (Charleroi)

first: Bernard

last: Grisart

address: Avenue Georges Lemaitre,25

department: Centre de génétique humaine

country: Belgium

institute: Institut de pathologie et de génétique

description: CGH analysis using standard Agilent hybridization procedure as recommended by Agilent : G4410-90010

hyb_protocol: Labelled DNA was hybridized according to manufactured instruction (Agilent G4410-90010) with Cot-1 DNA from Roche (11 581 074 001), 2µg.

scan_protocol: Scanned on an upgraded Agilent Scanner G2539A

data_processing: Extraction of data from scanned tiff files (Agilent type C scanner : upgraded scanner G2539A) was performed using feature extraction software (version 10.7.3.1) with an hg19 annotated design file (032482_D_F_20110208) and a modified Agilent provided extraction protocol (CGH_107_Sep09 ; "linear and lowess" normalization was used instead of linear normalization only as in the Agilent provided protocol).  Visualisation of the data (log2ratio) and aberration calling were performed using Genomic Work Bench (v.6.5.0.58)

source_name: DNA from a female patient with Kabuki phenotype

label_protocol: Patient and reference DNA was labeled by random priming using BioPrime Array CGH Genomic Labeling System (Invitrogen, 18095-012).  Patient DNA (250 ng) was labeled with Cyanine-5 dCTP (Amersham, PA55021) and reference DNA (250 ng of a pool of 7 sex-matched DNA) was labeled with Cyanine-3 dCTP (Amersham, PA53021).  Labeled DNA were pooled and were purified by ethanol precipitation and hybridized on Agilent 244K whole genome array for 24h using procedure recommended by Agilent (G4410-90010).

growth_protocol: No growth ; DNA directly extrated from blood of patients

extract_protocol: genomic DNA was extracted using QiaAmp DNA blood extraction kit (Ref 51106) from Qiagen using 200 µl of fresh blood according to Agilent recommendations (G4410-90010 : Agilent Oligonucleotide array-based CGH for genomic analysis).

value: whole blood

source_name: Pool of DNA from 7 normal female individuals


title: BAP-Treated at 500 µg/L for 24 Hour, Replicate 1

description: Biological replicate 1 of 5: BAP-treated at 500 µg/L for 24 Hr


title: Daphnia pulex SKC_1

city: Columbia

first: Jeffry

middle: L.

last: Dudycha

address: 715 Sumter Street

department: Biological Sciences

institute: University of South Carolina

hyb_protocol: 1 µg of each of the two paired labeled samples was hybridized at 42°C during 16 hours to microarrays. We used MAUI SC mixers, a 4-bay MAUI Hybridization system and Pronto Universal Microarray Hybridization kits (Corning) according to the manufacturer recommendations. Array washes after hybridizations were performed using the Pronto kit.

scan_protocol: slides were scanned on a Perkin Elmer ProScanArray Express HT scanner and the images quantified using Perkin Elmer ScanArray Express SP3 software

data_processing: All arrays were assayed for data quality, and normalized using print-tip loess without background correction because nearly all spot-background correlations were below 0.2.  Between-slide normalization was done with the Aquantile method.  All data processing was done in the limma package of R.

label: Alexafluor 555

organism: Daphnia pulex

source_name: whole animal, Lake Murray

label_protocol: 1.5 µg of each sample was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion) according to the manufacturer recommendations. 8 µg of amplified RNA was labeled with either Alexa Fluor 555 or Alexa Fluor 647 dyes (Invitrogen).

growth_protocol: Beakers of experimental animals were randomly distributed within an environmental chamber at 20°C on a 12:12 L:D cycle.  Experimental animals were fed a satiating level (at least 20,000 cells/ml) of the standard lab diet, vitamin-enriched A. falcatus, daily.  Animals were transferred to new beakers thrice a week until the experimental animals were 10 d old.

extract_protocol: total RNA was extracted from frozen tissue using a Qiagen RNeasy kit with the optional on-column DNase treatment

treatment_protocol: We collected epilimnetic lakewater from Lake Murray, brought it back to the lab and screened it through an 80 um mesh to remove any zooplankton.  This lakewater therefore contained the seston that forms the natural resource environment for zooplankton.  We conducted a 24-hr pulse experiment where half of the individuals, selected at random, were transferred into a beaker containing screened lakewater from Lake Murray; these were not fed A. falcatus that day.  The remaining beakers were transferred to filtered water from Lake Murray and fed A. falcatus at a density of 23,000 cells ml-1.  Thus the only difference between the Lake Murray seston treatment and the A. falcatus control was natural seston vs. lab food

value: female

label: Alexafluor 647

source_name: whole animal, Ankistrodesmus


title: Daphnia pulex POVI_11


title: Patient 3 : 253278210001_1_3_Processed


title: CSL7422

description: DAT

extract_protocol: Total RNA extracted with PAXgene Blood RNA kit

value: Female

value: DAT


title: kidney 48 hour--C

description: partial kidney homogenate

source_name: kidney 48 hour

value: kidney

value: 48 hour post-GalN


title: kidney 48 hour--B

description: partial kidney homogenate


title: CSL7871

description: DAT


title: BAP-Treated at 50 µg/L for 96 Hour, Replicate 6

description: Biological replicate 6 of 6: BAP-treated at 50 µg/L for 96 Hr

value: male

value: BAP-treated liver tissue

value: BAP-Treated at 50 ug/L


title: CSL8057

description: DAT

value: Adult


title: kidney 48 hour--A

description: partial kidney homogenate


title: liver 48 hour--C

description: partial liver homogenate

source_name: liver 48 hour

value: liver


title: liver sham--A

description: partial liver homogenate

value: 24 hour post-sham saline injection


title: CSL7750

description: DAT


title: BAP-Treated at 50 µg/L for 96 Hour, Replicate 5

description: Biological replicate 5 of 6: BAP-treated at 50 µg/L for 96 Hr

value: male and female

value: untreated


title: liver 48 hour--B

description: partial liver homogenate


title: Daphnia pulex WF_6


title: Daphnia pulex POVI_15


title: Patient 1 : 253278210001_1_1_Processed


title: CSL7462

description: Lepto

value: Juvenile

value: Lepto


title: liver 48 hour--A

description: partial liver homogenate


title: BAP-Treated at 50 µg/L for 96 Hour, Replicate 4

description: Biological replicate 4 of 6: BAP-treated at 50 µg/L for 96 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: BAP-Treated at 50 µg/L for 96 Hour, Replicate 3

description: Biological replicate 3 of 6: BAP-treated at 50 µg/L for 96 Hr


title: BAP-Treated at 50 µg/L for 96 Hour, Replicate 2

description: Biological replicate 2 of 6: BAP-treated at 50 µg/L for 96 Hr


title: CSL7926

description: DAT

value: Blood

value: Subadult


title: CSL7390

description: Outgroup

value: Male

value: Outgroup


title: BAP-Treated at 50 µg/L for 24 Hour, Replicate 7

description: Biological replicate 7 of 7: BAP-treated at 50 µg/L for 24 Hr


title: BAP-Treated at 50 µg/L for 96 Hour, Replicate 1

description: Biological replicate 1 of 6: BAP-treated at 50 µg/L for 96 Hr


title: Daphnia pulex BFP_2

value: female


title: kidney 24 hour--B

description: partial kidney homogenate

source_name: kidney 24 hour

value: kidney

value: 24 hour post-GalN


title: CSL7482

description: DAT

value: DAT


title: Daphnia pulex WF_3


title: Daphnia pulex WHIT_2


title: CSL7492

description: Lepto


title: Daphnia pulicaria 3L2_1

organism: Daphnia pulicaria


title: BAP-Treated at 50 µg/L for 24 Hour, Replicate 5

description: Biological replicate 5 of 7: BAP-treated at 50 µg/L for 24 Hr

value: male

value: BAP-treated liver tissue

value: BAP-Treated at 50 ug/L


title: kidney 24 hour--C

description: partial kidney homogenate


title: BAP-Treated at 50 µg/L for 24 Hour, Replicate 6

description: Biological replicate 6 of 7: BAP-treated at 50 µg/L for 24 Hr

value: liver


title: kidney 24 hour--A

description: partial kidney homogenate


title: Daphnia pulex COL_1


title: BAP-Treated at 50 µg/L for 24 Hour, Replicate 4

description: Biological replicate 4 of 7: BAP-treated at 50 µg/L for 24 Hr

value: male and female


title: liver 24 hour--B

description: partial liver homogenate

source_name: liver 24 hour


title: Daphnia pulicaria BAS_5


title: liver 24 hour--C

description: partial liver homogenate


title: liver 24 hour--A

description: partial liver homogenate


title: BAP-Treated at 50 µg/L for 24 Hour, Replicate 3

description: Biological replicate 3 of 7: BAP-treated at 50 µg/L for 24 Hr

value: untreated


title: CSL319

description: Healthy

value: Adult

value: Healthy


title: CSL606

description: Healthy


title: Daphnia pulicaria PINE_13


title: BAP-Treated at 50 µg/L for 24 Hour, Replicate 2

description: Biological replicate 2 of 7: BAP-treated at 50 µg/L for 24 Hr

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: CSL797

description: Healthy

value: Blood


title: Daphnia pulicaria XVI_11


title: Pineal gland from Crx-/- at ZT20, biological rep 3

city: Copenhagen

first: Louise

last: Rovsing

address: Blegdamsvej 3

department: Neuroscience and Pharmacology

institute: Copenhagen University

description:
CRX-/- ZT20 #3 Signal
Gene expression in the pineal gland of  a Crx-/- mouse at ZT20

hyb_protocol: Labeled cDNA was mixed with control oligonucleotides B2, 20x eukaryotic hybridization controls (Affymetrix), herring sperm DNA, acetylated BSA, 2x hybridization buffer, and DMSO according to the Affymetrix protocol.  cDNA was hybridized on Affymetrix mouse GeneChip 430_2 microarray chip for 18 to 24 hours at 45°C. The cips were washed and stained in the  Affymetrix GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned on an Affymetrix 3000 Scanner.

data_processing: GCOS software statistical algorithm (Affymetrix)

source_name: Crxsv at ZT20, pineal gland

label_protocol: Nugen Ovation RNA amplification system V2 was used to convert 100 ng RNA to cDNA following the manufacture’s protocol. Double stranded cDNA was SPIA® amplified using the same kit followed by purification (instead of using the washing buffer, the cDNA was washed twice in freshly prepared 80% ethanol).  3.75 µg cDNA was used for fragmentation and labeling (FL-Ovation cDNA Biotin Module V2).

growth_protocol: Control and Crx-/- mice (both genders, > 2 months of age) were bred and kept in a 12L:12D light cycle with food and water ad libitum.

extract_protocol: Total RNA was extracted with RNeasy (Qiagen) according to manufacturer's protocol

treatment_protocol: To collect pineal glands, animals were euthanized by CO2 followed by decapitation at ZT 6 and ZT20. Dim red light was used for killing the animals at ZT20.

tag: strain

value: Crx-/-

value: Pineal gland


title: Daphnia pulicaria WAR_19


title: CSL7367

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

institute: University of Ferrara

description: Outgroup

scan_protocol: Agilent B Scanner

data_processing: Agilent Feature Extraction, Rosetta Resolver

label_protocol: Agilent Quick Amp Labeling Kit, one-color, 500 ng RNA input  Quick Amp Labeling Kit, one-color   500ng input

value: Male

value: Juvenile

value: Outgroup


title: BAP-Treated at 50 µg/L for 24 Hour, Replicate 1

description: Biological replicate 1 of 7: BAP-treated at 50 µg/L for 24 Hr


title: CSL739

description: Healthy


title: CSL7594

description: DAT

value: Female


title: CSL7600

description: Lepto

value: Lepto


title: BAP-Treated at 5 µg/L for 96 Hour, Replicate 3

description: Biological replicate 3 of 5: BAP-treated at 5 µg/L for 95 Hr

value: male

value: BAP-Treated at 5 ug/L


title: BAP-Treated at 5 µg/L for 96 Hour, Replicate 4

description: Biological replicate 4 of 5: BAP-treated at 5 µg/L for 95 Hr

value: BAP-treated liver tissue


title: Daphnia pulicaria LMILL_11

value: female


title: BAP-Treated at 5 µg/L for 96 Hour, Replicate 5

description: Biological replicate 5 of 5: BAP-treated at 5 µg/L for 95 Hr

value: liver

value: male and female


title: Pineal gland from Crx-/- at ZT20, biological rep 2

description:
CRX-/- ZT20 #2 Signal
Gene expression in the pineal gland of  a Crx-/- mouse at ZT20


title: CSL7528

description: DAT

value: Subadult

value: DAT


title: Daphnia pulicaria BAKER_1


title: Pineal gland from Crx-/- at ZT6, biological rep 3

description:
CRX-/- ZT6 #3 Signal
Gene expression in the pineal gland of  a Crx-/- mouse at ZT6

source_name: Crxsv at ZT6, pineal gland


title: Daphnia pulicaria LAW_12


title: Pineal gland from Crx-/- at ZT20, biological rep 1

description:
CRX-/- ZT20 #1 Signal
Gene expression in the pineal gland of  a Crx-/- mouse at ZT20


title: Pineal gland from Crx-/- at ZT6, biological rep 2

description:
CRX-/- ZT6 #2 Signal
Gene expression in the pineal gland of  a Crx-/- mouse at ZT6


title: Pineal gland from Crx-/- at ZT6, biological rep 1

description:
CRX-/- ZT6 #1 Signal
Gene expression in the pineal gland of  a Crx-/- mouse at ZT6


title: BAP-Treated at 5 µg/L for 96 Hour, Replicate 2

description: Biological replicate 2 of 5: BAP-treated at 5 µg/L for 95 Hr

value: untreated

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Pineal gland from control mouse at ZT20, biological rep 3

description:
129sv ZT20 #3 Signal
Gene expression in the pineal gland of  a control mouse at ZT20

source_name: 129sv at ZT20, pineal gland

value: control


title: BAP-Treated at 5 µg/L for 24 Hour, Replicate 6

description: Biological replicate 6 of 6: BAP-treated at 5 µg/L for 24 Hr


title: CSL7478

description: Lepto

value: Blood


title: P2-2

city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

institute: University of Alabama in Huntsville

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: Drosophila mojavensis (ANZA 402.17)

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

growth_protocol: Flies were reared in opuntia/banana food in bottle at low density.

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).  Following RNA extraction, mRNA was amplified using the MessageAmp™ II aRNA amplification kit (Applied Biosystems/Ambion, Austin, TX, USA)

treatment_protocol: We used one D. mojavensis isofemale line collected from Anza Borrego Desert State Park (CA, USA) in April of 2002, and one D. arizonae isofemale line collected from Guaymas, Sonora, Mexico, in March of 2006 for our experiments.  We collected virgin males and females within 24 hours of emergence  and aged them separately for 10-12 days.  For mating experiments, one D. mojavensis female was introduced to a vial containing two D. mojavensis or D. arizonae males.  Following copulation males were removed from vials and females were kept in isolation until lower reproductive tracts were removed at either 15 minutes, two hours, or six hours postmating; we also removed lower reproductive tracts from virgin females at this time. Tissues were placed immediately in Trizol and frozen at -80°C until total RNA was extracted using a standard Trizol protocol. We performed two biological replicates for each timepoint by pooling 20-25 lower reproductive tracts for each sample (14 samples total).

tag: mating status

value: Conspecific

tag: time post-copulation


title: Pineal gland from control mouse at ZT20, biological rep 2

description:
129sv ZT20 #2 Signal
Gene expression in the pineal gland of  a control mouse at ZT20

value: Pineal gland


title: P15-2


title: BAP-Treated at 5 µg/L for 96 Hour, Replicate 1

description: Biological replicate 1 of 5: BAP-treated at 5 µg/L for 95 Hr

source_name: Male zebrafish liver tissue

tag: treatment


title: P2-1


title: Pineal gland from control mouse at ZT20, biological rep 1

description:
129sv ZT20 #1 Signal
Gene expression in the pineal gland of  a control mouse at ZT20


title: CSL7407

description: Lepto

value: Male


title: CSL7552

description: DAT

value: Female


title: CSL7414

description: Outgroup

value: Outgroup


title: BAP-Treated at 5 µg/L for 24 Hour, Replicate 5

description: Biological replicate 5 of 6: BAP-treated at 5 µg/L for 24 Hr

value: male

source_name: Male and female zebrafish liver tissue


title: Pineal gland from control mouse at ZT6, biological rep 2

description:
129sv ZT6 #2 Signal
Gene expression in the pineal gland of  a control mouse at ZT6

source_name: 129sv at ZT6, pineal gland


title: Pineal gland from control mouse at ZT6, biological rep 3

description:
129sv ZT6 #3 Signal
Gene expression in the pineal gland of  a control mouse at ZT6


title: CSL7513

description: Outgroup


title: CSL7581

description: Outgroup


title: BAP-Treated at 5 µg/L for 24 Hour, Replicate 4

description: Biological replicate 4 of 6: BAP-treated at 5 µg/L for 24 Hr

value: BAP-Treated at 5 ug/L


title: V2

value: Virgin


title: CSL7521

description: DAT


title: BAP-Treated at 5 µg/L for 24 Hour, Replicate 2

description: Biological replicate 2 of 6: BAP-treated at 5 µg/L for 24 Hr

value: BAP-treated liver tissue


title: BAP-Treated at 5 µg/L for 24 Hour, Replicate 1

description: Biological replicate 1 of 6: BAP-treated at 5 µg/L for 24 Hr

value: liver


title: BAP-Treated at 5 µg/L for 24 Hour, Replicate 3

description: Biological replicate 3 of 6: BAP-treated at 5 µg/L for 24 Hr

value: male and female


title: H15-2

value: Heterospecific


title: CSL7483 [2]

description: Lepto

value: Subadult

value: Lepto


title: V1


title: H6-1


title: P15-1


title: H6-2


title: Pineal gland from control mouse at ZT6, biological rep 1

description:
129sv ZT6 #1 Signal
Gene expression in the pineal gland of  a control mouse at ZT6


title: P6-1


title: htHSC sample 2 replicate 2

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description: 14.5dpc fetal liver HSC

hyb_protocol: 3.75 micrograms of biotinylated material was hybridized according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: GCRMA probe summarization and normalization using the Bioconductor gcrma package (http://www.bioconductor.org).

source_name: Sca-1+,Lin-,AA4.1+,c-Kit++ FLHSC from 15 embryos combined

label_protocol:
12ng of total RNA was amplified following the Ovation RNA amplification protocol.
12 nanograms of total RNA was amplified and processed to produce biotinylated cDNA targets using the NuGen Ovation Biotin labeling system.

extract_protocol: Qiagen RNeasy® micro kit following manufacturer's protocol.

tag: genetic background

value: Crebbp+/-

tag: cell type

value: Sca-1+,Lin-,AA4.1+,c-Kit++ FLHSC

value: 14 dpc


title: htHSC sample 1 replicate 2

description: 14.5dpc fetal liver HSC


title: htHSC sample 1 replicate 1

description: 14.5dpc fetal liver HSC


title: CSL7501

description: DAT

value: Blood

tag: developmental stage

value: DAT


title: htHSC sample 2 replicate 1

description: 14.5dpc fetal liver HSC


title: CSL7483

description: Lepto

value: Male


title: P6-2

value: Conspecific


title: CSL7332

description: Lepto

value: Female


title: H2-2


title: H15-1


title: wtHSC sample 2 replicate 2

description: 14.5dpc fetal liver HSC

value: wild type


title: CSL7428

description: DAT

value: Adult


title: oocyte from 12day HDAC1/2 conditional knocked-out mouse, biological rep1

status: Public on Dec 31 2011

city: Philadelphia

first: Hua

last: Pan

state: PA

address: 415 S University Avenue

department: Department of Biology

institute: University of Pennsylvania

description: Gene expression data from oocyte from 12day mouse

hyb_protocol: Following fragmentation, Four independent biological replicates were hybridized to Affymetrix GeneChip Mouse 1.1 ST microarrays

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

data_processing: Raw microarray  data were analyzed as previously described using MAS5, GeneSpring v7, SAM and  EASE software

label_protocol: FL-OvationTM cDNA Biotin Module V2 (NuGen)

growth_protocol: from 12 day old mouse ovary

extract_protocol: using the PicoPure RNA kit (Arcturus) according to the manufacturer's instructions.

treatment_protocol: To establish the in vivo role(s) of HDAC1 and HDAC2 during oocyte growth, we generated conditional mutant oocytes using Zp3-Cre transgenic mice (PMID 9016703, 12912906) in combination with conditional loss of function alleles of Hdac1 or/and Hdac2

tag: strain background

tag: genotype/variation

value: HDAC1/2 conditional knocked-out

tag: tissue source

value: ovary

value: oocyte


title: CSL7480

description: Lepto

tag: tissue

value: Juvenile


title: wtHSC sample 1 replicate 1

description: 14.5dpc fetal liver HSC

tag: genotype


title: wtHSC sample 2 replicate 1

description: 14.5dpc fetal liver HSC


title: oocyte from 12day HDAC1/2 conditional knocked-out mouse, biological rep2


title: H2-1

value: Heterospecific


title: wtHSC sample 1 replicate 2

description: 14.5dpc fetal liver HSC


title: oocyte from 12day HDAC2 conditional knocked-out mouse, biological rep3

value: HDAC2 conditional knocked-out


title: oocyte from 12day HDAC1/2 conditional knocked-out mouse, biological rep4


title: oocyte from 12day HDAC1 conditional knocked-out mouse, biological rep2

value: HDAC1 conditional knocked-out


title: oocyte from 12day HDAC1 conditional knocked-out mouse, biological rep3


title: oocyte from 12day HDAC2 conditional knocked-out mouse, biological rep4


title: oocyte from 12day wild-type mouse, biological rep4

source_name: oocyte from 12day wild type


title: oocyte from 12day HDAC1/2 conditional knocked-out mouse, biological rep3


title: oocyte from 12day wild-type mouse, biological rep2


title: oocyte from 12day HDAC2 conditional knocked-out mouse, biological rep1


title: oocyte from 12day HDAC2 conditional knocked-out mouse, biological rep2


title: oocyte from 12day HDAC1 conditional knocked-out mouse, biological rep1


title: oocyte from 12day wild-type mouse, biological rep3


title: oocyte from 12day HDAC1 conditional knocked-out mouse, biological rep4


title: oocyte from 12day wild-type mouse, biological rep1