title: Mouse 17 MA07 Array

description:
MC-S_17_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_150_F

status: Public on Mar 14 2012

type: RNA

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

country: USA

institute: Cleveland Clinic Lerner Research Institute

description: Bone marrow was flushed with DMEM and cells were grown for 10-14 days in Bone marrow macrophages complete media

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow derived macrophages from female DBA/2J x AKR/J F2 mice

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: gender

value: female

tag: strain

tag: cell type

value: bone marrow derived macrophages (BMM)


title: Mouse 16 MA07 Array

city: Philadelphia

first: Floyd

last: Dukes

state: PA

address: 3615 Civic Center Boulevard

institute: University of Pennsylvania

description:
MC-S_16_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.

hyb_protocol: Hybridization was in 2.5 ml Micro-Hyb (Research Genetics) at 42oC for 18 h.

scan_protocol: Scanned at 50-μm resolution on a Storm PhosphorImager, and visualized using ImageQuant (Molecular Dynamics).

data_processing: Local background median was subtracted from signal median as background-corrected signal. Background-corrected signals were divided by their median on the array as the normalized expression values.

source_name: Mouse lung, flaxseed diet and radiation

label_protocol: RNA target was labeled with 33P (3,000–5,000 Ci/mM) using reverse transcriptase.

extract_protocol: Acid guanidinium-thiocyanate phenol-chloroform extraction.

treatment_protocol: C57BL/6 black mice were fed a 10% flaxseed diet for 21 days and/or given 13.5Gy radiation and sacrificed 48hrs post radiation.

tag: tissue

value: lung

tag: treatment

value: 3 weeks 10% flaxseed diet + 13.5Gy radiation


title: BMM_F2A_138_F


title: Mouse 13 MA07 Array

description:
MC-S_13_MA07
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.

source_name: Mouse lung, radiation

value: 13.5Gy radiation


title: BMM_F2A_140_F


title: Mouse 15 MA07 Array

description:
MC-S_15_MA07
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_137_F


title: Mouse 09 MA07 Array

description:
MC-S_09_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.

source_name: Mouse lung, flaxseed diet

value: 3 weeks 10% flaxseed diet


title: Mouse 10 MA07 Array

description:
MC-S_10_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: BMM_F2A_135_F


title: BMM_F2A_132_F


title: BMM_F2A_133_F


title: Mouse 08 MA07 Array

description:
MC-S_08_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: Mouse 11 MA07 Array

description:
MC-S_11_MA07
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: Mouse 12 MA07 Array

description:
MC-S_12_MA07
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2D_133_F


title: Mouse 07 MA07 Array

description:
MC-S_07_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: BMM_F2D_132_F


title: BMM_F2A_103_F


title: BMM_F2A_136_F


title: BMM_F2A_131_F


title: Mouse 04 MA07 Array

description:
MC-S_04_MA07
C57BL/6 black mouse.

source_name: Mouse lung, untreated


title: BMM_F2A_145_F


title: BMM_F2A_130_F


title: Mouse 05 MA07 Array

description:
MC-S_05_MA07
C57BL/6 black mouse.


title: Mouse 03 MA07 Array

description:
MC-S_03_MA07
C57BL/6 black mouse.


title: Mouse 01 MA07 Array

description:
MC-S_01_MA07
C57BL/6 black mouse.


title: Mouse 02 MA07 Array

description:
MC-S_02_MA07
C57BL/6 black mouse.


title: Mouse 20 MA10 Array

description:
MC-S_20_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_134_F


title: BMM_F2A_129_F


title: BMM_F2A_125_F


title: BMM_F2A_126_F


title: BMM_F2A_124_F


title: BMM_F2A_123_F


title: BMM_F2A_128_F


title: BMM_F2D_49_M

source_name: Bone marrow derived macrophages from male DBA/2J x AKR/J F2 mice

value: male


title: BMM_F2D_50_M


title: BMM_F2D_47_M


title: BMM_F2D_48_M


title: BMM_F2A_122_F


title: BMM_F2D_42_M


title: BMM_F2D_46_M


title: BMM_F2D_45_M


title: BMM_F2A_127_F


title: BMM_F2D_41_M


title: BMM_F2D_43_M


title: BMM_F2D_40_M


title: BMM_F2D_27_M


title: BMM_F2D_23_M


title: Mouse 06 MA07 Array

description:
MC-S_06_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: BMM_F2D_44_M


title: BMM_F2D_24_M


title: BMM_F2D_22_M


title: BMM_F2D_19_M


title: BMM_F2D_25_M


title: BMM_F2D_18_M


title: BMM_F2D_12_M


title: BMM_F2D_16_M


title: BMM_F2D_20_M


title: BMM_F2D_17_M


title: BMM_F2D_21_M


title: BMM_F2D_26_M


title: BMM_F2D_9_M


title: BMM_F2D_8_M


title: BMM_F2D_11_M


title: BMM_F2D_10_M


title: BMM_F2D_13_M


title: BMM_F2D_7_M


title: BMM_F2D_6_M


title: uvmo-3_rep4

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

hyb_protocol: Hybridization was done using Affymetrix standard hybridization protocol for Gene ST 1.0 arrays

scan_protocol: Scanned using GCOS

data_processing: Partek was used to generate RMA.RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed.

label: biotin

source_name: CD4 T cell clone

label_protocol: RNA was labeled using Affymetrix standard WT protocol (non-Ambion) using 100ng total RNA.

growth_protocol: Usual growth medium (RPMI 1640; 10^-5M 2 mercaptoethanol; 1x glutamax-1 (gibco); recombinant IL-1a, IL-2, IL-6, IL-7, IL-15, TNF-a, IFN-4a, IFN-b)

extract_protocol: RNAeasy with DNAse1 treatment step (Qiagen)

treatment_protocol: harvested at 72 hours

tag: cd4 t cell clone

tag: t cell mechanism

value: iNOS independent


title: uvmo-3_rep3


title: CS+2R versus RCH+CS+2R, replicate 3

city: Columbus

first: Nicholas

middle: M

last: Teets

address: 300 Aronoff Laboratory, 318 W. 12th Ave.

department: Department of Entomology

institute: Ohio State University

description: CS+2R versus RCH+CS+2R, replicate 3 of 4.

hyb_protocol: 825 ng of Cy3-labeled and 825ng of Cy5-labeled aRNA were fragmented and hybridized with rotation at 65°C for 17 hours. The arrays were washed according to the manufacturer's protocol.

scan_protocol: The arrays were scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Data were extracted using Feature Extraction Software v. 9.5 and corrected to internal controls. Raw data files are not otherwise background corrected or normalized.  Fold changes were calculated using background correction, within array normalization using loess, and between array normalization using the scale method.

organism: Sarcophaga bullata

label_protocol: Starting with 500 ng of total RNA, Cy3- and Cy5-labeled cRNA were generated using the Low RNA Input Linear Amplification kit according to the manufacturer's protocol. Total RNA was first converted to cDNA, and then in vitro transcription was used to generate the labeled cRNA.

growth_protocol: Flesh flies were reared at 25°C, 15:9 LD to promote direct, nondiapause development. All flies in these experiments were at the red-eye, pharate adult stage of development.

extract_protocol: Pools of 4 individuals were homogenized in 4 ml of TRI Reagent, and RNA was extracted and purified using the Ambion RiboPure Kit according to the manufacturer's protocol.

treatment_protocol: Control (C) flies were held at 25°C; rapid cold-hardening (RCH) flies were held at 0°C for 2 h and immediately sampled; cold shock + recovery (CS+2R) flies were directly transferred to -10°C for 2 h, then allowed to recover at 25°C for 2 h before sampling; and RCH + cold shock + recovery (RCH+CS+2R) flies were held at 0°C for 2 h, transferred to -10°C for 2 h, and then allowed to recover at 25°C for 2 h before sampling.

value: whole body

tag: developmental stage

value: pharate adult


title: uvmo-3_rep1


title: BMM_F2D_1_M


title: uvmo-3_rep2


title: CS+2R versus RCH+CS+2R, replicate 1

description: CS+2R versus RCH+CS+2R, replicate 1 of 4.


title: C versus RCH+CS+2R, replicate 3

description: Control versus RCH+CS+2R, replicate 3 of 4.

value: C


title: CS+2R versus RCH+CS+2R, replicate 4

description: CS+2R versus RCH+CS+2R, replicate 4 of 4.


title: BMM_F2D_3_M


title: C versus RCH+CS+2R, replicate 1

description: Control versus RCH+CS+2R, replicate 1 of 4.


title: BMM_F2A_59_M

description: Bone marrow was flushed with DMEM and cells were grown for 10-14 days in Bone marrow macrophages complete media


title: C versus RCH+CS+2R, replicate 2

description: Control versus RCH+CS+2R, replicate 2 of 4.


title: C versus CS+2R, replicate 3

description: Control versus CS+2R, biological replicate 3 of 4.


title: CS+2R versus RCH+CS+2R, replicate 2

description: CS+2R versus RCH+CS+2R, replicate 2 of 4.


title: uvmo-2_rep4


title: BMM_F2D_2_M


title: C versus CS+2R, replicate 4

description: Control versus CS+2R, biological replicate 4 of 4.


title: BMM_F2A_57_M


title: C versus RCH+CS+2R, replicate 4

description: Control versus RCH+CS+2R, replicate 4 of 4.


title: uvmo-2_rep3


title: BMM_F2A_58_M


title: C versus CS+2R, replicate 2

description: Control versus CS+2R, biological replicate 2 of 4.


title: uvmo-2_rep1


title: C versus RCH, replicate 4

description: Control versus RCH, biological replicate 4 of 4.

value: RCH


title: Spl4-10_rep4

value: iNOS dependent


title: C versus RCH, replicate 3

description: Control versus RCH, biological replicate 3 of 4.


title: C versus RCH, replicate 2

description: Control versus RCH, biological replicate 2 of 4.


title: 20 min Oxidative stress replicate 2

city: Greifswald

first: Leif

last: Steil

address: Friedrich-Ludwig-Jahn Str. 15A

department: Genetics and Functional Genomics

country: Germany

institute: University of Greifswald

description: Biological replicate 2 of 2

hyb_protocol: The Cy3 and Cy5 labeled cDNA solutions (60 μl) were combined with 43.7 μl nuclease water, 43.5 μl 20x SSC (Ambion), 10.9 μl 2% SDS (diluted 1:10 with nuclease water from 20% SDS, Ambion) and 21.9 μl array block solution (GeneScan mixed). This hybridization solution was then denatured for 1 min at 100°C, cooled down for 5 min on ice and immediately pipetted onto the array. Two gene frames (ABgene, Epsom, UK) had been glued previously on top of the hybridization region creating a 240 μl chamber on the microarray according to the manufacturer’s instructions. The resulting chamber was filled with hybridization solution and closed with a flexible coverslip (ABgene) without air bubbles. The microarray was then inserted into a 50 ml tube covered with aluminum foil and incubated under rotation at 60°C for 16 hours. After hybridization, the gene frames with coverslip were carefully removed, and the array was reinserted in the 50 ml tube. Subsequently, the microarray in the 50 ml tubes was subjected to washing in the following buffers: 2x SSC, 0.1% SDS for 5 min at 65°C, 0.5% SSC for 5 min at 25°C, and 0.1x SSC for 10 min at 25°C. Finally, the arrays were placed in an empty 50 ml tubes and centrifuged at 2500 rpm for drying.

scan_protocol: Scanned on ScanArray Express microarray scanner (Perkin Elmer Lifesciences, Boston, USA; Cy3 at 543 nm, Cy5 at 633 nm). Images were quantified using AArray Vision 6.0 program (GE Healthcare).

data_processing:
Median trimmed density with the local background substracted Array Vision 6.0 software (GE Healthcare) was used. Thereafter the 3 replicate spots were flagged as present (P), marginal (M), or absent (A). A spot was flagged as present (P) if the S/N ratio >2 and the difference of the median spot intensities between replicate spots was less than 1.25 fold. Marginal spots had to meet the same S/N ratio, but the difference of the median spot intensities between replicate spots had to be less than 1.5 fold. Spots with a S/N ratio<2 or a difference of the median spot intensities between replicate spots greater than 1.5 fold were flagged as absent. Replicate spot intensities were combined using the median of the spots flagged as present or marginal. If none of the replicate spots was flagged as present or marginal, the spot intensity values of the absent flagged spots were taken to obtain a complete data matrix.
Generally, correction for systematic effects (e.g., dye effects) in dual dye microarray data is usually achieved using Lowess normalization. In our hybridization design, the wild type and sigB knock-out were always cohybridized, consequently  the gene expressions differs widely depending on stress condition and time point. The assumption of Lowess normalization that a fraction of genes/probes (our study 50%) has unchanged expressions is therefore not applicable for most of the hybridizations. Because of this we used the synthetic slide method to normalize our data. Synthetic slides were created from samples having similar/equivalent gene expression pattern. The equivalence of samples was determined using correlation analysis. Therefore we separated the signals of the Cy3 and Cy5 channel for all slides and did a correlation analysis using Pearsons product moment. Then we paired these datasets into synthetic slides, if their Pearsons correlation was above 0.8. To normalize for systematic effects, the paired datasets (synthetic slides) were normalized by Lowess (f = 0.5) using MicroPrep (van Hijum et al., 2003). In the next step we calculated the ratios of gene expression for the wild type strain with respect to the sigB knock-out strain. These ratio values were labelled as "Synthetic slide normalized ratio of wt/mutant (wt168/BSM29)"

organism: Bacillus subtilis

source_name: 20 min, oxidative

label_protocol: For annealing 12,5 µg of total RNA and 1,25 µl of 2µg/µl random hexamer primer were incubated in 14.5 µl deonized water at 65°C for 10 min. Reverse Transcription was conducted by adding 5 µL of 5 x First Strand Buffer, 2.5 µl of 0.1 M DTT, 1 µL of dNTP mix (5 mM dATP; 5 mM dCTP; 5 mM dGTP; 2 mM dTTP) (Roche Diagnostics), 1 ml of 1 mM Cy3-dUTP or Cy5 dUTP (GE Healthcare), 1 µL  SuperScript II reverse transcriptase (200U/µl, Invitrogen). The reaction mixture was incubated at 42 °C for 2 h. Subsequently, the remaining RNA was hydrolyzed by incubation with 5 µL of 1M NaOH at 65 °C for 10 min. After neutralization with 5 µL of 1M HCl and 100 µL of TE buffer (pH 8.0), the labeled cDNA was purified using the CyScribe GFX Purification Kit (GE Healthcare).

growth_protocol: The strains were precultured in Luria-Bertani (LB) medium, in case of BSM29 supplemented with 50 μg/ml spectinomycin. For the stress experiments, a defined minimal medium was selected (Stülke et al., 1993)

extract_protocol: Total RNA was isolated by the mechanical cell disruption/ acid phenol method (Petersohn et al., 2001).

treatment_protocol: Various stresses were applied to the cultures incubated at 37oC with shaking at 210 rpm: ethanol stress - the culture was treated with a final concentration of 4% (v/v) ethanol; salt stress - solid sodium chloride was added to a final concentration of 4% (w/v); butanol stress - the culture was treated with a final concentration of 1% (v/v) butanol (Helmann et al., 2003); heat stress – the culture was shifted from 37oC to 48oC (Helmann et al., 2001); oxidative stress – the culture was treated with hydrogen peroxide in a final sub-lethal concentration of 60 μM (Helmann et al., 2003). Samples were taken in regular time intervals of 5, 10, 15, 20 min after the imposition of the environmental stress factors. For low-temperature growth, the cultures were grown in minimal medium at 37oC to an OD540 of 0.1, and then the cultures were shifted to 15oC. Afterwards, the cultures were sampled at an OD540 of 0.9 and 1.0. Glucose limitation was triggered by growing the strains with growth-limiting amounts of 0.05% (w/v) glucose at 37°C. Oxygen limitation was induced by reducing the shaking speed at OD540 of 0.3 from 210 rpm to 50 rpm. The sampling for both glucose and oxygen limitation was conducted at the time intervals of 15, 30, 45, 60, 90 min after the induction of the limitation.

tag: time

value: 20 min

tag: stress

value: oxidative


title: Spl4-10_rep2


title: 20 min Oxidative stress dye swap

description: dye swap


title: 20 min Oxidative stress replicate 1

description: Biological replicate 1 of 2


title: uvmo-4-rep3


title: C versus CS+2R, replicate 1

description: Control versus CS+2R, biological replicate 1 of 4.


title: Spl4-10_rep3


title: C versus RCH, replicate 1

description: Control versus RCH, biological replicate 1 of 4.


title: BMM_F2A_53_M


title: BMM_F2A_50_M


title: 15 min Oxidative stress dye swap

description: dye swap

source_name: 15 min, oxidative

value: 15 min


title: BMM_F2A_54_M


title: BMM_F2A_52_M


title: uvmo-4-rep1


title: BMM_F2A_55_M


title: Spl4-10_rep1


title: uvmo-4-rep4


title: BMM_F2A_51_M


title: BMM_F2A_56_M


title: uvmo-4-rep2


title: 15 min Oxidative stress replicate 2

description: Biological replicate 2 of 2


title: 15 min Oxidative stress replicate 1

description: Biological replicate 1 of 2


title: uvmo-2_rep2


title: BMM_F2A_49_M


title: BMM_F2A_48_M


title: BMM_F2A_47_M


title: 10 min Oxidative stress replicate 1

description: Biological replicate 1 of 2

source_name: 10 min, oxidative

value: 10 min


title: 5 min Oxidative stress replicate 1

description: Biological replicate 1 of 2

source_name: 5 min, oxidative

value: 5 min


title: 5 min Oxidative stress dye swap

description: dye swap


title: 10 min Oxidative stress replicate 2

description: Biological replicate 2 of 2


title: 0 min Oxidative stress replicate 2

description: Biological replicate 2 of 2

source_name: 0 min, oxidative

value: 0 min


title: 20 min Osmotic stress dye swap

description: dye swap

source_name: 20 min, osmotic

value: osmotic


title: 0 min Oxidative stress replicate 1

description: Biological replicate 1 of 2


title: 20 min Osmotic stress replicate 1

description: Biological replicate 1 of 2


title: 0 min Oxidative stress dye swap

description: dye swap


title: 10 min Oxidative stress dye swap

description: dye swap


title: 15 min Osmotic stress dye swap

description: dye swap

source_name: 15 min, osmotic


title: 15 min Osmotic stress replicate 2

description: Biological replicate 2 of 2


title: 10 min Osmotic stress replicate 1

description: Biological replicate 1 of 2

source_name: 10 min, osmotic


title: 10 min Osmotic stress dye swap

description: dye swap


title: 20 min Osmotic stress replicate 2

description: Biological replicate 2 of 2


title: 5 min Oxidative stress replicate 2

description: Biological replicate 2 of 2


title: BMM_F2A_45_M

value: bone marrow derived macrophages (BMM)


title: BMM_F2A_44_M


title: BMM_F2A_46_M


title: BMM_F2A_41_M


title: BMM_F2A_43_M


title: 5 min Osmotic stress replicate 2

description: Biological replicate 2 of 2

source_name: 5 min, osmotic


title: 5 min Osmotic stress replicate 1

description: Biological replicate 1 of 2


title: 5 min Osmotic stress dye swap

description: dye swap


title: BMM_F2A_42_M


title: BMM_F2A_39_M


title: 0 min Osmotic stress replicate 2

description: Biological replicate 2 of 2

source_name: 0 min, osmotic


title: 0 min Osmotic stress dye swap

description: dye swap


title: 10 min Osmotic stress replicate 2

description: Biological replicate 2 of 2


title: 0 min Osmotic stress replicate 1

description: Biological replicate 1 of 2


title: BMM_F2A_38_M


title: 15 min Osmotic stress replicate 1

description: Biological replicate 1 of 2


title: SE971N_miR_str

city: Beppu

first: Koshi

last: Mimori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

country: Japan

institute: Kyushu university

description: SAMPLE 58

hyb_protocol: Each total RNA sample (100 ng) or cRNA was competitively hybridized to a microarray according to the manufacturer's protocol (Wang H, Ach RA, Curry B. Direct and sensitive miRNA profiling from low-input total RNA. RNA. 2007;13:151-9.).

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B).

data_processing: The intensity of each hybridization signal was evaluated using Extraction Software Version A.7.5.1 (Agilent Technologies), which used the locally weighted linear regression curve fit (LOWESS) normalization method.

label: Cyanine

organism: Homo sapiens

label_protocol: Cyanine (Cy)-labeled cRNA was prepared using T7 linear amplification as described in the Agilent Low RNA Input Fluorescent Linear Amplification Kit Manual (Agilent Technologies).

extract_protocol: Total RNA was extracted from tissue using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. Concentrations and purities of the total RNAs were assessed with a spectrophotometer and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies). OD260/OD280 ratios of 1.8 – 2.1 were accepted to be adequate for microarray.

treatment_protocol: Laser micro-dissection

tag: tissue type

value: normal

value: stroma

tag: source classification


title: SE971N_miR_epi

description: SAMPLE 57

value: epithelium


title: 90 min Oxygen limitation  replicate 2

description: Biological replicate 2 of 2

source_name: 90 min, oxygen limitation

value: 90 min

value: oxygen limitation


title: 90 min Oxygen limitation  replicate 1

description: Biological replicate 1 of 2


title: SE970N_miR_str

description: SAMPLE 55


title: 90 min Oxygen limitation  dye swap

description: dye swap


title: BMM_F2A_37_M

value: male


title: SE958N_miR_str

description: SAMPLE 51


title: SE970N_miR_epi

description: SAMPLE 54


title: 60 min Oxygen limitation  dye swap

description: dye swap

source_name: 60 min, oxygen limitation

value: 60 min


title: BMM_F2A_40_M


title: BMM_F2A_36_M


title: BMM_F2A_35_M


title: BMM_F2A_31_M


title: BMM_F2A_28_M


title: SE956N_miR_epi

description: SAMPLE 46


title: BMM_F2A_33_M


title: 60 min Oxygen limitation  replicate 1

description: Biological replicate 1 of 2


title: SE958N_miR_epi

description: SAMPLE 50


title: SE956N_miR_str

description: SAMPLE 47


title: 45 min Oxygen limitation  dye swap

description: dye swap

source_name: 45 min, oxygen limitation

value: 45 min


title: BMM_F2A_29_M


title: 45 min Oxygen limitation  replicate 1

description: Biological replicate 1 of 2


title: 45 min Oxygen limitation  replicate 2

description: Biological replicate 2 of 2


title: 60 min Oxygen limitation  replicate 2

description: Biological replicate 2 of 2


title: 30 min Oxygen limitation  dye swap

description: dye swap

source_name: 30 min, oxygen limitation

value: 30 min


title: BMM_F2A_27_M


title: NDMC01_miR_str

description: SAMPLE 40

tag: disease

value: colorectal cancer

value: cancer

value: female

tag: age


title: NDMC33_miR_str

description: SAMPLE 43


title: BMM_F2A_25_M


title: BMM_F2A_26_M


title: NCC210_miR_epi

description: SAMPLE 35


title: 30 min Oxygen limitation  replicate 2

description: Biological replicate 2 of 2


title: NCC210_miR_str

description: SAMPLE 36


title: 30 min Oxygen limitation  replicate 1

description: Biological replicate 1 of 2


title: 15 min Oxygen limitation  replicate 2

description: Biological replicate 2 of 2

source_name: 15 min, oxygen limitation

value: 15 min


title: NCC201_miR_epi

description: SAMPLE 32


title: NCC201_miR_str

description: SAMPLE 33


title: 15 min Oxygen limitation  replicate 1

description: Biological replicate 1 of 2


title: NCC197_miR_epi

description: SAMPLE 28


title: NCC197_miR_str

description: SAMPLE 29


title: 15 min Oxygen limitation  dye swap

description: dye swap


title: NCC173_miR_str

description: Clinical characteristics not available


title: 0 min Oxygen limitation  dye swap

description: dye swap

source_name: 0 min, oxygen limitation


title: 0 min Oxygen limitation  replicate 2

description: Biological replicate 2 of 2


title: 0 min Oxygen limitation  replicate 1

description: Biological replicate 1 of 2


title: BMM_F2A_30_M

source_name: Bone marrow derived macrophages from male DBA/2J x AKR/J F2 mice


title: NCC128_miR_epi

description: SAMPLE 21


title: BMM_F2A_24_M


title: NCC128_miR_str

description: SAMPLE 22


title: BMM_F2A_23_M


title: BMM_F2A_21_M


title: BMM_F2A_22_M


title: BMM_F2A_20_M


title: BMM_F2A_19_M


title: BMM_F2A_17_M


title: NCC037_miR_str

description: SAMPLE 12


title: 90 min Glucose limitation  replicate 2

description: Biological replicate 2 of 2

source_name: 90 min, glucose limitation

value: glucose limitation


title: 90 min Glucose limitation  dye swap

description: dye swap


title: 60 min Glucose limitation  dye swap

description: dye swap

source_name: 60 min, glucose limitation


title: NCC095_miR_str

description: SAMPLE 18


title: 60 min Glucose limitation  replicate 2

description: Biological replicate 2 of 2


title: KITA842_miR_str

description: SAMPLE 6


title: NCC036_miR_str

description: SAMPLE 9


title: 60 min Glucose limitation  replicate 1

description: Biological replicate 1 of 2


title: BMM_F2A_18_M


title: BMM_F2A_14_M


title: 45 min Glucose limitation  dye swap

description: dye swap

source_name: 45 min, glucose limitation


title: 90 min Glucose limitation  replicate 1

description: Biological replicate 1 of 2


title: BMM_F2A_15_M


title: KITA802_miR_str

description: SAMPLE 3


title: BMM_F2A_16_M


title: 45 min Glucose limitation  replicate 2

description: Biological replicate 2 of 2


title: 45 min Glucose limitation  replicate 1

description: Biological replicate 1 of 2


title: 30 min Glucose limitation  dye swap

description: dye swap

source_name: 30 min, glucose limitation


title: 30 min Glucose limitation  replicate 1

description: Biological replicate 1 of 2


title: BMM_F2A_12_M


title: 15 min Glucose limitation  dye swap

description: dye swap

source_name: 15 min, glucose limitation


title: BMM_F2A_9_M


title: BMM_F2A_11_M


title: BMM_F2A_10_M


title: 15 min Glucose limitation  replicate 2

description: Biological replicate 2 of 2


title: BMM_F2A_7_M


title: 15 min Glucose limitation  replicate 1

description: Biological replicate 1 of 2


title: BMM_F2A_8_M


title: BMM_F2A_6_M


title: 30 min Glucose limitation  replicate 2

description: Biological replicate 2 of 2


title: SE971N_gene_epi

description: SAMPLE 59


title: SE958N_gene_epi

description: SAMPLE 49


title: BMM_F2A_4_M


title: BMM_F2A_5_M


title: SE971N_gene_str

description: SAMPLE 56


title: SE970N_gene_epi

description: SAMPLE 52


title: SE970N_gene_str

description: SAMPLE 53


title: 0 min Glucose limitation  dye swap

description: dye swap

source_name: 0 min, glucose limitation

value: 0 min


title: SE958N_gene_str

description: SAMPLE 48


title: BMM_F2A_2_M


title: 0 min Glucose limitation  replicate 2

description: Biological replicate 2 of 2


title: SE956N_gene_str

description: SAMPLE 45


title: BMM_F2A_3_M


title: SE956N_gene_epi

description: SAMPLE 44


title: 0 min Glucose limitation  replicate 1

description: Biological replicate 1 of 2


title: OD 1.0 low temp replicate 2

description: Biological replicate 2 of 2

source_name: 0.9 OD, low temp

value: low temp


title: ECC_F2D_50_M

description: Endothelial cells were prepared from mouse aortic rings grown on matrigel wells in endothelial cell media.  After 10-14 days cultures were treated with dispase and and passaged to a second plate.

source_name: Primary aortic endothelial cells from male DBA/2J x AKR/J F2 mice

value: primary aortic endothelial cells


title: BMM_F2A_1_M

value: bone marrow derived macrophages (BMM)


title: OD 0.9 low temp replicate 8

description: Biological replicate 8 of 8


title: BMM_F2A_13_M


title: OD 1.0 low temp replicate 1

description: Biological replicate 1 of 2


title: NDMC01_gene_str

description: SAMPLE 39

value: stroma


title: ECC_F2D_40_M


title: ECC_F2D_44_M


title: ECC_F2D_49_M


title: NDMC33_gene_epi

description: SAMPLE 42

value: epithelium


title: OD 0.9 low temp replicate 7

description: Biological replicate 7 of 8


title: ECC_F2D_41_M


title: NDMC01_gene_epi

description: SAMPLE 38


title: OD 0.9 low temp replicate 5

description: Biological replicate 5 of 8


title: OD 0.9 low temp replicate 6

description: Biological replicate 6 of 8


title: NDMC33_gene_str

description: SAMPLE 41


title: OD 0.9 low temp replicate 4

description: Biological replicate 4 of 8


title: ECC_F2D_19_M


title: NCC210_gene_epi

description: SAMPLE 37


title: ECC_F2D_34_M


title: NCC210_gene_str

description: SAMPLE 34


title: ECC_F2D_14_M


title: NCC201_gene_epi

description: SAMPLE 30


title: OD 0.9 low temp replicate 2

description: Biological replicate 2 of 8


title: NCC197_gene_str

description: SAMPLE 27


title: OD 0.9 low temp replicate 3

description: Biological replicate 3 of 8


title: ECC_F2D_13_M


title: OD 0.9 low temp replicate 1

description: Biological replicate 1 of 8


title: ECC_F2A_59_M


title: ECC_F2D_3_M


title: NCC201_gene_str

description: SAMPLE 31


title: NCC197_gene_epi

description: SAMPLE 26


title: 15 min Butanol stress replicate 1

description: Biological replicate 1 of 2

source_name: 15 min, butanol

value: butanol


title: ECC_F2D_1_M


title: 10 min Butanol stress replicate 1

description: Biological replicate 1 of 2

source_name: 10 min, butanol

value: 10 min


title: 20 min Butanol stress replicate 1

description: Biological replicate 1 of 2

source_name: 20 min, butanol

value: 20 min


title: NCC173_gene_epi

description: Clinical characteristics not available


title: NCC128_gene_str

description: SAMPLE 20

value: male


title: ECC_F2A_58_M


title: NCC173_gene_str

description: Clinical characteristics not available


title: 5 min Butanol stress replicate 1

description: Biological replicate 1 of 2

source_name: 5 min, butanol

value: 5 min


title: NCC128_gene_epi

description: SAMPLE 19


title: 0 min Butanol stress replicate 1

description: Biological replicate 1 of 2

source_name: 0 min, butanol


title: NCC095_gene_epi

description: SAMPLE 16


title: 20 min Heat shock dye swap

description: dye swap

source_name: 20 min, heat

value: heat


title: ECC_F2A_54_M


title: ECC_F2A_57_M


title: 20 min Heat shock replicate 2

description: Biological replicate 2 of 2


title: 20 min Heat shock replicate 1

description: Biological replicate 1 of 2


title: ECC_F2A_53_M


title: NCC042_miR_str

description: SAMPLE 15

value: colorectal cancer


title: NCC042_gene_str

description: SAMPLE 14

value: cancer


title: ECC_F2A_48_M


title: NCC095_gene_str

description: SAMPLE 17

value: female


title: ECC_F2A_46_M


title: ECC_F2A_52_M


title: NCC037_gene_epi

description: SAMPLE 10


title: NCC042_gene_epi

description: SAMPLE 13


title: ECC_F2A_47_M


title: NCC037_gene_str

description: SAMPLE 11


title: 15 min Heat shock replicate 2

description: Biological replicate 2 of 2

source_name: 15 min, heat

value: 15 min


title: 15 min Heat shock replicate 1

description: Biological replicate 1 of 2


title: 15 min Heat shock dye swap

description: dye swap


title: 10 min Heat shock dye swap

description: dye swap

source_name: 10 min, heat


title: NCC036_gene_str

description: SAMPLE 8


title: ECC_F2A_50_M


title: 10 min Heat shock replicate 2

description: Biological replicate 2 of 2


title: ECC_F2A_45_M


title: 10 min Heat shock replicate 1

description: Biological replicate 1 of 2


title: NCC036_gene_epi

description: SAMPLE 7


title: KITA842_gene_str

description: SAMPLE 5


title: ECC_F2A_42_M


title: KITA802_gene_str

description: SAMPLE 2


title: 5 min Heat shock dye swap

description: dye swap

source_name: 5 min, heat


title: 5 min Heat shock replicate 2

description: Biological replicate 2 of 2


title: ECC_F2A_43_M


title: OB Neu

city: Tsukuba

first: Makoto

last: Asashima

state: Ibaraki

address: 1-1-1 Higashi

department: Tsukuba Central 4

institute: National Institute of Advanced Industrial Science Technology (AIST)

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014879_D_20070820).

organism: Rattus norvegicus

source_name: OB Neu

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using ISOGEN (Nippon Gene, Toyama, Japan) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: fisher 344 rat

value: neurons derived from the OB NSCs


title: ECC_F2A_44_M


title: KITA842_gene_epi

description: SAMPLE 4


title: HPC NSC

source_name: HPC NSC

value: hippocampal derived neural stem cells


title: 5 min Heat shock replicate 1

description: Biological replicate 1 of 2


title: ECC_F2A_38_M

value: primary aortic endothelial cells


title: ECC_F2A_41_M


title: OB NSC

source_name: OB NSC

value: Olfactory bulb-derived neural stem cells


title: HPC neu

source_name: HPC neu

value: neurons derived from the HPC NSCs


title: 0 min Heat shock dye swap

description: dye swap

source_name: 0 min, heat

value: 0 min


title: KITA802_gene_epi

description: SAMPLE 1

value: epithelium


title: ECC_F2A_36_M


title: 0 min Heat shock replicate 2

description: Biological replicate 2 of 2


title: 0 min Heat shock replicate 1

description: Biological replicate 1 of 2


title: miR-NC_2

city: Tokyo

first: Toru

last: Furukawa

address: 8-1 Kawadacho, Shinjuku-ku

department: Institute for Integrated Medical Sciences

institute: Tokyo Women's Medical University

description: Gene expression 48 hours after transfection of a negative precursor miRNA

hyb_protocol: 1.65 µg of cRNAs were fragmented at 60 ˚C for 30 minutes using Gene Expression Hybridization Kit (Agilent Technologies) and hybridized at 65 ˚C for 17 hours to the 4×44K Whole Human Genome Microarray slide containing 45,015 features representing 41,000 unique probes (Catalog # G4112F, Agilent Technologies) by the method of the manufacturer’s instructions, including 2 biological replications.

scan_protocol: Microarrays were scanned using Agilent Array Scanner (Agilent technologies). Reproducibility and reliability of each single microarray was assessed using Quality Control report data which were extracted with Agilent feature extraction software (version 10.5.1.1) using the GE1-v5_10_Apr08 protocol.

data_processing:
Data processing was conducted using GeneSpring GX 10.0 software (Agilent Technologies). Expression levels were normalized to the 75 percentile, and baseline transformations were conducted employing the median of control samples in each cell line. Genes whose expressions altered more than 2.5-folds or higher with statistical significance (P < 0.05) in cells transfected with a negative precursor miRNA compated to those transfected with the precursor of miR-193b were listed. Fold change results are available on the Series record (IKEDA_data.txt)
gProcessedSignal data provided by Agilent feature extraction software

source_name: Human pancreatic cancer cells, MIA PaCa-2, transfected with a negative precursor miRNA

label_protocol: cRNAs labeled with Cyanin 3 were synthesized by the T7-liner amplification method from 500 ng of the total RNAs employing Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) and purified using RNeasy mini kit (Qiagen).

growth_protocol: Human pancreatic cancer cell line, MIA PaCa-2, cultured with DMEM supplemented with 10% fetal bovine serum at 37˚C in 5% CO2 with appropriate humidity

extract_protocol: Total RNA was extracted using mirVana miRNA Isoraion Kit (Life technologies) according to manufacturer’s instructions.

treatment_protocol: Cells were seeded at 2×105/well in 6-well plate and transfected with precursor of miR-193b or with negative controlprecursor (Life technologies) at 30 nM using siPORT NeoFX (Life Technologies) according to the manufacturer’s instructions.

value: pancreatic cancer cells

tag: cell line

value: MIA PaCa-2

tag: transfectant

value: negative precursor miRNA


title: Wnt3A W3A1 rep 1

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: Labeled material was hybridized for 17 hours at 65°C to an Agilent Whole Mouse Genome Oligo Microarrays 4 x 44K array. Microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescenct signals of the hybridized Agilent microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

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

source_name: mouse stromal cell line OP9

label_protocol: Labeling, hybridization, washing and scanning was performed by Miltenyi Biotec. Protocols provided here are from their service report. RNA was amplifed using a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: OP9 cells were maintained in MEM containing 20% fetal calf serum, 100 U/ml penicillin, 100 mg/mL streptomycin, and 2 mM L-glutamine.

extract_protocol: Cells were lyzed with SuperAmp lysis buffer following the instructions of the SuperAmp Preparation Kit (Miltenyi Biotec).

treatment_protocol: OP9 cells were transfected with the retroviral vector LZRS-IRES-GFP either lacking or containing the Wnt3A gene. Two separate replicates for each condition were analyzed.

tag: vector

value: LZRS-IRES-GFP retroviral vector with Wnt3A gene


title: ECC_F2A_31_M

source_name: Primary aortic endothelial cells from male DBA/2J x AKR/J F2 mice

tag: gender

value: male


title: 20 min Ethanol stress dye swap

description: dye swap

source_name: 20 min, ethanol

value: 20 min

value: ethanol

tag: strain


title: ECC_F2A_30_M

tag: cell type


title: Control LZR1 rep 1

value: LZRS-IRES-GFP retroviral vector


title: 20 min Ethanol stress replicate 2

description: Biological replicate 2 of 2


title: Wnt3A W3A2 rep 2


title: miR-193b_1

description: Gene expression 48 hours after transfection of precursor of miR-193b

source_name: Human pancreatic cancer cells, MIA PaCa-2, transfected with precursor of miR-193b

value: precursor of miR-193b


title: miR-NC_1


title: 20 min Ethanol stress replicate 1

description: Biological replicate 1 of 2


title: Control LZR2 rep 2


title: ECC_F2A_20_M


title: ECC_F2A_29_M


title: ECC_F2A_23_M


title: miR-193b_2


title: ECC_F2A_18_M


title: 15 min Ethanol stress dye swap

description: dye swap

source_name: 15 min, ethanol

value: 15 min


title: ovary-day2-control

city: Ithaca

first: Susan

last: Quirk

state: NY

address: 431 Morrison Hall

department: Animal Science

institute: Cornell University

description: Raw data file: 100702-Cowan-D2C.CEL

hyb_protocol: cRNA was hybridized to 430v2 chips.

scan_protocol: GeneChip Scanner 3000

data_processing: Affymetrix GCOS software

source_name: Day 2 ovary

label_protocol: Biotinylated cRNA were prepared from 1 ug total RNA using standard Affymetrix protocols.

growth_protocol: Ovaries were dissected from 2 day old mice. 8 control mice and 8 mutant mice were used

extract_protocol: RNA samples, each representing ovaries from a single mouse,  were prepared using Qiagen Rneasy Micro Kit. Equal amounts of RNA from ovaries of 8 mice were pooled for each sample.

treatment_protocol: Ovaries were frozen and stored at -80C until extraction

tag: genotype/variation

value: Amhr2(+/+)-SmoM2 control

value: 2 days

tag: tissue

value: ovary


title: ECC_F2A_25_M

value: primary aortic endothelial cells


title: K7M2/ezrinT567A-GFP rep3

city: Bethesda

first: Chand

last: Khanna

state: MD

address: 37 Convent Drive, Suite 2144

department: Pediatric Oncology Branch

institute: NCI

hyb_protocol: Biotinylated fragmented cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 for 16 hours according to the standard Affymetrix protocol

scan_protocol: Affymetrix genechip scanner 3000 was used

data_processing: The .CEL file was exported from Affymetrix AGCC software and the data was processed with RMA using Affymetrix Power Tool

source_name: K7M2 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle eukaryotic target labeling assay protocol

growth_protocol: Cells were grown in DMEM medium + 10%FBS  at 37 degree with 5% CO2

extract_protocol: Total RNA is extracted using Qiagen RNA mini kit

tag: overexpression


title: ECC_F2A_17_M


title: ECC_F2A_19_M


title: ovary-day2-mutant

description: Raw data file: 100702-Cowan-D2M.CEL

value: Amhr2(cre/+)-SmoM2 mutant


title: 15 min Ethanol stress replicate 1

description: Biological replicate 1 of 2


title: K7M2/ezrinT567A-GFP rep2


title: 10 min Ethanol stress dye swap

description: dye swap

source_name: 10 min, ethanol

value: 10 min


title: 10 min Ethanol stress replicate 2

description: Biological replicate 2 of 2


title: 10 min Ethanol stress replicate 1

description: Biological replicate 1 of 2


title: K7M2/GFP

value: GFP


title: K7M2/ezrinT567A-GFP rep1


title: 5 min Ethanol stress dye swap

description: dye swap

source_name: 5 min, ethanol

value: 5 min


title: ECC_F2A_14_M


title: KO1

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Stat5-null (knockout) MEFs

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

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

data_processing: Expression values were determined with GeneChip Operating Software (GCOS) v1.1.1 software. RMA signals were summarized using GeneSpring GX 10.0.1 (Agilent) and normalized by quantile normalization. All data analysis was performed with GeneSpring software GX 10.01.

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

extract_protocol: Total cellular RNA from each group of the MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions

tag: genotype/varation

value: KO

value: mouse embryonic fibroblasts

tag: stimulation


title: 5 min Ethanol stress replicate 2

description: Biological replicate 2 of 2

tag: time


title: ECC_F2A_16_M


title: KO-gh1

description: Stat5-null (knockout) MEFs

value: growth hormone for 120 minutes


title: ECC_F2A_11_M

value: male


title: WT-gh2

description: wild-type MEFs

value: WT


title: ECC_F2A_10_M


title: KO2

description: Stat5-null (knockout) MEFs


title: ECC_F2A_9_M


title: ECC_F2A_8_M


title: KO-gh2

description: Stat5-null (knockout) MEFs


title: 0 min Ethanol stress dye swap

description: dye swap

source_name: 0 min, ethanol

value: 0 min

tag: stress

value: ethanol


title: ECC_F2A_12_M


title: 0 min Ethanol stress replicate 2

description: Biological replicate 2 of 2


title: WT-gh1

description: wild-type MEFs


title: WT2

description: wild-type MEFs


title: 5 min Ethanol stress replicate 1

description: Biological replicate 1 of 2


title: 0 min Ethanol stress replicate 1

description: Biological replicate 1 of 2


title: WT1

description: wild-type MEFs


title: S5-gh1

description: STAT5A-containing vector was introduced into Stat5-null MEFs by retroviral infection


title: ECC_F2A_7_M


title: ECC_F2A_1_M


title: ECC_F2A_3_M


title: S5-gh2


title: Mouse 20 MA11 Array

description:
MC-S_20_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.

source_name: Mouse lung, flaxseed diet and radiation

value: lung

tag: treatment

value: 3 weeks 10% flaxseed diet + 13.5Gy radiation


title: Mouse 19 MA11 Array

description:
MC-S_19_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: gene expression profiling in CD69 positive blood cells selected from HTLV-1-infected patients_2

city: LYON

first: Pascale

last: GIRAUDON

address: rue Guillaume Paradin

department: Faculty of Medicine Laennec

country: France

institute: CRNL-U1028 Inserm

hyb_protocol: Biotin-labelled aRNA (10 ug) was fragmented using 5ug of fragmentation buffer in a final volume of 25 ul, then mixed with 240 ug of Amersham hybridization solution (GE Healthcare Europe GmbH, Freiburg, Germany) and injected on Codelink Uniset I Bioarrays containing around 20,000 human oligonucleotide geneprobes (GE Healthcare Europe GmbH, Freiburg, Germany). The arrays were hybridized overnight at 37°C at 15g in an incubator, then washed in stringent TNT buffer at 46°C for 1 h before performing streptavidin-cy5 (GE Healthcare) detection step.

scan_protocol: The arrays were scanned using a Genepix 4000B scanner (Axon, Union City, CA, USA) and Genepix software, with a laser set at 635 nm, the laser power at 60% and the photomultiplier tube voltage at 60%.

data_processing: The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and a normalized hybridization signal for each spot on the array. CodeLink software was used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control samples in the array: spot with signal intensity below this threshold was referred as ‘absent’. The quality of processing was evaluated by generating scatter plots of positive signal distribution.

source_name: human blood immune cells selected on CD69

label_protocol: Total RNA (2ug) was amplified and biotin-labelled by a round of in vitro transcription using a MessageAmp aRNA kit (Ambion, Austin, Texas, USA)

extract_protocol: RNA was extracted from cells with the use of RNA PLUSTM (Qbiogen, Illkirch, France) and was precipitated with ethanol

tag: donor

value: infected patient

value: CD69 positive blood cells


title: S51


title: gene expression profiling in CD69 positive blood cells selected from Healthy blood Donors_1

value: healthy donor


title: gene expression profiling in CD69 positive blood cells selected from Healthy blood Donors_2


title: Mouse 18 MA11 Array

description:
MC-S_18_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: ECC_F2A_24_M

value: primary aortic endothelial cells


title: Mouse 15 MA11 Array

description:
MC-S_15_MA11
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.

source_name: Mouse lung, radiation

value: 13.5Gy radiation


title: Mouse 14 MA11 Array

description:
MC-S_14_MA11
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: rapid-male-4

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: The cRNA samples were then fragmented and hybridised onto NuGO-Hs1a520180 (Scienion) Arrays from Affymetrix as performed by ServiceXS (www.servicexs.com)

scan_protocol: GCOS software (Affymetrix) was used to monitor scanning and to convert the raw image files into cell intensity files (‘.CEL’).

data_processing: CEL files were processed with the BioConductor gcrma function from the simpleaffy pacakge

source_name: whole blood, globin mRNA reduced, rapid growth, male

label_protocol: After treatment with the GeneChip Globin-Reduction Kit,  2ug of RNA was biotin labeled with the Affymetrix One-Cycle Target Labeling Kit according to manufacturers instructions

growth_protocol: Whole blood was drawn into PAXgene tubes prior to RNA extraction

extract_protocol: RNA is purified with the PAXgene Blood RNA kit

treatment_protocol: Slow and rapid growth was determined by difference in Z score for weight between term and term plus 12 weeks

tag: growth

value: rapid

tag: sex

value: M


title: rapid-female-6

source_name: whole blood, globin mRNA reduced, rapid growth, female

value: F


title: rapid-male-5


title: Mouse 17 MA11 Array

description:
MC-S_17_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: rapid-female-4


title: rapid-male-2


title: gene expression profiling in CD69 positive blood cells selected from HTLV-1-infected patients_1


title: Mouse 11 MA11 Array

description:
MC-S_11_MA11
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: rapid-male-1


title: Mouse 10 MA11 Array

description:
MC-S_10_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.

source_name: Mouse lung, flaxseed diet

value: 3 weeks 10% flaxseed diet


title: Mouse 12 MA11 Array

description:
MC-S_12_MA11
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: rapid-male-3


title: Mouse 08 MA11 Array

description:
MC-S_08_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: Mouse 09 MA11 Array

description:
MC-S_09_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: Mouse 13 MA11 Array

description:
MC-S_13_MA11
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: rapid-female-1


title: slow-female-6

source_name: whole blood, globin mRNA reduced, slow growth, female

value: slow


title: slow-male-6

source_name: whole blood, globin mRNA reduced, slow growth, male


title: Mouse 04 MA11 Array

description:
MC-S_04_MA11
C57BL/6 black mouse.

source_name: Mouse lung, untreated


title: rapid-female-3


title: Mouse 05 MA11 Array

description:
MC-S_05_MA11
C57BL/6 black mouse.


title: Mouse 03 MA11 Array

description:
MC-S_03_MA11
C57BL/6 black mouse.


title: rapid-female-2


title: Mouse 06 MA11 Array

description:
MC-S_06_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: Mouse 07 MA11 Array

description:
MC-S_07_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: slow-female-4


title: slow-male-5


title: slow-male-4


title: Mouse 16 MA11 Array

description:
MC-S_16_MA11
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: Mouse 02 MA11 Array

description:
MC-S_02_MA11
C57BL/6 black mouse.


title: slow-female-5


title: slow-female-3


title: Mouse 01 MA11 Array

description:
MC-S_01_MA11
C57BL/6 black mouse.


title: slow-male-1


title: slow-male-3


title: slow-female-1


title: slow-female-2


title: 15 min Ethanol stress replicate 2

description: Biological replicate 2 of 2

value: 15 min


title: slow-male-2


title: E8.5 foregut endoderm 1

status: Public on Mar 13 2012

city: Westmead

first: David

middle: A. F.

last: Loebel

state: NSW

address: 214 Hawkesbury Road

department: Embryology Unit

country: Australia

institute: Children's Medical Research Institute

description:
endoderm 1
RNA from pooled foregut endodern samples from 4-5 somite mouse embryos.

hyb_protocol: Standard Affymetrix protocol. Hybridization was performed by the Australian Genome Research Facility.

scan_protocol: Affymetrix scanner 3000 7G. Scanning was performed by the Australian Genome Research Facility.

data_processing: Data were processed using tools in GenePattern. CEL files were imported into Expression File Creator and subjected to RMA normalization with quantile normalization.

source_name: foregut endoderm from mouse embryos 3-5 somite stage

label_protocol: Biotin labelled using two rounds of amplification with the Affymetrix IVT kit following standard procedures. RNA amplification labelling was performed by the Australian Genome Research Facility.

growth_protocol: Mouse embryos were collected at the 4-5 somite stage.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini columns following the standard protocol. Concentration and integrity were tested by spectrophotometry and Bioanalyzer analyses.

treatment_protocol: Tissues were separated by mechanical dissection (endoderm 1 and mes/ectoderm 1) or trypsin/pancreatin digestion and mechanical dissection (endoderm 2 and mes/ectoderm 2). 15-20 individual tissue pieces (foregut endoderm, or combined mesoderm/ectoderm from head and heart tissues) were pooled per sample.

value: ARC/s

value: foregut endoderm

tag: age

tag: developmental stage

value: 4-5 somites


title: E8.5 foregut endoderm 2

description:
ectoderm 2
RNA from pooled foregut endodern samples from 4-5 somite mouse embryos.


title: E8.5 combined heart mesoderm and head mesoderm/ectoderm 1

description:
mes/ectoderm 1
RNA from pooled heart/head mesoderm and ectoderm from 4-5 somite mouse embryos.

source_name: mesoderm/ectoderm from mouse embryos 3-5 somite stage

value: mesoderm/ectoderm from heart/head fold


title: PaxCre GABAergic AC subset, rep1

city: Cambridge

first: Jeremy

middle: N

last: Kay

state: MA

address: 52 Oxford Street

institute: Harvard University

description: PaxCre-B

hyb_protocol: 20ug of aRNA were fragmented and hybridized according to standard Affymetrix protocols for 16 h at 45 degrees C. Arrays were washed and stained in Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were analyzed in dChip.

source_name: GFP+ retinal cells

label_protocol: MessageAmp II-biotin system (Ambion). Two rounds of amplification were used.

growth_protocol: Postnatal day 6 mice.

extract_protocol: PicoPure RNA Isolation Kit (MDS).

treatment_protocol: Papain-dissociated retinal cell suspension.

value: postnatal day 6

value: retina

value: GFP+ retinal cells

tag: neuron subtype

value: PaxCre GABAergic amacrine cell (AC) subset


title: W3 RGCs, rep1

source_name: YFP+ Thy1+ retinal cells

value: YFP+ Thy1+ retinal cells

value: W3 retinal ganglion cells (RGCs)


title: ON bipolar cells, rep1

description: ON BC-C

value: ON bipolar cells


title: J-RGCs, rep2

value: J-retinal ganglion cells (RGCs)


title: Isl2+ RGCs, rep1

source_name: bgal+ Thy1+ retinal cells

value: bgal+ Thy1+ retinal cells

value: Isl2+ retinal ganglion cells (RGCs)


title: Isl2+ RGCs, rep2


title: E8.5 combined heart mesoderm and head mesoderm/ectoderm 2

description:
mes/ectoderm 2
RNA from pooled heart/head mesoderm and ectoderm from 4-5 somite mouse embryos.


title: ON bipolar cells, rep2

description: ON BC-E


title: J-RGCs, rep1


title: PaxCre GABAergic AC subset, rep2

description: PaxCre-D


title: W7 RGCs, rep2

value: W7 retinal ganglion cells (RGCs)


title: Cdh3 BAC RGC subset, rep2

source_name: GFP+ Thy1+ retinal cells

value: Swiss Webster x C57BL/8

value: GFP+ Thy1+ retinal cells

value: Cdh3 BAC retinal ganglion cell (RGC) subset


title: J glycinergic AC subset, rep1

source_name: YFP+ retinal cells

value: YFP+ retinal cells

value: J glycinergic amacrine cell (AC) subset


title: Cdh3 BAC RGC subset, rep1

value: Swiss Webster x C57BL/7


title: W7 RGCs, rep1

value: postnatal day 6


title: W3 RGCs, rep2

value: retina


title: J glycinergic AC subset, rep2


title: AII amacrine cells, rep1

value: Swiss Webster x C57BL/6

value: GFP+ retinal cells

value: aII amacrine cells


title: AII amacrine cells, rep2


title: MP-positive bipolars, rep1

source_name: CFP+VC1.1– retinal cells

value: mixed C57BL/6 x CD1

value: CFP+VC1.1– retinal cells

value: MP-positive bipolars


title: MP-positive amacrine, rep2

source_name: CFP+VC1.1+ retinal cells

value: CFP+VC1.1+ retinal cells

value: MP-positive amacrine


title: MP-positive bipolars, rep2


title: BD RGCs, rep1

description: BD-C

value: YFP+ Thy1+ retinal cells

value: bistratified dendrite-retinal ganglion cells (BD-RGCs)


title: MP-positive amacrine, rep1


title: rapid-female-5

value: rapid

value: F


title: Starburst amacrine, rep2

description: SAC-C

source_name: Kusabira Orange+Thy1– retinal cells

value: Kusabira Orange+Thy1– retinal cells

value: starburst amacrine


title: conidia at T8, in the presence of 3 µM natamycin, biological rep2

city: Utrecht

first: Martin

middle: Richard

last: van Leeuwen

address: Uppsalalaan 8

department: Applied and Industrial Mycology

country: Netherlands

institute: CBS-KNAW/Fungal Biodiversity Centre

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1.1 software. Normalization was done using the MAS5.0 algorithm using a baseline correction of the median (the Value '0' was  transformed into 12 to enable calculations).

organism: Aspergillus niger

source_name: germinating A. niger conidia, 8h post inoculation in the presence of 3 µM natamycin

label_protocol: Biotin-labeled antisense cRNA was produced from 2 μg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: For spore isolation, Aspergillus niger N402 was grown for 12 days at 25 °C on complete medium (CM). Conidia were harvested in ice-cold ACES-buffer (10 mM ACES, 0.02 % Tween-80, pH 6.8). To this end, the colony surface was gently rubbed with a sterile T-spatula and the conidial suspension was filtered through sterile glass wool. Conidia were washed in ice-cold ACES-buffer, resuspended in CM and kept on ice until further processing on the same day.

extract_protocol: The conidial pellet was kept frozen in liquid nitrogen and homogenized with the Qiagen Tissuelyser® (2 times 2 min at 30 strokes sec-1) in a stainless steel grinding jar that had been cooled with liquid nitrogen (Qiagen, Venlo, The Netherlands). After homogenizing, 2 ml RLT buffer (supplied with the Qiagen RNeasy® Maxi kit) was added. All the material of the samples taken at 0 h and 2 h, half of the material taken at 4 h and a third of the material taken at 6 h and 8 h were transferred to a 50 ml Greiner tube. RNA was extracted following the protocol of the RNeasy® Maxi kit (Qiagen) with some modifications. 15 ml RLT buffer supplemented with 170 µl ß-mercaptoethanol was added. After centrifugation (3000 x g, 10 min, 4 ºC) the supernatant was mixed thoroughly with 15 ml 70 % ethanol in a 50 ml Greiner tube and transferred to a RNeasy Maxi column. After centrifugation (3000 g, 5 min, 4 °C) the column was washed with 10 ml RW1 and twice with 10 ml RPE buffer (with 2 and 10 min centrifugation, respectively, at 3000 g at 4 °C). This was followed by addition of 800 µl of RNase-free water to elute the RNA. After 2 min the column was centrifuged at 4 °C for 3 min at 3000 g, followed by an additional elution with 800 µl of RNase-free water. The volume of the aqueous RNA solution was reduced to approximately 100-400 µl with a SpeedVac® (Savant DNA 110). Subsequently, 600 µl of 2 x T & C lysis buffer (Epicentre, Landgraaf, The Netherlands) was added and the mixture was kept on ice. After 5 min, 350 µl of MPC Protein Precipitation Reagent (Epicentre, Landgraaf, The Netherlands) was added, thoroughly mixed, and centrifuged (12.000 x g, 10 min, 4 °C) The supernatant was transferred to a clean micro-centrifuge tube and gently mixed with 1000 µl isopropanol. RNA was precipitated at 12.000 x g (10 min, 4 °C) and the pellet was air-dried for 5 min. The pellet was then resuspended in 100 µl RNase-free water. This was followed by addition of 700 µl of RLT buffer (without ß-mercaptoethanol) and 500 µl 96 % ethanol. RNA was further purified using the RNeasy® Mini kit (Qiagen) according to the RNA Cleanup protocol.

treatment_protocol: Control samples of germinating conidia of Aspergillus niger N402 were taken in triplo at 0h (dormant), 2h, and 8h after inoculation in CM.  Natamycin treated samples were taken in triplo at 2h and 8h after inoculation in CM either supplemented with 3 µM or 10 µM natamycin. A single experiment comprises three cultures of 300 ml CM with 3 x 109 conidia, shaken at 125 rpm and 25°C. At each time point, 15 ml was taken from each culture and pooled, resulting in 4.5 x 108 conidia per 45 ml. The conidial suspensions were centrifuged at 1100 x g at 5°C for 5 min. Pellets were frozen in liquid nitrogen and kept at -80°C.

value: germinating conidia

tag: conidial age

value: 12 days


title: conidia at T2, in the presence of 10 µM natamycin, biological rep3

source_name: germinating A. niger conidia, 2h post inoculation in the presence of 10 µM natamycin

tag: strain


title: conidia at T2, in the presence of 3 µM natamycin, biological rep2

source_name: germinating A. niger conidia, 2h post inoculation in the presence of 3 µM natamycin


title: S52

description: STAT5A-containing vector was introduced into Stat5-null MEFs by retroviral infection

tag: cell type

value: mouse embryonic fibroblasts


title: Starburst amacrine, rep1

value: postnatal day 6

value: retina


title: conidia at T2, in the presence of 10 µM natamycin, biological rep2


title: conidia at T8, in the presence of 10 µM natamycin, biological rep2

source_name: germinating A. niger conidia, 8h post inoculation in the presence of 10 µM natamycin


title: conidia at T8, in the presence of 10 µM natamycin, biological rep3


title: conidia at T8, in the presence of 3 µM natamycin, biological rep3


title: conidia at T8, in the presence of 3 µM natamycin, biological rep1


title: conidia at T2, in the presence of 3 µM natamycin, biological rep3


title: conidia at T8, in the presence of 10 µM natamycin, biological rep1


title: conidia at T6, biological rep2

data_processing: Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1.1 software. Normalization was done using the MAS5.0 algorithm using a baseline correction of the median (the Value '0' was  transformed into "12" to enable calculations).

source_name: germinating A. niger conidia, 6h post inoculation

extract_protocol: The conidial pellet was kept frozen in liquid nitrogen and homogenized with the Qiagen Tissuelyser® (2 times 2 min at 30 strokes sec-1) in a stainless steel grinding jar that had been cooled with liquid nitrogen (Qiagen, Venlo, The Netherlands). After homogenizing, 2 ml RLT buffer (supplied with the Qiagen RNeasy® Maxi kit) was added. All the material of the samples taken at 0 h and 2 h, half of the material taken at 4 h and a third of the material taken at 6 h and 8 h were transferred to a 50 ml Greiner tube. RNA was extracted following the protocol of the RNeasy® Maxi kit (Qiagen) with some modifications. 15 ml RLT buffer supplemented with 170 µl ß-mercaptoethanol was added. After centrifugation (3000 x g, 10 min, 4C) the supernatant was mixed thoroughly with 15 ml 70 % ethanol in a 50 ml Greiner tube and transferred to a RNeasy Maxi column. After centrifugation (3000 g, 5 min, 4 °C) the column was washed with 10 ml RW1 and twice with 10 ml RPE buffer (with 2 and 10 min centrifugation, respectively, at 3000 g at 4 °C). This was followed by addition of 800 µl of RNase-free water to elute the RNA. After 2 min the column was centrifuged at 4 °C for 3 min at 3000 g, followed by an additional elution with 800 µl of RNase-free water. The volume of the aqueous RNA solution was reduced to approximately 100-400 µl with a SpeedVac® (Savant DNA 110). Subsequently, 600 µl of 2 x T & C lysis buffer (Epicentre, Landgraaf, The Netherlands) was added and the mixture was kept on ice. After 5 min, 350 µl of MPC Protein Precipitation Reagent (Epicentre, Landgraaf, The Netherlands) was added, thoroughly mixed, and centrifuged (12.000 x g, 10 min, 4 °C) The supernatant was transferred to a clean micro-centrifuge tube and gently mixed with 1000 µl isopropanol. RNA was precipitated at 12.000 x g (10 min, 4 °C) and the pellet was air-dried for 5 min. The pellet was then resuspended in 100 µl RNase-free water. This was followed by addition of 700 µl of RLT buffer (without ß-mercaptoethanol) and 500 µl 96 % ethanol. RNA was further purified using the RNeasy® Mini kit (Qiagen) according to the RNA Cleanup protocol.

treatment_protocol: Samples of germinating conidia of Aspergillus niger N402 were taken in triplo at 0h (dormant), 2h, 4h, 6h and 8h after inoculation in CM.  A single experiment comprises three cultures of 300 ml CM with 3 x 109 conidia, shaken at 125 rpm and 25°C. At each time point, 15 ml was taken from each culture and pooled, resulting in 4.5 x 108 conidia per 45 ml. The conidial suspensions were centrifuged at 1100 x g at 5°C for 5 min. Pellets were frozen in liquid nitrogen and kept at -80°C.


title: BD RGCs, rep2

description: BD-D


title: conidia at T6, biological rep3


title: conidia at T8, biological rep1

source_name: germinating A. niger conidia, 8h post inoculation


title: conidia at T2, in the presence of 10 µM natamycin, biological rep1


title: conidia at T4, biological rep1

source_name: germinating A. niger conidia, 4h post inoculation


title: conidia at T8, biological rep3


title: conidia at T8, biological rep2


title: conidia at T2, biological rep3

source_name: germinating A. niger conidia, 2h post inoculation


title: conidia at T6, biological rep1


title: conidia at T2, biological rep2


title: conidia at T4, biological rep3


title: conidia at T2, in the presence of 3 µM natamycin, biological rep1


title: conidia at T2, biological rep1


title: conidia at T4, biological rep2


title: conidia at T0, biological rep2

source_name: dormant A. niger conidia


title: conidia at T0, biological rep3


title: conidia at T0, biological rep1


title: WEC_RA_2h_199_1

status: Public on Mar 12 2012

city: Bilthoven

first: Joshua

middle: F

last: Robinson

address: Leeuwenhoeklaan 9

department: Laboratory for Health Protection Research

institute: National Institute for Public Health and the Environment (RIVM)

hyb_protocol: Fragmentation reaction of the cRNA sample was performed using 7.5ug cRNA from each sample.  Fragmented cRNA with a concentration of 0.0375ng/ul was utilized for the hybridization on the Affymetrix HT RG 230 PM Aray Plate.  HWS Kit (#901530) was used for hybridization, washing and staining of the chips.

scan_protocol: Scanning of the Array Plates was perfomred using the Affymetrix GeneTitan scanner.

data_processing: Microarray Analysis-Data Processing:  Quality of microarray images was inspected visually and raw values were examined for average background scale factors, 3`/5` ratios of glyceraldehydes 3-phosphate dehydrogenase and 3`/5` ratios of Bactin, and NUSE and RLE signal quality metrics.  Affymetrix CEL files were normalized using the Robust Multichip Average algotrithm (Irizarry et al., 2003) using the Brainarray custom CDF version 13.0.0 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/entrezg.download/HTRat230PM_Rn_ENTREZG_13.0.0.zip) (Dai et al., 2005).  Affymetrix internal controls ID were not used in further analyses, leaving a total of 11,521 probe sets for EntrezGeneID mapped genes.

source_name: whole embryo

label_protocol: Service XS:  The Affymetrix 3' IVT-Express Labeling Kit (#901229) was used to synthesize Biotin labeled cRNA.  From each RNA sample 100ng was used as input for the labeling reactions.

growth_protocol: Animal Care  As described previously (Robinson et al., 2010; Luijten et al., 2010), animal studies were approved and conducted in accordance with the National Institute for Public Health and the Environment Animal Care facility and federal regulations.  HsdCpd:WU rats (Harlan, the Netherlands) were housed at the RIVM in a climate controlled room with a 12h on/off light cycle.  After acclimating for at least 2 weeks, virgin female rats were housed with adult male rats for a 3h mating period (9:00-12:00).  Females showing evidence of a copulatory plug (declared GD0) were housed in separate cages.  Animals were monitored daily for general health for the extent of the study.  Water and food were provided ad libitum.    Rat Postimplantation Whole Embryo Culture  Following previously published methods (New, 1978; Piersma et al., 2004), on gestational day (GD) 10, rat embryos were extracted from the uterus with the yolk sac and ectoplancental cone left intact.  Embryos with 1-5 somites were used at the onset of culture.  For gene expression studies, only embryos with 2-4 somites were used.  The pre-selection of this range of embryos for RNA-studies was based on our previous studies indicating similar RA-induced effects (degree and significance) on gene expression in embryos of 2-4 somites (Luijten et al., 2010).  Embryos were cultured in a serum mixture (Biochrom, Germany, #S900) consisting of 80% pregnant bovine serum, 10% rat serum, 1.57 mg/ml D-glucose, 75 ug/ml L-methionine and supplemented 10% Hank’s solution (Gibco).  The use of bovine-serum mixture instead of 100% rat serum significantly reduces the usage of animals for this experiment.  Furthermore, our previous studies indicate that the use of this serum mixture versus heat inactivated 100% rat serum, results in only a reduction of ~1 somite after 48h in culture (Luijten et al., 2010).  Using increasing concentrations of oxygen, gassing occurred five times during culture: on the first day for 30s at 9:00 (~-1h) and 16:00 (~7h) (5% O2, 5% CO2, 90% N2), on the second day for 30s at 9:00 (~23h) and 16:00 (~30h) (20% O2, 5% CO2, 75% N2) and on the third day for 10s at 9:00 (~47h) (40% O2, 5% CO2, 55% N2).  Euthanization of pregnant dams was performed via intracardiac injection of T61R (Intervet, Netherlands).

extract_protocol: Embryo Isolation for Gene Expression Analysis in WEC  Following 2, 4, 6, 12, 24 and 48h post-exposure, embryos were isolated and scored for total somites and development of the neural tube and heart.  The yolk sac and ectoplacental cone were completely removed.  Embryos collected for each time point were extracted from at least 3 different pregnant dams.  Embryo Isolation for Gene Expression Analysis In Vivo  On GD 10 + 2, 4, 6, 12, 24 and 48h, pregnant dams were euthanized via intracardiac injection of T61R (Intervet, Netherlands) and embryos were extracted from the uterus.  All extraembryonic membranes were removed.  Embryos were scored for total somites and development of the neural tube.

treatment_protocol: Rat Postimplantation Whole Embryo Culture:  All-trans-retinoic acid (RA, CAS No. 302-79-4) (MP Biomedical, Irvine, CA) at a concentration of 0.5µg/mL or vehicle control (dimethyl sulfoxide (DMSO), 1µl/mL) were added to 2mL of culture medium prior to culturing (8:00-9:00).  Dosing of RA at the selected concentration was based on previous studies suggesting a ~25-30% decline in TMS and moderate teratogenicity after 48h exposure (Luijten et al., 2010).  New solutions were completed in the morning of each culture day. Previous studies from our lab indicate the concentration of DMSO in this study does not significantly alter morphology or gene expression (Robinson et al., 2010).  In Vivo Rat Gestational Exposure Studies to Retinoic Acid:  During the same general time period as WEC experiments, in vivo-exposure studies were conducted within the RIVM Animal Care facility.  RA was administered via oral gavage at a dose of 50 mg/kg BW on GD 10.  RA was administered at 50 mg/kg BW due to previous studies (Tembe et al., 1996) suggesting this dose induces a similar malformation rate and specific malformations (neural tube, craniofacial abnormalities) as observed with 0.5µg/mL RA in WEC (Luijten et al., 2010).  As previously indicated (Tembe et al., 1996), the dose selected did not induce significant embryonic death nor signs of maternal toxicity.  RA solutions were prepared the day of administration in corn oil.  Total volumes of vehicles did not exceed 2ml/kg body weight.  In a similar fashion, controls were also dosed with corn oil via oral gavage.

tag: model

value: WEC

tag: agent

value: All-trans-retinoic acid

tag: time point

tag: duration (gd10 + xhours)

tag: date isolated

tag: animal number

value: D

tag: embryo number

tag: neural tube development

tag: initial somites

tag: somite number

tag: somitediff

tag: lab sample number

tag: sample number

tag: classification


title: INVIVO_RA_12h_182_1

value: INVIVO


title: INVIVO_RA_6h_183_1


title: INVIVO_RA_2h_189_1


title: WEC_CON_6h_186_2

value: vehicle control

value: B


title: WEC_CON_24h_184_1

value: A


title: INVIVO_RA_24h_188_1


title: INVIVO_RA_4h_191_1


title: INVIVO_RA_48h_192_1


title: WEC_RA_2h_190_1

value: C


title: WEC_CON_6h_186_1


title: WEC_CON_2h_187_1


title: INVIVO_RA_12h_185_1


title: C. elegans: B. thuringiensis DB27 vs. E. coli OP50 exposure; 4hours, Biological Replicate 1

city: Ipswich

first: Amit

last: Sinha

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 1 of 3. Dye-swap sample.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent C. elegans oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the ÒnormexpÓ method (Ritchie et al., 2007). The arrays were lowess normalized individually (ÒnormalizeWithinArrays option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Caenorhabditis elegans

source_name: C. elegans young adults, fed E.coli OP50, 4 hours

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

treatment_protocol: For each biological replicate, about 200 young adult hermaphrodites were picked onto control E. coli OP50 plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

tag: developmental stage

value: young adults

value: N2 Bristol

tag: bacteria

value: E. coli OP50

tag: timepoint

value: 4 hour feeding / exposure

source_name: C. elegans young adults, fed Bacillus thuringiensis DB27, 4 hours

treatment_protocol: For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Bacillus thuringiensis DB27 plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

value: Bacillus thurigiensis DB27


title: WEC_CON_2h_180_1

tag: model


title: INVIVO_RA_6h_176_1

tag: agent


title: INVIVO_RA_48h_174_1

tag: time point


title: C. elegans: B. thuringiensis DB27 vs. E. coli OP50 exposure; 4hours, Biological Replicate 3

description: Biological replicate 3 of 3.

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the “normexp” method (Ritchie et al., 2007). The arrays were lowess normalized individually (“normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto pathogen Bacillus thuringiensis DB27 plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

tag: strain

growth_protocol: Synchronized populations of C. elegans were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 plates at 20C. For each biological replicate, about 200 young adult hermaphrodites were picked onto control E. coli OP50 plates for 4 hours of exposure, after which they were collected into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.


title: WEC_CON_6h_175_1

tag: duration (gd10 + xhours)

tag: date isolated


title: WEC_CON_2h_177_1

tag: animal number

tag: embryo number


title: INVIVO_CON_6h_178_1

tag: neural tube development

tag: initial somites


title: WEC_CON_12h_173_1

tag: somite number

tag: somitediff


title: INVIVO_RA_24h_181_1

tag: lab sample number

tag: sample number


title: C. elegans: B. thuringiensis DB27 vs. E. coli OP50 exposure; 4hours, Biological Replicate 2

description: Biological replicate 2 of 3.

tag: developmental stage


title: WEC_CON_6h_175_2

tag: classification


title: WEC_RA_12h_179_1


title: WEC_CON_4h_169_1


title: INVIVO_CON_12h_158_1


title: INVIVO_RA_12h_170_1


title: WEC_CON_4h_157_1


title: WEC_RA_24h_171_1


title: WEC_CON_48h_167_1


title: WEC_RA_48h_159_1


title: WEC_RA_6h_156_1


title: INVIVO_RA_4h_164_1


title: INVIVO_RA_12h_163_1


title: INVIVO_RA_48h_168_1


title: WEC_CON_6h_160_1


title: WEC_CON_6h_168_1


title: WEC_CON_2h_172_1


title: WEC_RA_2h_162_1

value: E


title: WEC_RA_6h_154_1


title: INVIVO_CON_4h_166_1


title: INVIVO_RA_6h_161_1


title: INVIVO_CON_4h_150_1


title: WEC_RA_12h_148_1


title: WEC_RA_12h_149_1


title: INVIVO_CON_24h_152_1


title: WEC_CON_24h_147_1


title: INVIVO_CON_2h_155_1


title: INVIVO_CON_4h_150_2


title: WEC_RA_6h_154_2


title: INVIVO_CON_2h_139_1


title: WEC_RA_2h_143_1


title: WEC_CON_48h_153_1


title: INVIVO_CON_24h_145_1


title: WEC_RA_6h_151_1


title: INVIVO_RA_2h_138_1


title: WEC_CON_48h_144_1


title: WEC_RA_4h_146_1


title: WEC_RA_4h_134_1


title: INVIVO_CON_48h_137_1


title: INVIVO_RA_24h_135_1


title: INVIVO_RA_6h_142_1


title: INVIVO_RA_24h_136_1


title: INVIVO_CON_12h_141_1


title: INVIVO_CON_24h_140_1


title: WEC_CON_12h_133_1


title: WEC_RA_2h_132_1


title: WEC_RA_48h_121_1


title: INVIVO_CON_24h_131_1


title: WEC_CON_24h_122_1


title: INVIVO_CON_48h_120_1


title: INVIVO_RA_4h_116_1


title: INVIVO_RA_48h_108_1


title: INVIVO_RA_4h_110_1


title: INVIVO_CON_6h_129_1


title: WEC_RA_6h_127_1


title: WEC_RA_4h_130_1


title: INVIVO_CON_48h_123_1


title: WEC_CON_12h_118_1


title: INVIVO_CON_48h_111_1


title: INVIVO_CON_4h_119_1


title: WEC_RA_4h_117_1


title: WEC_RA_24h_115_1


title: INVIVO_RA_2h_128_1


title: WEC_CON_24h_107_1


title: WEC_RA_24h_112_1


title: INVIVO_CON_2h_126_2


title: INVIVO_CON_2h_126_1


title: WEC_CON_48h_125_1


title: INVIVO_CON_12h_106_1


title: WEC_RA_24h_113_1


title: INVIVO_CON_2h_114_1


title: INVIVO_CON_6h_124_1


title: WEC_CON_4h_109_1


title: WEC_RA_12h_99_1


title: WEC_CON_4h_102_1


title: INVIVO_RA_2h_104_1


title: WEC_CON_4h_90_1


title: WEC_CON_12h_103_1


title: WEC_CON_4h_96_1


title: WEC_RA_48h_94_1


title: INVIVO_CON_12h_100_1


title: WEC_CON_24h_88_1


title: INVIVO_CON_4h_87_1


title: INVIVO_CON_4h_97_1


title: INVIVO_CON_6h_101_1


title: WEC_CON_2h_89_1


title: WEC_RA_48h_98_1


title: WEC_CON_6h_91_1


title: INVIVO_CON_12h_92_1


title: INVIVO_CON_4h_87_2


title: WEC_CON_48h_81_1


title: WEC_CON_4h_86_1


title: WEC_RA_48h_105_1


title: INVIVO_RA_6h_93_1


title: WEC_CON_4h_85_2


title: INVIVO_RA_24h_95_1


title: INVIVO_CON_2h_82_1


title: INVIVO_CON_2h_84_1


title: WEC_CON_48h_83_1


title: INVIVO_CON_12h_79_1


title: WEC_CON_4h_85_1


title: INVIVO_RA_24h_80_1


title: INVIVO_CON_6h_75_1


title: INVIVO_RA_6h_74_2


title: WEC_CON_6h_73_1


title: WEC_RA_24h_69_1


title: INVIVO_RA_48h_78_1


title: WEC_CON_2h_70_1


title: INVIVO_RA_6h_68_1


title: INVIVO_RA_2h_64_1


title: INVIVO_CON_6h_57_1


title: WEC_CON_2h_76_1


title: WEC_RA_2h_62_2


title: INVIVO_RA_6h_74_1


title: INVIVO_RA_12h_67_1


title: WEC_RA_12h_71_1


title: WEC_RA_12h_60_1


title: INVIVO_RA_24h_72_1


title: WEC_RA_2h_62_1


title: INVIVO_CON_48h_63_1


title: WEC_CON_12h_66_1


title: WEC_RA_4h_59_1


title: INVIVO_CON_6h_57_2


title: WEC_RA_6h_77_1


title: INVIVO_RA_12h_61_1


title: WEC_CON_2h_58_1


title: INVIVO_CON_24h_65_1


title: WEC_RA_24h_51_1


title: WEC_RA_6h_52_1


title: INVIVO_RA_6h_50_1


title: INVIVO_RA_2h_56_1


title: INVIVO_RA_4h_54_1


title: INVIVO_RA_2h_56_2


title: INVIVO_CON_24h_53_1


title: WEC_RA_6h_43_1


title: INVIVO_RA_12h_47_1


title: INVIVO_RA_12h_47_2


title: INVIVO_CON_4h_48_1


title: WEC_CON_6h_44_1


title: INVIVO_RA_2h_55_1


title: INVIVO_CON_2h_46_1


title: INVIVO_CON_4h_40_1


title: WEC_CON_48h_45_1


title: INVIVO_RA_4h_41_1


title: WEC_CON_12h_42_1


title: WEC_RA_12h_38_1


title: INVIVO_CON_6h_37_1


title: WEC_RA_2h_34_1


title: WEC_CON_6h_49_1


title: INVIVO_RA_48h_35_1


title: WEC_CON_12h_32_1


title: WEC_RA_2h_39_1


title: INVIVO_CON_48h_30_1


title: WEC_RA_48h_29_1


title: WEC_RA_48h_26_1


title: INVIVO_CON_2h_27_1


title: INVIVO_RA_4h_25_1


title: INVIVO_CON_24h_28_1


title: WEC_CON_24h_22_1


title: INVIVO_RA_48h_15_1


title: INVIVO_CON_48h_21_1


title: WEC_RA_4h_23_1


title: INVIVO_RA_12h_16_1


title: INVIVO_CON_48h_14_1


title: WEC_RA_4h_13_1


title: WEC_RA_6h_10_1


title: INVIVO_CON_4h_24_1


title: INVIVO_RA_4h_33_1


title: INVIVO_RA_24h_19_1


title: INVIVO_CON_24h_11_1


title: WEC_RA_48h_20_1


title: INVIVO_RA_48h_18_1


title: WEC_CON_24h_9_1


title: INVIVO_CON_6h_12_1


title: WEC_RA_24h_8_1


title: WEC_RA_24h_17_1


title: WEC_RA_12h_5_1


title: WEC_CON_48h_7_1


title: WEC_RA_4h_6_1


title: INVIVO_RA_2h_4_1


title: WEC_CON_12h_3_1


title: INVIVO_CON_12h_1_1


title: RNA isolated from PBMCs (HS_4)

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

description: miRNA expression in healthy subject

hyb_protocol: Cy3-labeled RNA from each sample was hybridized to an Agilent Human miRNA Version 2 Microarray using the miRNA v1 Protocol

scan_protocol: The hybridized array was then washed and scanned according to Agilent specifications and data was extracted from the scanned image using Feature Extraction version 9.5.1.1. (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (Grid: 019118_D_20080214) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Healthy Subject

label_protocol: 600ng of total RNA from each sample was dephosphorylated with Calf Intestinal Alkaline Phosphatase (CIP) at 37ºC for 30’ following a denaturalization and then a ligation for 2h at 16ºC using Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies; Palo Alto, CA). In this step a molecule of Cyanine3-pCp is incorporated to the 3’ end of RNA molecules.

extract_protocol: miRNAs were extracted using Qiagen miRNeasy kit according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Blood sample was drawn into Lithium Heparin blood collection tube

tag: disease state

tag: urinalysis

value: negative


title: RNA isolated from PBMCs (HS_1)

description: miRNA expression in healthy subject

source_name: healthy Subject


title: RNA isolated from PBMCs (HS_3)

description: miRNA expression in healthy subject


title: RNA isolated from PBMCs (IgAN_6)

description: miRNA expression in IgAN patient

source_name: IgAN Patient with a Nomal Renal Function

value: IgAN

tag: status

value: normal renal function

tag: creatinine clearance

value: >90 ml/min/1.73 m2 body surface area (evaluated by Cockcroft-Gault formula)

tag: serum creatinine

tag: clinical follow up

value: At least 7 years


title: RNA isolated from PBMCs (HS_2)

description: miRNA expression in healthy subject


title: RNA isolated from PBMCs (HS_5)

description: miRNA expression in healthy subject


title: RNA isolated from PBMCs (IgAN_7)

description: miRNA expression in IgAN patient


title: WEC_CON_24h_2_1

tag: model

value: WEC

tag: agent

tag: time point

tag: duration (gd10 + xhours)

tag: date isolated


title: RNA isolated from PBMCs (IgAN_4)

description: miRNA expression in IgAN patient


title: RNA isolated from PBMCs (HS_7)

description: miRNA expression in healthy subject


title: RNA isolated from PBMCs (HS_6)

description: miRNA expression in healthy subject


title: RNA isolated from PBMCs (IgAN_3)

description: miRNA expression in IgAN patient


title: RSV_4

city: COLUMBUS

first: IOANNIS

last: IOANNIDIS

address: 700 CHILDRENS DRIVE

department: VACCINES AND IMMUNITY

institute: NATIONWIDE CHILDRENS HOSPITAL

description: gene expression after 2h rsv infection (harvested 48h after treatment)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: 2h_RSV_ infection

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

growth_protocol: Human airway tracheobronchial epithelial cells from non-cystic fibrosis patients were obtained from airway specimens resected at lung transplantation following Nationwide Children’s Hospital Institutional Review Board-approved protocols. Epithelial cells were removed from the mainstream bronchi by protease digestion and plastic adherence, and plated at a density of 300,000 cells per well on permeable Transwell-Col supports. Cultures were maintained under air-liquid interface (ALI) for 4 to 6 weeks to form well differentiated, polarized cultures that resemble the in vivo pseudostratified mucociliary epithelium as previously described (Pickles et al., 1998).

extract_protocol: RNA was isolated from the AEC cultures after direct lysis of cells with TRIzol (Invitrogen) and application of the resulting aqueous phase to Qiagen RNeasy Mini Columns. 2 ug of total RNA was reversed transcribed in a 20 ul volume using Applied Biosystem’s high capacity reverse transcription Kit. mRNA expression was determined for 1ul of cDNA with the PRISM 7500 sequence detection system (Applied Biosystems) using SYBR green dye and gene specific primers designed using Primer express software. Primer sets for the P protein of RSV were (F) 5’ AGTGCAGGACCTACATCTGCTC and (R) 5’ AGCTGTTGGCTATGTCCTTGG , while for the NP protein of Influenza virus  were (F) 5 ’ CCAGGAAATGCTGAGATCGAAG  and (R)  5’ TACACACAGGCAGGCAGACAAG 3’. Data were normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), for which the set of primers we used were (F) 5’ GCAAATTCCATGGCACCGT and (R) 5’ TCGCCCCACTTGATTTTGG. The fold increase in mRNA expression was determined using the ddCt method with mock-treated cultures as calibrator.

treatment_protocol: Influenza A/Udorn/72 (H3N2) viruses were grown in eggs, and virus titers were determined by an immunofluorescence foci assay. A laboratory stock of rgRSV244 (Hallak et al., 2000) was propagated in HEp-2 cells, and RSV infectivity was determined by plaque assay. hAEC cultures were exposed to 2 x 105 PFU influenza Udorn (MOI of apical cells of 1), 1 x 106 PFU rgRSV244 (MOI of apical cells of 5), or mock treated for 2 h, and harvested after 24 and 48 hours of incubation, respectively.

tag: cell type

value: primary polarized airway epithelial cell cultures


title: RNA isolated from PBMCs (IgAN_2)

description: miRNA expression in IgAN patient


title: RNA isolated from PBMCs (IgAN_1)

description: miRNA expression in IgAN patient


title: INFLUENZA_4

description: gene expression after 2h influenza infection (harvested 24h after treatment)


title: RSV_1


title: LS_011_bC

city: Tuebingen

first: Stefan

last: Henz

address: Spemannstrasse 37-39

department: Department of Molecular Biology

institute: Max Planck Institute for Developmental Biology

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

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

data_processing:
The exact procedure of how probes were selected and mapped to the TAIR annotation (here we used the TAIR8 annotation) as well as the used algorithms and software to get log2 expression values are the same as described in Laubinger et al., Genome Biol, 2008, Naouar et al., Plant J., 2009.
The only additional appplied filtering step for the probes was the following:
All probes that were not identically conserved in the genomes of Col-0, Bur-0 and C24 were also excluded.
Processed data is available on Series record.

organism: Arabidopsis thaliana

source_name: WT, Bur-0 23°C, LL, whole inflorescences, replicate C

label_protocol: 7.5 µg dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Plants were grown on soil at 23°C and LL until flowering.

extract_protocol: Qiagen RNeasy Plant Mini Kit was used for the total RNA extractions. For synthesis of targets, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).

treatment_protocol: none.

tag: ecotype

tag: tissue

value: whole inflorescense


title: INFLUENZA_3


title: RSV_3


title: RSV_2


title: INFLUENZA_2


title: LS_008_bA

source_name: WT, C24 23°C, LL, whole inflorecsences, replicate A


title: LS_011_bA

source_name: WT, Bur-0 23°C, LL, whole inflorescences, replicate A


title: epiRIL12_rep3

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

description: epiRIL12 Arabidopsis RNA chip 3

hyb_protocol: Approximately 7.5 μg of fragmented cDNA was hybridized for 16 hours at 60 rpm

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

data_processing:
Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94
R_processed_results_file.txt, this file contains the expression values of wt compared to mutants (log2) and their corresponding p-value resulting from the data processing in R

source_name: whole seedlings RNA

label_protocol: Ribosomal RNA (rRNA) reduction was carried out on 3 μg-aliquots of total RNA using the RiboMinusTM Plant Kit for RNA-Seq (Invitrogen). The rRNA-depleted RNA fraction was reverse transcribed using T7-(N)6 primer and Superscript II and the second strand synthesized by DNA polymerase I employing the GeneChip® WT Amplified Double Stranded cDNA Synthsis Kit (Affymetrix, P/N 900811). cDNA was then amplified using IVT (Affymetrix). The resulting cRNA was cleaned up with the GeneChip® Sample Cleanup Module (Affymetrix, P/N 900371). cRNA (7-μg aliquots) was then reverse transcribed and made double-stranded in the presence of dUTP. Following cleanup (GeneChip® Sample Cleanup Module), the cDNA was fragmented and labeled using the GeneChip® WT Double Stranded DNA Terminal Labeling Kit (Affymetrix, P/N 900812).

growth_protocol: Plants were grown under standard growth condition with 16 hours of light (long day)

extract_protocol: RNA was extracted using the Ambion miRVANA RNA isolation kit

treatment_protocol: no treatment was performed

tag: strain/ecotype

tag: age

value: 14 days

value: rosette leaves


title: RNA isolated from PBMCs (IgAN_5)

description: miRNA expression in IgAN patient


title: LS_008_bC

source_name: WT, C24 23°C, LL, whole inflorescences, replicate C


title: LS_005_bC

source_name: WT, Col-0 23°C, LL, whole inflorescenses, replicate C


title: LS_005_bA

source_name: WT Col-0 23°C, LL, whole inflorescences, replicate A


title: epiRIL12_rep2

description: epiRIL12 Arabidopsis RNA chip 2


title: LS_005_bB

source_name: WT, Col-0 23°C, LL, whole inflorescenses, replicate B


title: Col_rep3

description: Col Arabidopsis RNA chip 3

value: Col


title: epiRIL12_rep1

description: epiRIL12 Arabidopsis RNA chip 1


title: INFLUENZA_1


title: INVIVO_CON_12h_36_1

value: INVIVO

value: vehicle control

tag: animal number

tag: embryo number

tag: neural tube development

tag: initial somites

tag: somite number

tag: somitediff

tag: lab sample number

tag: sample number

tag: classification


title: MOCK_1 (for Influenza)

description: gene expression after 2h mock treatment (harvested 24h after treatment)

source_name: 2h_mock treatment_for influenza


title: MOCK_2 (for RSV)

description: gene expression after 2h mock treatment (harvested 48h after treatment)

source_name: 2h_mock treatment_for RSV


title: MOCK_2 (for Influenza)


title: MOCK_1 (for RSV)


title: LS_011_bB

source_name: WT, Bur-0 23°C, LL,  whole inflorescences, replicate B


title: LS_008_bB

source_name: WT, C24 23°C, LL,  whole inflorescences, replicate B


title: Col_rep2

description: Col Arabidopsis RNA chip 2


title: Col_rep1

description: Col Arabidopsis RNA chip 1