title: IL-23p19-/- 0 hours sample 3

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
material isolated 0 hours post infection
Total mouse liver RNA

hyb_protocol: Amplification, labeling and hybridization was performed using the WT Plus Reagent Kit (Affymetrix) according to manufacturers instructions.

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

data_processing: Data was processed using the software provided by Affymetrix (Expression Console) and background corrected/normalized using RMA procedure/quantile normalization.

label: Biotin

source_name: IL-23p19-/- mouse infected intra-hepaticallywith E. histolytica trophozoites, 0 hours post-infection

growth_protocol: IL-23p19-/- and respective C57BL/6 control mice were bred in the animal facilities at the University of Kiel, Germany, and the Research Center Borstel, Germany, respectively. All mouse strains were backcrossed against the genetic C57BL/6 background for more than 10 generations. Mice were male and aged 8–12 weeks.

extract_protocol: Total liver RNA was isolated using the Rneasy Mini Kit (qiagen). RNA integrity was checked on an Bioanalyzer 2100 (Agilent).

treatment_protocol: Mice were infected by intrahepatic injection of 1.25 × 10^5 in vitro-cultured trophozoites of the highly pathogenic cell line B, generated from E. histolytica trophozoites (HM-1:IMSS).

tag: mouse genotype

tag: background strain

value: liver

tag: infection status

value: infected intra-hepatically with E. histolytica trophozoites


title: wholebody_VEG_m_rep4

status: Public on Oct 03 2016

type: RNA

city: Saint-Pée sur Nivelle

first: Viviana

last: Lazzarotto

address: Quartier Ibarron

country: France

institute: INRA

description:
Gene expression after 3 weeks feeding
VEG_M_4

hyb_protocol: Cy3-labelled cRNA sample yields (> 0.825µg cRNA) and specific activity (> 6pmol of Cy3/µg of cRNA) were verified using a NanoDrop ND-1000: 600ng of Cy3-cRNA were fragmented and hybridized on a sub-array, following the LIQA kit instructions. The hybridization reactions were allowed to continue for 17 hours in a rotating hybridization oven (65°C), prior to washing according to the manufacturer’s instructions.

scan_protocol: Slides were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm – 20 bits).

data_processing:
Data were then obtained with the Agilent Feature Extraction software (10.7.1.1), according to the appropriate GE protocol (GE1_107_Sep09). Data were analysed using GeneSpring software (v. 12.6).
Data were scale-normalized using the median value of each array to identify differentially expressed genes between conditions

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: whole-body alevins_3 weeks feeding_VEG-M

label_protocol: Cy3-labelled experimental cRNA samples were generated using the Agilent “One-Color Microarray-based Gene Expression Analysis” (Low Input Quick Amp Labeling-LIQA) kit, according to manufacturer’s instructions. The method uses T7 RNA Polymerase Blend, which simultaneously amplifies target material and incorporates Cyanine 3-CTP (Cy3). For each sample 150ng of total RNA were used to generate fluorescent cRNA. Agilent Spike-In was included in each reaction. After the denaturation step (10 min in circulating bath at 65°C) and cRNA synthesis step (2hr at 40°C), the reactions were incubated at 70°C for 15 min to inactivate the AffinityScript enzyme. To perform the labelling reaction, cRNA samples were each mixed with 6µL of Transcription Master Mix cocktail, containing Cy3-dye, and then incubated at 40°C for two hours. Purification was performed using Quiagen RNeasy mini spin columns, eluting in 30uL of RNase-free water.

extract_protocol: Total RNA was extracted from whole body alevins collected before the first feeding and after three weeks of feeding using the TRIZOL reagent method.

tag: Stage

value: alevins

tag: broodstock group

value: VEG-fed broodstock

tag: time point

value: 3 weeks fed

tag: maternal diet

value: VEG

tag: experimental diet

value: VEG-M

tag: tissue

value: whole body


title: IL-23p19-/- 6 hours sample 1

description:
material isolated 6 hours post infection
Total mouse liver RNA

organism: Mus musculus

source_name: IL-23p19-/- mouse infected intra-hepaticallywith E. histolytica trophozoites, 6 hours post-infection

label_protocol: Amplification, labeling and hybridization was performed using the WT Plus Reagent Kit (Affymetrix) according to manufacturers instructions.


title: wholebody_COM_v_rep8

description:
Gene expression after 3 weeks feeding
COM_V_8

source_name: whole-body alevins_3 weeks feeding_COM-V

value: COM-fed broodstock

value: COM

value: COM-V


title: IL-23p19-/- 6 hours sample 2


title: IL-23p19-/- 6 hours sample 3


title: wholebody_VEG_m_rep3

description:
Gene expression after 3 weeks feeding
VEG_M_3


title: IL-23p19-/- 0 hours sample 2


title: wholebody_VEG_m_rep2

description:
Gene expression after 3 weeks feeding
VEG_M_2


title: wholebody_COM_v_rep4

description:
Gene expression after 3 weeks feeding
COM_V_4


title: wholebody_COM_v_rep6

description:
Gene expression after 3 weeks feeding
COM_V_6


title: IL-23p19-/- 0 hours sample 1


title: wholebody_VEG_m_rep1

description:
Gene expression after 3 weeks feeding
VEG_M_1


title: wholebody_COM_v_rep5

description:
Gene expression after 3 weeks feeding
COM_V_5


title: wholebody_COM_v_rep7

description:
Gene expression after 3 weeks feeding
COM_V_7


title: wholebody_COM_v_rep3

description:
Gene expression after 3 weeks feeding
COM_V_3


title: Wild type 6 hours sample 3

source_name: Wild type mouse infected intra-hepaticallywith E. histolytica trophozoites, 6 hours post-infection

value: Wild type


title: No treatment control-1

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

country: USA

institute: PHRI, NJMS, Rutgers the State University of NJ

hyb_protocol: The biotin labeled cDNA was hybridized to  the array for 16 hours at 45°C using the GeneChip® Hybridization Oven 640. Washing  and staining with streptavidin-phycoerythrin was performed using the GeneChip®  Hybridization, Wash and Stain Kit, and the GeneChip® Fluidics Station 450.standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute was used for all the experiments

scan_protocol: The biotin labeled cDNA was hybridized to the array for 16 hours at 45°C using the GeneChip® Hybridization Oven 640. Washing and staining with streptavidin-phycoerythrin was performed using the GeneChip®Hybridization, Wash and Stain Kit, and the GeneChip® Fluidics Station 450.  Standard protocol used can be found at <http://www.cag.icph.org> from the center for advanced genomics of the Public Health Research Institute  was used for all the experiments.

data_processing: Scanned Images were acquired using the GeneChip® Scanner 3000 7G and the GeneChip® Command Console® Software. Normalized and background-corrected, raw probe intensity values  were uploaded to Partek Genomics Suite ver 6.5 (PARTEK Inc, St. Louis, MO) for further analysis.

label: biotin

organism: Homo sapiens

source_name: PBMC-no treatment

label_protocol: cRNA was obtained by an in vitro transcription reaction, and was then used as the template for generating 1st strand cDNA. The cDNA  was fragmented and end-labeled with biotin as suggested by the array manufacturer (affymetrix)

growth_protocol: PBMCs were isolated from the blood of healthy human donors by Histopaque®-1077 gradient centrifugation and MDM were isolated as per standard protocols

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (Qiagen), and was converted to cDNA following the  GeneChip® WT Plus Reagent Kit protocol. Briefly, total RNA (300 ng) was used for 1st and 2nd strand cDNA synthesis.

treatment_protocol: MDMs were  treated with various concentrations of IFNε for 6 hours or 24 h. Un-treated cells were included as controls.

tag: cell type

value: MDM

tag: treatment

value: no treatment

tag: time

value: control


title: No treatment control-2


title: Wild type 6 hours sample 1


title: Wild type 0 hours sample 3

source_name: Wild type mouse infected intra-hepaticallywith E. histolytica trophozoites, 0 hours post-infection


title: Wild type 6 hours sample 2


title: Wild type 0 hours sample 2


title: wholebody_COM_v_rep2

description:
Gene expression after 3 weeks feeding
COM_V_2


title: wholebody_COM_v_rep1

description:
Gene expression after 3 weeks feeding
COM_V_1


title: Wild type 0 hours sample 1


title: wholebody_COM_c_rep8

description:
Gene expression after 3 weeks feeding
COM_C_8

source_name: whole-body alevins_3 weeks feeding_COM-C

value: COM-C


title: wholebody_COM_c_rep6

description:
Gene expression after 3 weeks feeding
COM_C_6


title: Rosiglitazone_1

city: ann arbor

first: Jun

last: Wu

state: MI

address: 210 washtenaw ave.

institute: University of Michigan

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C on Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: The label, hyb and scan were performed by the Dana-Farber Cancer institute Core facility using affymetrix Gene Chip Mouse Genome 430 2.0 arrays according to established methods.

data_processing: The data were normalized using the DNA-chip Anaylzer (dChip) software.

source_name: Rosiglitazone, differentiated inguinal fat cells

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

growth_protocol: Differentiated inguinal fat cells

extract_protocol: Total RNA was isolated by TRIzol extraction and purification using QIAGEN Rneasy mini columns according to the manufacturer's instructions.

treatment_protocol: 1 uM rosiglitazone for 4 d

value: Differentiated inguinal fat cells

value: Rosiglitazone

tag: treatment effect

value: Beiging


title: wholebody_COM_c_rep4

description:
Gene expression after 3 weeks feeding
COM_C_4

value: alevins


title: wholebody_COM_c_rep2

description:
Gene expression after 3 weeks feeding
COM_C_2


title: Rosiglitazone_2


title: wholebody_COM_c_rep7

description:
Gene expression after 3 weeks feeding
COM_C_7


title: wholebody_COM_c_rep5

description:
Gene expression after 3 weeks feeding
COM_C_5


title: Control_2

source_name: Control, differentiated inguinal fat cells

value: Control

value: Non-activated


title: wholebody_COM_c_rep3

description:
Gene expression after 3 weeks feeding
COM_C_3

value: 3 weeks fed


title: wholebody_COM_c_rep1

description:
Gene expression after 3 weeks feeding
COM_C_1


title: Control_3


title: Control_1


title: wholebody_COM_m_rep8

description:
Gene expression after 3 weeks feeding
COM_M_8

source_name: whole-body alevins_3 weeks feeding_COM-M

value: COM-M


title: wholebody_COM_m_rep7

description:
Gene expression after 3 weeks feeding
COM_M_7

value: whole body


title: abdominal wall myofascial layer_silver containing polypropylene mesh_infected_rep 3

city: Barcelona

first: Maria

middle: Teresa

last: Quiles

address: Pg Vall Hebron 119-129

department: General Surgery Research Group

country: Spain

institute: Vall Hebron Research Institute - Vall Hebron University Hospital

description: Pooled RNA: Total RNA extracted from three animals of the same group (equal quantities) and pooled into one sample.

hyb_protocol: Approximately 5μg of fragmented and labeled ssDNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 17 hours at 45° at the Gene Titan platform

scan_protocol: Arrays were scanned on an Affymetrix Gene Titan platform.

data_processing: RMA algorithm was used to normalize the arrays and summarize probe-level intensity

organism: Rattus norvegicus

source_name: anterior abdominal wall myofascial layer, silver-containing polypropylene mesh,  infected (S. aureus Xen29 inoculation; 1x107 CFU)

label_protocol: A quantity of 5.5μg of ssDNA was fragmented and labeled using the WT Plus kit (Affymetrix) following protocol guides

growth_protocol: Animals were pair-housed in plastic cages in a temperature and relative-humidity controlled room (22 °C; 50-70%, respectively) with 12:12 hour light-dark cycles and given ad libitum access to food and water.

extract_protocol: Total RNA was extracted from cryo-preserved tissues using TRIzol™ plus PureLink® RNA Mini Kit columns (Ambion) in accordance to the manufacturer's instructions. To prevent any DNA contamination of the RNA, samples were treated with DNAse I solution (Qiagen). The RNA quality and quantity were determined using the Agilent 2100 Bioanalyzer and the Nanodrop® ND-1000 Spectrophotometer. Total RNA was pooled into groups containing three individual biological replicates. Each pool contained an equal quantity of RNA (1 μg) from each individual animal. Three different pools were analyzed per treatment.

treatment_protocol: Surgical meshes (conventional polypropylene and silver containing polypropylene (250 ppm)) were implanted subcutaneously in male 7-wk-old Sprague-Dawley Hairless rats (8 replicates per mesh type were implanted into 8 different animals) . A longitudinal incision on the central abdominal surface and a subcutaneous pocket was made with blunt forceps. Single sheets of each mesh were placed onto the pre-fascia avascular plane and fixed. Half of the implanted meshes (n=4 for each mesh type) were directly inoculated with a suspension of Staphylococcus aureus Xen 29 strain (107 CFU) and skin was closured. Animals were monitored until recovery of anaesthesia and housed on-site as per standard practices. After 10 days, rats were euthanized by CO2 asphyxiation and the engrafted prostheses together with the surrounding tissues were explanted by cutting around the area. For each implant, tissue fragments were cut and snap-frozen for RNA extraction and hybridization on Affymetrix microarrays.

tag: gender

value: Male

tag: age

value: 7 weeks

tag: strain

value: Sprague Dawley Hairless


title: wholebody_COM_m_rep6

description:
Gene expression after 3 weeks feeding
COM_M_6

value: COM-fed broodstock

value: COM


title: abdominal wall myofascial layer_silver containing polypropylene mesh_infected_rep 2

value: anterior abdominal wall myofascial layer


title: IFNa-treatment-6hours-4

value: MDM

value: IFNa


title: Rosiglitazone_3

value: Differentiated inguinal fat cells


title: Day0WTATII

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

description: Gene expression data from WT D0 ATII

hyb_protocol: Hybridization targets were prepared with the Ovation Pico WT Amp V2 kit (NuGen, San Carlos, CA) and the Encore Biotin Module (NuGen, San Carlos, CA) from total RNA, hybridized to GeneChip® mouse 430.2 arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Command Console Scan Control 3.2.3.1515

data_processing: GeneSpring GX

source_name: WT

label_protocol: cDNA were amplyfied by Ovation Pico WT Amp V2 kit and labeling were done by the Encore Biotin Module (NuGen, San Carlos, CA)

growth_protocol: AEC2 cells were flow sorted from either untreated lungs or the lungs 4 days after bleomycin. The AEC2 cells were pooled from 4 – 5 mouse lungs each category.

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

tag: genotype/variation

value: wild type

value: untreated


title: wholebody_COM_m_rep4

description:
Gene expression after 3 weeks feeding
COM_M_4

value: alevins


title: wholebody_COM_m_rep5

description:
Gene expression after 3 weeks feeding
COM_M_5


title: Day0TLR4koATII

description: Gene expression data from TLR4-/- D0 ATII


title: Day4WTATII

description: Gene expression data from WT D4 ATII

value: 4 days after bleomycin


title: wholebody_COM_m_rep2

description:
Gene expression after 3 weeks feeding
COM_M_2


title: Day4TLR4koATII

description: Gene expression data from TLR4-/- D4 ATII


title: wholebody_COM_m_rep3

description:
Gene expression after 3 weeks feeding
COM_M_3


title: IFNe-treatment-6hours-3

value: IFNe


title: wholebody_VEG_rep8

description:
Gene expression before first feeding
VEG_8

source_name: whole-body alevins_before first feeding_VEG

value: VEG-fed broodstock

value: before first feeding

value: VEG


title: wholebody_COM_m_rep1

description:
Gene expression after 3 weeks feeding
COM_M_1

value: 3 weeks fed

value: COM-M

value: whole body


title: abdominal wall myofascial layer_conventional polypropylene mesh_infected_rep 2

source_name: anterior abdominal wall myofascial layer, conventional polypropylene mesh, infected (S. aureus Xen29 inoculation; 1x107 CFU)

value: Male

value: 7 weeks

value: Sprague Dawley Hairless


title: wholebody_VEG_rep7

description:
Gene expression before first feeding
VEG_7


title: wholebody_VEG_rep6

description:
Gene expression before first feeding
VEG_6


title: wholebody_VEG_rep5

description:
Gene expression before first feeding
VEG_5


title: abdominal wall myofascial layer_conventional polypropylene mesh_infected_rep 3

value: anterior abdominal wall myofascial layer


title: abdominal wall myofascial layer_silver containing polypropylene mesh_non infected_rep 1

source_name: anterior abdominal wall myofascial layer, silver containing polypropylene mesh, non infected


title: abdominal wall myofascial layer_conventional polypropylene mesh_infected_rep 1


title: abdominal wall myofascial layer_silver containing polypropylene mesh_non infected_rep 2


title: NEG_J3_rep4

city: Quebec

first: Chloe

last: Fortin

state: Quebec

address: 2440 boulevard hochelaga

country: Canada

institute: Universite Laval

description: NEGJ3 rep4

hyb_protocol: Samples were hybridized on the human gene expression 4 × 44K v2 microarray (Agilent) using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing:
Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.
The normalized_data.txt contains normalized log2 ratio (Cy5/Cy3)

label_protocol: The labelling aRNA was done using  the ULS Fluorescent Labelling Kit for Agilent arrays (Cy3-Cy5) (Kreatech Diagnostics, Amsterdam, Netherlands). ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol: Total RNA was extracted from follicular cells using TRIzol® reagent (Invitrogen, Burlington, ON, Canada) following the manufacturer’s protocol. The RNA was purified further using the ARCTURUS® PicoPure® RNA Isolation Kit protocol (Applied Biosystems, Burlington, ON, Canada) including the optional treatment with the RNase-free DNase Set (Qiagen) directly on the extraction column. Total RNA quality, purity and concentration were analyzed using the Agilent Bioanalyzer 2100 (Agilent technologies Inc., Santa Clara, CA, USA) with the RNA 6000 Nano Kit (Agilent Technologies). To generate enough material for hybridization, the samples were linearly amplified. Anti-sense RNA (aRNA) was produced using the RiboAmp Plus RNA amplification kit (Applied Biosystems). The resulting aRNA amplified output was quantified using the NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: The oocytes and surrounding cumulus cells of the patient were removed for the IVF/ICSI procedure. Follicle fluid remaining in the dishes after removal of the oocyte-cumulus complex was pooled into a single sample, which was then centrifuged at room temperature for 10 min at 800 xg to isolate follicle cells containing mural granulosa cells. The resulting pellet was suspended in 500 µL of phosphate-buffered saline solution at 4°C and transferred to a cryovial. After centrifugation at 2000 xg for 1 min (room temperature), the supernatant was removed and cells were frozen quickly in liquid nitrogen until extraction.

value: granulosa cells (preovulatory follicles 34h post trigger)

tag: ivf outcome

value: Negative

value: Positive


title: abdominal wall myofascial layer_conventional polypropylene mesh_ non infected_rep 3

source_name: anterior abdominal wall myofascial layer, conventional polypropylene mesh, non infected


title: NEG_J3_rep3

description: NEGJ3 rep3


title: NEG_J3_rep2

description: NEGJ3 rep2


title: NEG_J3_rep1

description: NEGJ3 rep1


title: abdominal wall myofascial layer_silver containing polypropylene mesh_infected_rep 1


title: abdominal wall myofascial layer_silver containing polypropylene mesh_non infected_rep 3


title: wholebody_VEG_rep3

description:
Gene expression before first feeding
VEG_3


title: wholebody_VEG_rep4

description:
Gene expression before first feeding
VEG_4


title: abdominal wall myofascial layer_conventional polypropylene mesh_ non infected_rep 2


title: wholebody_VEG_rep1

description:
Gene expression before first feeding
VEG_1


title: wholebody_VEG_rep2

description:
Gene expression before first feeding
VEG_2


title: IL-4 8 h_HCAEC

city: Zürich

first: TOM

last: SKARIA

address: Rämistr. 100

department: INTERNAL MEDICINE

country: Switzerland

institute: UNIVERSITY HOSPITAL ZURICH

description: Human coronary artery endothelial cells (HCAEC) treated with IL-4 for 8 h

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN) 825 ng of Cy3 and Cy5 labeled cRNA were competitively hybridized for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on a Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.7.3.1. Spot values were normalized using the default linear-lowess normalization.
We imported the calculated and lowess-normalized log10 ratios of the Feature Extraction result text files directly into Genesrping GX 9.0 Software (Agilent Tech. Inc.) and Metacore GeneGO (Thomson Reuters, http://portal.genego.com) software without further normalization.
As feature extraction software already performed a linear-lowess normalization of the microarray data, we must not perform any further normalization. Further data processing, i.e. selecting genes regulated atleast 2 fold up or down in their expression were performed using Genespring GX 9.0 Software (Agilent Tech. Inc.) with default settings for two color arrays. As per the MIAME guidelines, it is not necessary to provide a Matrix data table with data containing genes satisfying a particular fold cut off.

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: Human Coronary Artery Endothelial Cells (HCAEC) obtained from Lonza were cultured in EBM-2 medium (Clonetics, Lonza) supplemented with EGM-2MV Single Quots (Clonetics, Lonza) and 5% FBS.

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >9.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: HCAEC were treated with recombinant (rec.) human (h) IL-4 (4 ng/mL; PeproTech, USA) for 4 h and 8 h. Treatments were performed by replacing culture medium containing 5% FBS by one with 2% FBS added with suitable stimuli.

value: HCAEC

value: no treatment

tag: incubation time

value: 8 h

value: IL-4  4 ng/mL


title: abdominal wall myofascial layer_conventional polypropylene mesh_ non infected_rep 1

description: Pooled RNA: Total RNA extracted from three animals of the same group (equal quantities) and pooled into one sample.


title: wholebody_COM_rep6

description:
Gene expression before first feeding
COM_6

source_name: whole-body alevins_before first feeding_COM

value: alevins

value: COM-fed broodstock

value: COM


title: IL-1β 4 h_HCAEC

description: Human coronary artery endothelial cells (HCAEC) treated with IL-1β for 4 h as a positive control for inflamed endothelium

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.5.1.1. Spot values were normalized using the default linear-lowess normalization.

source_name: HCAEC - no treatment

treatment_protocol: HCAEC were treated with recombinant (rec.) mouse/human (h) Wnt5A (250 ng/mL; R&D systems, USA), rec. h IL1β (20 U/mL; PeproTech, USA) for 4 h and 8 h. Treatments were performed by replacing culture medium containing 5% FBS by one with 2% FBS added with suitable stimuli.

value: Human Coronary Artery Endothelial Cells

value: 4 h

source_name: HCAEC - treated: IL-1β 20 U/mL

value: IL-1β 20 U/mL


title: wholebody_COM_rep8

description:
Gene expression before first feeding
COM_8

value: before first feeding

value: whole body


title: IL-4 4 h_HCAEC

description: Human coronary artery endothelial cells (HCAEC) treated with IL-4 for 4 h

source_name: Human Coronary Artery Endothelial Cells (HCAEC)


title: wholebody_COM_rep5

description:
Gene expression before first feeding
COM_5


title: IL-1β 8 h_HCAEC

description: Human coronary artery endothelial cells (HCAEC) treated with IL-1β for 8 h as a positive control for inflamed endothelium


title: wholebody_COM_rep7

description:
Gene expression before first feeding
COM_7


title: wholebody_COM_rep4

description:
Gene expression before first feeding
COM_4


title: Wnt5A 4 h_HCAEC

description: Human coronary artery endothelial cells (HCAEC) treated with Wnt5A for 4 h

source_name: HCAEC - treated: Wnt5A 250 ng/mL

value: Wnt5A 250 ng/mL


title: Wnt5A 8 h_HCAEC

description: Human coronary artery endothelial cells (HCAEC) treated with Wnt5A for 8 h


title: wholebody_COM_rep3

description:
Gene expression before first feeding
COM_3


title: wholebody_COM_rep2

description:
Gene expression before first feeding
COM_2


title: wholebody_COM_rep1

description:
Gene expression before first feeding
COM_1


title: spleen_tem_2

status: Public on Oct 02 2016

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

country: Australia

institute: University of Melbourne

hyb_protocol: Performed using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix), at Ramaciotti Centre for Genomics, University of New South Wales, Australia.

scan_protocol: Performed using GeneChip Scanner 7G (Affymetrix), at Ramaciotti Centre for Genomics, University of New South Wales, Australia.

data_processing: The following analyses were conducted in R. CEL files were normalised with background correction using RMA, quantile normalization, probe-specific background correction using MAS, and summarization using the median polish algorithm.

source_name: C57/BL6 spleen, irradiated sporozoites, 30 days p.i.

label_protocol: Performed using Encore Biotin module (Nugen), at Ramaciotti Centre for Genomics, University of New South Wales, Australia.

extract_protocol: Liver and spleen were processed as described in (Fernandez-Ruiz D, et al. 2015 Nature, submitted). Briefly, livers and spleens were finely chopped to form single cell suspensions. Liver cell suspensions were filtered and then separated by density using percoll. Red blood cells in both liver and spleen cell suspensions were lysed.

value: Spleen

value: T cells (tem)


title: spleen_tem_1


title: liver_tem_1

source_name: C57/BL6 liver, irradiated sporozoites, 30 days p.i.

value: Liver


title: liver_tem_3


title: spleen_tem_3


title: liver_trm_1

value: T cells (trm)


title: liver_tem_2


title: liver_trm_2


title: Q45_liver_high fat diet_QHD_4 weeks

status: Public on Oct 01 2016

city: Shanhgai

first: Qin

last: Feng

address: 528 Zhangheng Road

department: institute of Liver diseases

country: China

institute: Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine

description:
Gene expression data from liver
Sample name: Q45

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

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. The raw data were normalized by Expression Console with MAS 5.0.

source_name: liver,high fat diet,QHD,4 weeks

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

growth_protocol: The rats were maintained in a temperature-controlled room (25 ± 1◦C) on a 12 h: 12 h light-dark cycle in the animal center.

treatment_protocol: QHD group were fed with HFD for 4 weeks followed by daily gavage of 0.1ml/kg QHD in addition to HFD for additional 4 weeks; rats in the GC group were fed with HFD for 4 weeks followed by daily gavage of a mixture of geniposide and chlorogenic acid (weight ratio) in addition to HFD for additional 4 weeks.  All rats were sacrificed for tissue collection at the end of 4-week therapy.

value: Sprague-Dawley

value: liver

tag: diet

value: high fat


title: Ovarian granulosa cells_PKA-CQR Lentivirus, biological rep3

city: Pittsburgh

first: Anthony

last: Zeleznik

address: 204 Craft Avenue

department: Obstetrics Gynecology and Reproductive Sciences

institute: University of Pittsburgh

description:
AZ38_(Rat230_2), biological rep3
Ovarian granulosa cells transduced with PKA-CQR Lentivirus

hyb_protocol: Fifteen micrograms of the fragmented RNA was added to a final volume of 300 μl hybridization cocktail (1X hybridization buffer, 100 μg/ml Herring sperm DNA, 50 μg/ml Acetylated BSA, 50 pM Affymetrix Control Oligo B2, 1X Affymetrix Eukaryotic Hybridization Control).

scan_protocol: The chip was  scanned using the GeneArray® 3000 scanner

data_processing: For data analysis, cel files were RMA normalized and reduced to single probe per gene using IQR by R. The data was imported into BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for differential expression (DE) analysis. DE genes were identified using the Student t test (p<0.001) in BRB.

source_name: 24 day-old Rat Ovarian granulosa cells

label_protocol: Labeled cRNA was prepared using the 3’IVT Express kit (Affymetrix) according to manufacturer instructions

growth_protocol: Ovarian granulosa cultures were established in M199 medium.

extract_protocol: Total RNA was extracted from the cells 24 hr. later using RNA-Bee solution, frozen at −80 C,

treatment_protocol: The following treatments were applied: 1) EGFP lentivirus 24hr (n=2), 2) EGFP lentivirus 24h + FSH (100 ng/ml) for 24h (n=3), 3) PKA-CQR lentivirus 24h (n=3)

value: 24 days-old

value: ovary

value: granulosa cell

value: PKA-CQR lentivirus 24h


title: Q46_liver_high fat diet_QHD_4 weeks

description:
Gene expression data from liver
Sample name: Q46


title: Ovarian granulosa cells_PKA-CQR Lentivirus, biological rep2

description:
AZ34_(Rat230_2), biological rep2
Ovarian granulosa cells transduced with PKA-CQR Lentivirus


title: E5_w

city: Bonn

first: Jutta

last: Kirfel

state: NRW

department: Institute of Pathology

institute: University Hospital

description: Replicate w

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: The normalization was calculated with the RMA (Robust Multiarray Analysis) algorithm.

source_name: MEF

label_protocol: Illumina protocol

growth_protocol: The mouse embryonic fibroblast cells (MEFs) were cultured in Dulbecco's modified Eagle's medium (DMEM) with High Glucose (4,5g/l) and pyruvate containing 10 % fetal bovine serum, 1 % L-glutamine, 1 % penicillin / streptomycin, 1% essential amino acids and 1 % non essential amino acids (all from Invitrogen, Darmstadt, Germany) at 37°C in a humidified 5 % CO2 atmosphere.

extract_protocol: RNA was extracted with PureLinkTM RNA Mini Kit (Invitrogen, Darmstadt, Germany) according to the manufacturer's protocol. For the microarray experiments MouseWG-6 v2.0 Expression BeadChip (Illumina, San Diego, USA) were used. RNA was extracted using the PureLink™ RNA Mini Kit (Life Technologies, Carlsbad, USA). RNA quality was tested using the Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). For the transcriptome array, 100 ng of total RNA were used. The arrays were washed and stained according to the manufacturer’s recommendations (Illumina, Fulbourn, UK)

treatment_protocol: To induce HA-Fbxl10 expression 1 µg/ml doxycycline was added to growth medium for 48 hours, changing medium after 24 hours. Not induced MEFs (without doxycycline) served as control.

tag: protocol

value: non-induced (without doxycycline)

value: embryo


title: E5_w/o

description: Replicate w/o

value: induced with doxycycline


title: E4_w

description: Replicate w


title: AP37_liver_high fat diet_GC_4 weeks

description:
Gene expression data from liver
Sample name: AP37

source_name: liver,high fat diet,GC,4 weeks


title: Q47_liver_high fat diet_QHD_4 weeks

description:
Gene expression data from liver
Sample name: Q47


title: M87_liver_high fat diet_4 weeks

description:
Gene expression data from liver
Sample name: M87

source_name: liver,high fat diet,4 weeks


title: liver_trm_3


title: M36_liver_high fat diet_4 weeks

description:
Gene expression data from liver
Sample name: M36


title: AP35_liver_high fat diet_GC_4 weeks

description:
Gene expression data from liver
Sample name: AP35


title: AP55_liver_high fat diet_GC_4 weeks

description:
Gene expression data from liver
Sample name: AP55


title: Ovarian granulosa cells_EGFP Lentivirus and treated with FSH, biological rep3

description:
AZ36_(Rat230_2), biological rep3
Ovarian granulosa cells transduced with EGFP Lentivirus and treated with FSH

value: EGFP lentivirus 24h + FSH (100 ng/ml) for 24h


title: N2_liver_normal diet_4 weeks

description:
Gene expression data from liver
Sample name: N2

source_name: liver,normal diet,4 weeks

value: normal


title: Ovarian granulosa cells_EGFP Lentivirus, biological rep2

description:
AZ35_(Rat230_2), biological rep2
Ovarian granulosa cells transduced with EGFP Lentivirus

value: EGFP lentivirus 24hr


title: Ovarian granulosa cells_EGFP Lentivirus and treated with FSH, biological rep2

description:
AZ32_(Rat230_2), biological rep2
Ovarian granulosa cells transduced with EGFP Lentivirus and treated with FSH


title: E4_w/o

description: Replicate w/o


title: E3_w

description: Replicate w


title: E3_w/o

description: Replicate w/o


title: N3_liver_normal diet_4 weeks

description:
Gene expression data from liver
Sample name: N3


title: N4_liver_normal diet_4 weeks

description:
Gene expression data from liver
Sample name: N4


title: Ovarian granulosa cells_PKA-CQR Lentivirus, biological rep1

description:
AZ30_(Rat230_2), biological rep1
Ovarian granulosa cells transduced with PKA-CQR Lentivirus


title: Ovarian granulosa cells_EGFP Lentivirus, biological rep1

description:
AZ27_(Rat230_2), biological rep1
Ovarian granulosa cells transduced with EGFP Lentivirus


title: Blood_Ly-6Clo_YFPneg_2

city: St. Louis

first: Xiaodi

state: Missouri

address: 4940 Parkview Pl

institute: Washington University/HHMI

hyb_protocol: Biotinylated cRNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix)

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high resolution scanner

data_processing: Expression values were analyzed after RMA background correction and quantile normalization using ArrayStar software (DNASTAR)

source_name: Blood Ly-6C(lo) YFP(-) monocytes

label_protocol: Target preparation was performed using the GeneChip WT Pico Kit (Affymetrix)

growth_protocol: Mice were bred and maintained in a specific pathogen–free animal facility according to institutional guidelines and under approved protocols

extract_protocol: Total RNA was isolated from cells using an RNAqueous-Micro Kit (Ambion)

treatment_protocol: Cheek pouch (submandibular) blood samples were collected using BD Microtainer Tubes with EDTA after venipuncture using a 4-mm Golden Rod Animal Lancet (MEDIpoint)

tag: backgroud strain

value: C57BL/6N x C57BL/6J F1 hybrid

value: Ly-6C(lo) monocyte, YFP(-)


title: M24_liver_high fat diet_4 weeks

description:
Gene expression data from liver
Sample name: M24


title: Blood_Ly-6Clo_YFPneg_1


title: Blood_Ly-6Clo_YFPpos_1

source_name: Blood Ly-6C(lo) YFP(+) monocytes

value: Ly-6C(lo) monocyte, YFP(+)


title: MBH_19_CON_1

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

institute: University of Lübeck

description: control

hyb_protocol: 17 hours, 60 rpm, 45C

scan_protocol: GeneChip Scanner 3000

data_processing: Data were extracted from CEL files and normalized using Expression Console (Affymetrix) software.

source_name: Mediobasal hypothalamus

label_protocol: Labelling was with GeneChip WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was isolated using Trizol Reagent (Invitrogen)

treatment_protocol: TSR mice were kept awake using 'gentle handing' method from ZT0 until ZT6 for 5 consecutive days, left to sleep ad libitum for 2 days, and sleep restrictiong was repeated for another 5 days. Control mice were kepts undisturbed in parallel.

value: Mediobasal hypothalamus

tag: background strain


title: MBH_13_CON_1

description: control


title: Ovarian granulosa cells_EGFP Lentivirus and treated with FSH, biological rep1

description:
AZ28_(Rat230_2), biological rep1
Ovarian granulosa cells transduced with EGFP Lentivirus and treated with FSH

value: Sprague-Dawley


title: Blood_Ly-6Clo_YFPpos_2


title: MBH_19_CON_2

description: control


title: MBH_7_CON_2

description: control


title: MBH_13_CON_3

description: control


title: MBH_13_CON_2

description: control


title: MBH_7_CON_1

description: control


title: Blood_Ly-6Chi_2

source_name: Blood Ly-6C(hi) monocytes

value: Ly-6C(hi) monocyte


title: MBH_13_TSR_3

description: sleep-restricted group


title: MBH_1_CON_1

description: control


title: MBH_19_CON_3

description: control


title: MBH_1_CON_2

description: control


title: MBH_1_CON_3

description: control


title: MBH_7_CON_3

description: control


title: MBH_7_TSR_2

description: sleep-restricted group


title: MBH_19_TSR_2

description: sleep-restricted group


title: MBH_1_TSR_1

description: sleep-restricted group


title: MBH_7_TSR_3

description: sleep-restricted group


title: MBH_13_TSR_2

description: sleep-restricted group


title: MBH_19_TSR_3

description: sleep-restricted group


title: MBH_1_TSR_3

description: sleep-restricted group


title: Blood_Ly-6Chi_1


title: MBH_19_TSR_1

description: sleep-restricted group


title: MBH_1_TSR_2

description: sleep-restricted group


title: MBH_13_TSR_1

description: sleep-restricted group


title: C24_12d-seedlings_2

city: KONGLOON TOON

first: SHOUDONG

last: ZHANG

address: WATERLOO ROAD

department: BIOLOGY

country: Hong Kong

institute: HONG KONG BAPTIST UNIVERSITY

description:
gene expression of 12 day old seedling
US10123789_252116911419_S01_GE1_107_Sep09_1_2.txt

hyb_protocol: Labeled RNA probes (1.65 mg) were fragmented using the fragmentation buffer (Agilent) and hybridized to the Arabidopsis arrays in the presence of the Gene Expression Hybridization buffer HI-RPM and the blocking agent (Agilent) for 17 h at 65 °C with a 10-rpm rotation speed in a hybridization oven (Agilent). The arrays were then washed using low stringency wash buffer 1 (Agilent) at room temperature for 1 min followed by a high-stringency wash using wash buffer 2 (Agilent) at 37 °C.

scan_protocol: The arrays were air-dried and scanned using the high-resolution array scanner (Agilent) with the appropriate settings for one-color gene expression arrays. The signal intensities were extracted from the scanned images with the aid of Feature extraction software 10.7.1.1 (Agilent) and subjected to background subtraction and spatial detrending GeneSpring GX (Agilent) was used to calculate the intensity ratios and fold changes. Genes with P < 0.05 and change above 2-fold were chosen for the enrichment analysis.

data_processing: The outliers and the abnormal features were flagged, and the data were normalized using intraarray percentile shift normalization (threshold of 75 and above) and median-based interarray normalization.

organism: Arabidopsis thaliana

label_protocol: Total RNA (150 ng) was used to prepare Cy3-labeled probe using the low-RNA-input linear amplification/labeling kit (Agilent).

growth_protocol: Plants were grown onfull MS plates with 3% sucrose

extract_protocol: For total RNA extraction, 100 mg of seedlings were harvested after cold treatment (4°C, 1 d) and extracted using an RNeasy plant kit (Qiagen).  The extracted total RNAs were treated with DNAse I and cleaned up with an RNA mini-column

treatment_protocol: at 21°C with 16 h of light and 8 h of darkness.

tag: genotype

value: seedling


title: MBH_7_TSR_1

description: sleep-restricted group


title: C24_12d-seedlings_1

description:
gene expression of 12 day old seedling
US10123789_252116911419_S01_GE1_107_Sep09_1_1.txt


title: ros1_12d-seedlings_1

description:
gene expression of 12 day old seedling
US10123789_252116911416_S01_GE1_107_Sep09_1_4.txt


title: ros1hda6-9_12d-seedlings_1

description:
gene expression of 12 day old seedling
US10123789_252116911417_S01_GE1_107_Sep09_1_4.txt

value: ros1, hda6-9


title: ros1hda6-9_12d-seedlings_2

description:
gene expression of 12 day old seedling
US10123789_252116911418_S01_GE1_107_Sep09_1_1.txt


title: L2.1 vs wt nitrate

city: Málaga

first: Marina

last: Rueda López

state: Málaga

address: Campus Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

description:
L2.1-wt-N
Biological replicate 1 - Technical replicate 2 of wt vs transgenic Arabidopsis plants grown with nitrate

hyb_protocol: Standard Agilent protocol

scan_protocol: Scanned using GenePix 4100A scanner with a resolution of 5 µm/pixel. Data were extracted from the scanned images using the GenePix v6.0 software.

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. Genes were declared as differentially expressed with adjusted p-value < 0.05 and log FC 1

source_name: Line 2.1 transgenic Arabidopsis plants overexpressing PpDof5

label_protocol: 600 ng of total RNA was used for each sample. Microarray labelling, hybridization and slide washing were performed accoding to the manufacturer´s protocol Low Input Quick Amp Labelling Kit - two color (Agilent Technologies; cat#5190-2306)

growth_protocol: Plants were grown 10 days in vitro conditions with MS medium containing 30 mM KNO3 or NH4Cl of unique nitrogen source.

extract_protocol: Total RNA extracted as described by Canales el al. (2010)

value: Line 2.1 transgenic overexpressing PpDof5

tag: growth conditions

value: modified MS medium with 30 mM KNO3

value: 10 days in vitro conditions

source_name: wt Arabidopsis thalina

value: wt

tag: growth condition


title: L2.2 vs wt nitrate

description:
L2.2-wt-N
Biological replicate 2 - Technical replicate 2 of wt vs transgenic Arabidospsis plants grown with nitrate

source_name: Line 2.2 transgenic Arabidopsis plants overexpressing PpDof5

value: Line 2.2 transgenic overexpressing PpDof5


title: ros1_12d-seedlings_2

description:
gene expression of 12 day old seedling
US10123789_252116911417_S01_GE1_107_Sep09_1_1.txt

tag: tissue


title: ros1hda6-10_12d-seedlings_2

description:
gene expression of 12 day old seedling
US10123789_252116911416_S01_GE1_107_Sep09_1_3.txt

value: ros1, hda6-10


title: wt vs L2.2 nitrate

description:
wt-L2.2-N
Biological replicate 2 - Technical replicate 1 of wt vs transgenic Arabidopsis plants grown with nitrate


title: L2.2 vs wt ammonium

description:
L2.2-wt-A
Biological replicate 2 - Technical replicate 2 of wt vs transgenic Arabidopsis plants grown with ammonium

value: modified MS medium with 30 mM NH4Cl


title: wt vs L2.2 ammonium

description:
wt-L2.2-A
Biological replicate 2 - Technical replicate 1 of wt vs transgenic Arabidopsis plants grown with ammonium

source_name: Line 2.2 transgenic Arabidospsis plants overexpressing PpDof5


title: IB116T

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

institute: Cancer Research Center of Toulouse

description: Sample name: 064752_IB116T_1_4

hyb_protocol: Gene expression analysis was carried out using Agilent Whole human 44K Genome Oligo Array (G4112F; Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s protocol.

scan_protocol: the scan was performed according to manufacturer’s recommendations with scanning resolution of 5µm

data_processing: For each series all microarrays were simultaneously normalized using the Quantile algorithm.

source_name: tumor

label_protocol: RNA was labeled according to manufacturer’s protocol.

extract_protocol: Total RNA were extracted from frozen tumor samples using the miRNeasy® Mini Kit (Qiagen) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Frozen tissue and cell line

tag: sample type

value: tumor

tag: sample id

tag: diagnosis

value: myxofibrosarcoma

tag: tumor site

value: left thigh

tag: cgh profile type

value: flat

tag: fnclcc grading


title: wt vs L2.1 nitrate

description:
wt-L2.1-N
Biological replicate 1 - Technical replicate 1 of wt vs transgenic Arabidopsis plants grown with nitrate

tag: genotype/variation

tag: age


title: ros1hda6-10_12d-seedlings_1

description:
gene expression of 12 day old seedling
US10123789_252116911416_S01_GE1_107_Sep09_1_1.txt


title: wt vs L2.1 ammonium

description:
wt-L2.1-A
Biological replicate 1 - Technical replicate 1 of wt vs transgenic Arabidopsis grown with ammonium


title: IB116_L

description: Sample name: 064753_IB116L_1_1

source_name: late cell line

value: cell line

value: complex with arms


title: IB117T

description: Sample name: 064752_IB117T_1_2

value: right thigh

value: complex


title: IB115_L

description: Sample name: 064749_IB115L_1_3

value: dedifferentiated liposarcoma

value: paratesticular

value: amplicons


title: IB115T

description: Sample name: 064752_IB115T_1_3


title: IB116_E

description: Sample name: 064847_IB116E_1_3

source_name: early cell line


title: IB117_E

description: Sample name: 064847_IB117E_1_2


title: IB115_E

description: Sample name: 064848_IB115E_1_3


title: IB114_E

description: Sample name: 064847_IB114E_1_1


title: IB117_L

description: Sample name: 064750_IB117L_1_4


title: IB111_L

description: Sample name: 064751_IB111L_1_3

value: axillary

value: complex with amplicons


title: IB114T

description: Sample name: 064753_IB114T_1_2


title: L2.1 vs wt ammonium

description:
L2.1-wt-A
Biological replicate 1 - Technical replicate 2 of wt vs transgenic Arabidopsis grown with ammonium

value: Line 2.1 transgenic overexpressing PpDof5

value: 10 days in vitro conditions

value: wt


title: IB105/106T

description: Sample name: 064752_IB105106T_1_1

value: unclassified sarcoma

value: paravertebral


title: IB111_E

description: Sample name: 064848_IB111E_1_1


title: IB114_L

description: Sample name: 064749_IB114L_1_4

value: myxofibrosarcoma


title: IB106_E

description: Sample name: 049917_IB106E_1_2


title: sdg8 sdg26 seedlings Replicate 1

city: Changsha

first: Ying

last: Ruan

state: Hunan

address: No.1 YuanDa Road

department: College of Bioscience and Biotechnology

institute: Hunan Agricultural University

description: sdg8 sdg26_1

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: sdg8 sdg26 seedlings

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

growth_protocol: wild-type and mutant seedlings grown at 22°C under LD

extract_protocol: 6-day-old seedlings grown at 22°C under long-day (LD; 16-h light/8-h dark) conditions were collected and quickly frozen in liquid nitrogen to extract total RNA using a TRIzol Reagent (Invitrogen；http://www.lifetechnologies.com).

value: sdg8 sdg26 mutant

value: aerial part of seedlings


title: IB105_L

description: Sample name: 064751_IB105L_1_1

value: cell line


title: Wild-type seedlings Replicate 2

source_name: Wild-type seedlings

value: wild type


title: sdg26 seedlings Replicate 2

source_name: sdg26 seedlings

value: sdg26 mutant


title: IB106_L

description: Sample name: 064751_IB106L_1_2

value: complex


title: Total RNA  from BL2 AID-/- cells rep1

city: New Haven

first: Yang

last: Xi

address: 300 George St

department: Cancer Center

institute: Yale University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol according to Illumina® Whole-Genome Gene Expression Direct Hybridization Assay  system

scan_protocol: Standard Illumina scanning protocol according to Illumina® Whole-Genome Gene Expression Direct Hybridization Assay  system

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

source_name: BL2 AID-/- cells

label_protocol: Total RNA was labeled by Cy3-Streptavidin according to the protocol in Illumina® Whole-Genome Gene Expression Direct Hybridization Assay  system

extract_protocol: RNA was extracted with Trizol reagent, followed with Illumina TotalPrep RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: disease

value: Burkitt lymphoma


title: IB111T

description: Sample name: 064753_IB111T_1_4

value: tumor

value: dedifferentiated liposarcoma


title: sdg8 sdg26 seedlings Replicate 2

description: sdg8 sdg26_2


title: Wild-type seedlings Replicate 1


title: IB105_E

description: Sample name: 049917_IB105E_1_3


title: sdg8 seedlings Replicate 1

source_name: sdg8 seedlings

value: sdg8 mutant


title: sdg26 seedlings Replicate 1


title: Total RNA from BL2 cells rep1

description: replicate 1

source_name: BL2  cells


title: Total RNA from BL2 cells rep3

description: replicate 3


title: sdg8 seedlings Replicate 2


title: Total RNA  from BL2 AID-/- cells rep3

description: replicate 3


title: Total RNA  from BL2 AID-/- cells rep2

description: replicate 2


title: Total RNA from BL2 cells rep2

description: replicate 2


title: dsDNA Ab stimulation rep1

city: Bangkok

first: Pattarin

last: TANGTANATAKUL

state: กรุงเทพมหานคร

address: Thoethai Road

country: Thailand

institute: Chulalongkorn University

description: SAMPLE 4

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: Human mesangial cells_dsDNA Ab stimulation

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: Human mesangial cells were purchased from available company.  The cells (1x106) were growth arrest in serum free medium for 24 hours before treated with anti-dsDNA antibodies or normal IgG controls (100 µg/mL).

extract_protocol: Total RNA and small RNA was extracted using miRNA Purification kit (Cat. N0. 21300, Norgen Biotek Corp., Ontario) according to the manufacturers’ protocol.  After processing with DNase digestion, clean-up procedures, RNA samples were quantified using nanodrop 1000 (Thermo Fisher Sciencitific), aliquoted and stored at -80°C until use.  For quality control, RNA purity and integrity were analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Anti-dsDNA antibodies or normal IgG controls (100 µg/mL) with normal serum 1:100 were added into culture medium period after 24 hours cell growth arrest and collected after 3 hours stimulation.

tag: cell type

value: human mesangial cells

tag: stimulated with

value: anti-dsDNA antibodies (100 µg/mL)


title: human neural progenitor cell line_TCF4_siRNA s13864_replicate2

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

country: United Kingdom

institute: Cardiff University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Sample probe profile were exported from GenomeStudio. Data were then imported into lumi (bioconductor) and Variance Stabilizing transformation applied, Robust Spline Normalized and log2 transformed.

source_name: CTXOE03 cell line

label_protocol: Biotinylated cDNA were prepared using the Custom Illumina® TotalPrep™-96 Kit (Ambion)

growth_protocol: Cells were maintained as described by Pollock K et al, Exp Neurol. 2006 May;199(1):143-55.

extract_protocol: Standard Trizol, RNA dissolved in water.

treatment_protocol: Transfection of siRNA, either control or two separate siRNAs targeting TCF4 (s13863 or s13864) using the N-Ter transfection system(Sigma). Cells were harvested using acutase 96 hours after transfection.

tag: cell line

tag: gender

value: Male

value: Neural progenitor

tag: brain region of origin

value: Fetal cortical neuroepithelium


title: IgG stimulation rep3

state: กรุงเทพมหานคร

description: SAMPLE 3

source_name: Human mesangial cells_IgG stimulation

value: non-specific polyclonal IgG


title: human neural progenitor cell line_TCF4_siRNA s13864_replicate1


title: human neural progenitor cell line_TCF4_siRNA s13864_replicate4


title: IgG stimulation rep2

state: กรุงเทพมหานคร

description: SAMPLE 2


title: dsDNA Ab stimulation rep2

state: กรุงเทพมหานคร

description: SAMPLE 5


title: IgG stimulation rep1

state: กรุงเทพมหานคร

description: SAMPLE 1


title: human neural progenitor cell line_TCF4_siRNA s13863_replicate4


title: human neural progenitor cell line_TCF4_siRNA s13864_replicate3


title: 200ppmOTA_rep4

city: Valencia

first: Markus

last: Proft

address: Jaime Roig 11

institute: Inst. Biomedicina Valencia IBV CSIC

hyb_protocol: 0.825 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast Gene Expression 8*15K Microarray (G4813A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately washing in acetonitrile at RT for 10 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1. (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 016322_D_F_20131129) to obtain background subtracted and spatially detrended Processed Signal intensities. Quantile method was used to normalize signal intensity.

organism: Saccharomyces cerevisiae

source_name: pdr5 mutant_200ppm ochratoxin A

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by NucleoSpin RNA Clean-up XS column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells from Saccharomyces cerevisiae pdr5 mutant were grown in SD medium until exponential phase

extract_protocol: Total RNA was isolated by acid phenol extraction protocol and purifyed with the RNeasy Mini kit (Qiagen) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were subjected to four different conditions: control (60min), citrinin (200 ppm for 60 min), ochratoxin A (200 ppm for 30 min), and a combination of both mycotoxins (100 ppm each for 30 min). Cells were harvested by centrifugation to extract RNA.

tag: strain background

value: pdr5 mutant cells

tag: treatment group

value: ochratoxin A (200 ppm for 30 min)


title: 100ppmCIT_100ppmOTA_rep4

source_name: pdr5 mutant_100ppm citrinin + 100ppm ochratoxin A

value: a combination of both mycotoxins (100 ppm each for 30 min)


title: human neural progenitor cell line_Control_siRNA_replicate4


title: human neural progenitor cell line_TCF4_siRNA s13863_replicate3


title: human neural progenitor cell line_TCF4_siRNA s13863_replicate1


title: human neural progenitor cell line_Control_siRNA_replicate3


title: 100ppmCIT_100ppmOTA_rep1


title: human neural progenitor cell line_Control_siRNA_replicate1


title: human neural progenitor cell line_Control_siRNA_replicate2


title: 100ppmCIT_100ppmOTA_rep3


title: O4_CMP

city: Ulm

first: Martin

middle: David

last: Burkhalter

state: Badern-Württemberg

address: Albert-Einstein-Allee 11

department: Institute for Biochemistry and Molecular Biology

institute: Ulm University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the the Agilent Scan Control Version A.8.4.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). To process raw data Genespring 13 software was used (Agilent). Acceptable flags werde Detected and Not Detected. 100% of values had to be met in at least 1 out of 1 condition. To normalize values, the threshold raw signals was set to 1.0. Percentile shift was calculated with percentile target 75. Baseline was set to the median of all samples (Normalized data can be found in GSE74093.txt.gz file).

source_name: common myeloid progenitor cells from 22-24 months old mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: mice were kept in a pathogen-free environment

extract_protocol: RNA was isolated using PeqGOLD TriFas (Peqlab) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: mice were untreated

tag: strain

value: FACS-sorted common myeloid progenitor cells

tag: genotype

value: wildtype


title: 200ppmOTA_rep3


title: O5_CMP


title: 200ppmOTA_rep2


title: O3_CMP


title: 100ppmCIT_100ppmOTA_rep2


title: 200ppmOTA_rep1


title: human neural progenitor cell line_TCF4_siRNA s13863_replicate2


title: O2_CMP


title: 200ppmCIT_rep4

source_name: pdr5 mutant_200ppm citrinin

value: citrinin (200 ppm for 60 min)


title: 200ppmCIT_rep3


title: 200ppmCIT_rep2


title: Y6_CMP

source_name: common myeloid progenitor cells from 2-3 months old mice


title: control_rep4

source_name: pdr5 mutant_non-treatment

value: control (60min)


title: 200ppmCIT_rep1


title: Y5_CMP


title: control_rep1


title: Y3_CMP


title: Y4_CMP


title: dsDNA Ab stimulation rep3

state: กรุงเทพมหานคร

description: SAMPLE 6


title: 534331A09 - Control_8h+2h_BR2 vs Stress_8h+2h_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: In temperate species, low temperatures adversely affect plant growth and development, constraining spatial expansion and productivity. Cold can trigger adaptive process or lead to alterations in physiological traits when stress intensity exceeds a certain threshold. Grapevine flower development and fruit set are influenced by cold nights in the vineyard. The correct formation of sexual organs and the success of reproduction are dependent upon sugar supply which can be affected by low temperatures. Many pathways of carbon metabolism may be affected by low temperatures however limited information is available about fluctuations in carbon metabolism in inflorescences.

hyb_protocol: Stress_8h+2h_BR2 Cy5 / Control_8h+2h_BR2 Cy3 : 30pmol.

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

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Vitis vinifera

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  . (PT-SIGMA-01_30-10-2012_T.pdf)

growth_protocol: flower - Cuttings were planted in pots containing a perlite/sand mixture (1/2, v/v) and transferred to a growth chamber at 25°C/19°C (day/night), at a relative humidity of 60% and a 16 h light/8 h dark photoperiod. Photosynthetically active radiation, PAR = 300 µmol.m-2.s-1.

extract_protocol: Stress 8h+2h BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:0°C and night 8h+2h 25°C - environmental treatment - temperature,frost:time 8hour . Plants were placed at 0°C for a 8h night. Inflorescences were collected after 1h of cold. Additional time point was performed 2h after the end of the cold night by placing the inflorescence at 25°C after the end of the cold night.

tag: harvest date

extract_protocol: Control 8h+2h BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 19°C 8h + 25°C 2h - environmental treatment - temperature,frost:time 8hour . Control plants were maintained in a growth chamber for 8 h at 19°C. Additional time point was performed 2h after the end by placing the inflorescence at 25°C


title: 534331A11 - Control_0h_BR2 vs Stress_1h_BR2

hyb_protocol: Stress_1h_BR2 Cy5 / Control_0h_BR2 Cy3 : 30pmol.

extract_protocol: Stress 1h BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:0°C and night 1h - environmental treatment - temperature,frost:time 1hour . Plants were placed at 0°C for a 1h night. Inflorescences were collected after 1h of cold.

extract_protocol: Control 0h BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment


title: 561832A10 - Control_lower_BR4 vs Tilted_lower_BR4

description: The experiments were designed to identify genes responding to the gravitropic stimulus in the xylem of poplar stem independently of phototropic responses.

hyb_protocol: Tilted_lower_BR4 Cy5 / Control_lower_BR4 Cy3 : 30pmol.

organism: Populus tremula x Populus alba

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

growth_protocol: stem - Media=potting soil hygrometry=N/A Temperature=24°C (Day) / 18°C (night) Light=16h (Day) / 8h (night)

treatment_protocol: Name:Light - abiotic stress - light,light:time 30min . young poplar trees were staked one week before use. For the experiment, the plants were placed in an isotropic light environment and were tilted at 35° during 30 min. Control plants were kept straight in the isotropic light device. Xylem samples were collected from the upper and lower face of the stems.

tag: treatment

value: tilted

tag: face of the stem

value: lower

tag: cultivar

value: 73 days

value: control


title: mmu_SPL_CD19_CD38_IgG2ab_rep2

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: IgG2b+ memory B cells from spleen of pet shop mice

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Mouse MG 430_2 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the BioRetis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the BioRetis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 2 chips of one group (Experiment group) were compared to the 2 chips of any other group (Baseline group) and chips within one group were compared to each other in both directions. This results in 15 different comparisons of 6 groups. Of relevance for this publication were the comparisons of groups 1 vs. 2, groups 3 vs. 4, and groups 5 vs. 6. The following parameters of absolute and comparative analysis were included in the BioRetis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 4 SLR values of Experiment group vs. Baseline group and 4 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.385E-07) or more than 50% of non-parametrically calculated Change calls (one-sided Wilcoxon’s signed rank test after Tukey-Biweight reduction of outliers, calculated by GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction and not No Changed. Significantly differentially expressed genes were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chips comparisons (one direction).

growth_protocol: Cells were isolated ex vivo from wild type C57BL/6J mice or mice obtained at a pet shop without treatment of live mice or isolated cells.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

value: IgG2b+ memory B cells

tag: mouse strain/origin

value: pet shop mice

tag: tissue

value: spleen


title: C57Bl6_SPL_CD19_IgG2b_rep2

description: IgG2b+ memory B cells from spleen of C57BL/6J

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Mouse MG 430_2 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.


title: 561832A04 - Tilted_lower_BR2 vs Control_lower_BR2

hyb_protocol: Control_lower_BR2 Cy5 / Tilted_lower_BR2 Cy3 : 30pmol.

tag: age


title: 561832A07 - Control_lower_BR3 vs Tilted_lower_BR3

hyb_protocol: Tilted_lower_BR3 Cy5 / Control_lower_BR3 Cy3 : 30pmol.


title: 534107A07 - Stress_8h_BR1 vs Stress_8h+2h_BR1

hyb_protocol: Stress_8h+2h_BR1 Cy5 / Stress_8h_BR1 Cy3 : 30pmol.

extract_protocol: Stress 8h+2h BR1:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: Stress 8h BR1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:0°C and night 8h - environmental treatment - temperature,frost:time 8hour . Plants were placed at 0°C for a 8h night. Inflorescences were collected after 1h of cold.


title: 534331A12 - Stress_1h_BR2 vs Control_0h_BR2

hyb_protocol: Control_0h_BR2 Cy5 / Stress_1h_BR2 Cy3 : 30pmol.


title: 534331A10 - Stress_8h+2h_BR2 vs Control_8h+2h_BR2

hyb_protocol: Control_8h+2h_BR2 Cy5 / Stress_8h+2h_BR2 Cy3 : 30pmol.


title: 561832A09 - Tilted_lower_BR3 vs Control_lower_BR3

hyb_protocol: Control_lower_BR3 Cy5 / Tilted_lower_BR3 Cy3 : 30pmol.


title: C57Bl6_SPL_CD19_IgG2b_rep1

source_name: IgG2b+ memory B cells from spleen of C57BL/6J


title: mmu_BM_CD19_CD38_IgG2ab_rep1

description: IgG2b+ memory B cells from bone marrow of pet shop mice

value: bone marrow


title: 561832A03 - Control_lower_BR2 vs Tilted_lower_BR2

hyb_protocol: Tilted_lower_BR2 Cy5 / Control_lower_BR2 Cy3 : 30pmol.


title: 561832A02 - Control_lower_BR1 vs Tilted_lower_BR1

hyb_protocol: Tilted_lower_BR1 Cy5 / Control_lower_BR1 Cy3 : 30pmol.


title: 534107A08 - Stress_8h+2h_BR1 vs Stress_8h_BR1

hyb_protocol: Stress_8h_BR1 Cy5 / Stress_8h+2h_BR1 Cy3 : 30pmol.


title: 561827A04 - Tilted_upper_BR2 vs Control_upper_BR2

hyb_protocol: Control_upper_BR2 Cy5 / Tilted_upper_BR2 Cy3 : 30pmol.

value: upper


title: 561832A01 - Tilted_lower_BR1 vs Control_lower_BR1

hyb_protocol: Control_lower_BR1 Cy5 / Tilted_lower_BR1 Cy3 : 30pmol.


title: 561827A07 - Control_upper_BR3 vs Tilted_upper_BR3

hyb_protocol: Tilted_upper_BR3 Cy5 / Control_upper_BR3 Cy3 : 30pmol.


title: 561827A03 - Control_upper_BR2 vs Tilted_upper_BR2

hyb_protocol: Tilted_upper_BR2 Cy5 / Control_upper_BR2 Cy3 : 30pmol.


title: 534331A08 - Stress_8h+2h_BR2 vs Stress_8h_BR2

hyb_protocol: Stress_8h_BR2 Cy5 / Stress_8h+2h_BR2 Cy3 : 30pmol.

extract_protocol: Stress 8h BR2:10ug. (Qiagen_RNeasy.pdf)


title: 561827A08 - Tilted_upper_BR3 vs Control_upper_BR3

hyb_protocol: Control_upper_BR3 Cy5 / Tilted_upper_BR3 Cy3 : 30pmol.


title: 561827A10 - Tilted_upper_BR4 vs Control_upper_BR4

hyb_protocol: Control_upper_BR4 Cy5 / Tilted_upper_BR4 Cy3 : 30pmol.


title: 561827A09 - Control_upper_BR4 vs Tilted_upper_BR4

hyb_protocol: Tilted_upper_BR4 Cy5 / Control_upper_BR4 Cy3 : 30pmol.


title: 561827A01 - Control_upper_BR1 vs Tilted_upper_BR1

hyb_protocol: Tilted_upper_BR1 Cy5 / Control_upper_BR1 Cy3 : 30pmol.


title: 534331A07 - Stress_8h_BR2 vs Stress_8h+2h_BR2

hyb_protocol: Stress_8h+2h_BR2 Cy5 / Stress_8h_BR2 Cy3 : 30pmol.


title: 561832A08 - Tilted_lower_BR4 vs Control_lower_BR4

hyb_protocol: Control_lower_BR4 Cy5 / Tilted_lower_BR4 Cy3 : 30pmol.


title: 561827A02 - Tilted_upper_BR1 vs Control_upper_BR1

hyb_protocol: Control_upper_BR1 Cy5 / Tilted_upper_BR1 Cy3 : 30pmol.


title: C57Bl6_BM_CD19_IgG2b_rep2

description: IgG2b+ memory B cells from bone marrow of C57BL/6J

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The Mouse MG 430_2 arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.


title: 534331A05 - Control_8h_BR2 vs Stress_8h_BR2

hyb_protocol: Stress_8h_BR2 Cy5 / Control_8h_BR2 Cy3 : 30pmol.

extract_protocol: Control 8h BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 19°C 8h - environmental treatment - temperature,frost:time 8hour . Control plants were maintained in a growth chamber for 8h at 19°C.


title: 534331A06 - Stress_8h_BR2 vs Control_8h_BR2

hyb_protocol: Control_8h_BR2 Cy5 / Stress_8h_BR2 Cy3 : 30pmol.


title: 534107A12 - Stress_1h_BR1 vs Control_0h_BR1

hyb_protocol: Control_0h_BR1 Cy5 / Stress_1h_BR1 Cy3 : 30pmol.

extract_protocol: Control 0h BR1:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: Stress 1h BR1:10ug. (Qiagen_RNeasy.pdf)


title: 534331A03 - Stress_1h_BR2 vs Stress_8h_BR2

hyb_protocol: Stress_8h_BR2 Cy5 / Stress_1h_BR2 Cy3 : 30pmol.


title: 534331A02 - Stress_1h_BR2 vs Control_1h_BR2

hyb_protocol: Control_1h_BR2 Cy5 / Stress_1h_BR2 Cy3 : 30pmol.

extract_protocol: Control 1h BR2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:control 19°C 1h - environmental treatment - temperature,frost:time 1hour . Control plants were maintained in a growth chamber for 1h at 19°C.


title: control_rep2

hyb_protocol: 0.825 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast Gene Expression 8*15K Microarray (G4813A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately washing in acetonitrile at RT for 10 seconds.

tag: genotype/variation


title: DT40 cells infected with vvIBDV LX at 36 hpi, biological rep1

city: Beijing

first: Rong

last: Quan

address: No. 9 Shuguang Garden Middle Road, Haidian District

institute: Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences

hyb_protocol: Array hybridization and washing were performed using the GeneChip Hybridization, Wash and Stain Kit in a Hybridization Oven 645 and a Fluidics Station 450 according to the manufacturer’s instructions.

scan_protocol: Slides were scanned using a GeneChip Scanner 3000 and Command Console Software 3.1 with default settings.

data_processing:
The raw data were normalized using the MAS 5.0 algorithm
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.28061

organism: Gallus gallus

label_protocol: After quality assessment, the RNA was used for cDNA synthesis. The cDNA was then transcribed to cRNA, which was tagged with biotin using the GeneChip 3’IVT Express Kit (Affymetrix).

growth_protocol: The DT40 cell line was maintained in RPMI 1640 medium supplemented with 8% heat-inactivated fetal bovine serum (FBS), 2% heat-inactivated chicken serum, 10% tryptose phosphate broth, 1 mM sodium pyruvate, 100 U/ml penicillin G, and 100 μl/ml streptomycin at 37°C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was isolated using an miRNeasy Mini Kit (QIAGEN). Both the integrity and concentration of RNA were evaluated using an Agilent Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: DT40 cells were infected with vvIBDV strain LX at an MOI of 5 EID50 and collected at 12,18,24,36,48 hours post-infection (pi).  Mock-infected DT40 cells were used as negative controls.

tag: cell type

value: Chicken B cell line

tag: infected with

value: very virulent infectious bursal disease virus (vvIBDV) strain LX

tag: time point

value: 36 hpi


title: 534331A01 - Control_1h_BR2 vs Stress_1h_BR2

hyb_protocol: Stress_1h_BR2 Cy5 / Control_1h_BR2 Cy3 : 30pmol.


title: C57Bl6_BM_CD19_IgG2b_rep1

description: IgG2b+ memory B cells from bone marrow of C57BL/6J IgG2b+ memory B cells from bone marrow of C57BL/6J


title: DT40 cells, mock treated biological rep1

tag: cell line

value: none (mock control)


title: DT40 cells infected with vvIBDV LX at 48 hpi, biological rep1

value: 48 hpi


title: control_rep3

value: pdr5 mutant cells


title: DT40 cells infected with vvIBDV LX at 24 hpi, biological rep1

value: 24 hpi


title: DT40 cells infected with vvIBDV LX at 18 hpi, biological rep1

description: BH12069-2_DT40-LX 18h_(Chicken).mas5

value: 18 hpi


title: 534107A11 - Control_0h_BR1 vs Stress_1h_BR1

hyb_protocol: Stress_1h_BR1 Cy5 / Control_0h_BR1 Cy3 : 30pmol.


title: PCC6803_IsaR1OE_6h_copper_addition_2

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays for the iron depletion Experiment. For the overexpression experiment a G2505C scanner was used with the same Software and protocol version.

data_processing: Raw data were processed with the R package Limma. Median signal intensity was normexp background substracted and quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis 6803 liquid cultures

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis wild type strain was grown at 30 °C in a modified version of BG11 medium (YBG11) containing a higher amount of EDTA (16 μM instead of 2.8 μM in BG11) and a lower iron concentration (Shcolnick, Shaked et al. 2007). Light intensity was adjusted to 50 μmol photons m−2·s−1 of white light. Cultures were aerated with normal air for the iron stress experiment and shaked without aeration for the overexpression experiment. IsaR1OE and WT_pVZ were grown in presence of 2 µg mL-1 gentamicin.

extract_protocol: Synechocystis 6803 liquid cultures were collected by quenching on ice and immediate centrifugation at 4 °C.  RNA was extracted following the protocol by  Pinto et al., 2009 (Pinto, Thapper et al. 2009) with an additional phenol/chloroform/Isoamyl alcohol (25:24:1 v/v) extraction preceding the RNA precipitation

treatment_protocol: Desferrioxamine B (endconcentration 100µM) was added to the liquid cultures, and samples were taken before treatment and 3,12, 24, 48 and 72 h after DFB addition. IsaR1 overexpression was induced by addition of  CuSO4 to a final concentration of 2 µM.

tag: timepoint

value: CuSO4 to a final concentration of 2 µM


title: 534107A06 - Stress_8h_BR1 vs Control_8h_BR1

hyb_protocol: Control_8h_BR1 Cy5 / Stress_8h_BR1 Cy3 : 30pmol.

extract_protocol: Control 8h BR1:10ug. (Qiagen_RNeasy.pdf)


title: PCC6803_IsaR1OE_0h_copper_addition_1


title: PCC6803_IsaR1OE_6h_copper_addition_1


title: DT40 cells infected with vvIBDV LX at 12 hpi, biological rep1

description: BH12069-2_DT40-LX 12h_(Chicken).mas5

value: 12 hpi


title: 534107A10 - Stress_8h+2h_BR1 vs Control_8h+2h_BR1

hyb_protocol: Control_8h+2h_BR1 Cy5 / Stress_8h+2h_BR1 Cy3 : 30pmol.

extract_protocol: Control 8h+2h BR1:10ug. (Qiagen_RNeasy.pdf)


title: PCC6803_WT_pVZ_6h_copper_addition_2


title: 534107A05 - Control_8h_BR1 vs Stress_8h_BR1

hyb_protocol: Stress_8h_BR1 Cy5 / Control_8h_BR1 Cy3 : 30pmol.


title: 534107A04 - Stress_8h_BR1 vs Stress_1h_BR1

hyb_protocol: Stress_1h_BR1 Cy5 / Stress_8h_BR1 Cy3 : 30pmol.


title: 534107A02 - Stress_1h_BR1 vs Control_1h_BR1

hyb_protocol: Control_1h_BR1 Cy5 / Stress_1h_BR1 Cy3 : 30pmol.

extract_protocol: Control 1h BR1:10ug. (Qiagen_RNeasy.pdf)


title: PCC6803_IsaR1OE_0h_copper_addition_2


title: PCC6803_WT_pVZ_0h_copper_addition_2


title: PCC6803_[delta]isaR1_48h_DFB_addition_2

value: Desferrioxamine B (endconcentration 100µM)


title: PCC6803_[delta]isaR1_72h_DFB_addition_1


title: PCC6803_[delta]isaR1_24h_DFB_addition_1


title: PCC6803_WT_pVZ_0h_copper_addition_1


title: 534107A01 - Control_1h_BR1 vs Stress_1h_BR1

hyb_protocol: Stress_1h_BR1 Cy5 / Control_1h_BR1 Cy3 : 30pmol.


title: PCC6803_[delta]isaR1_48h_DFB_addition_1


title: PCC6803_[delta]isaR1_72h_DFB_addition_2


title: PCC6803_[delta]isaR1_24h_DFB_addition_2


title: PCC6803_[delta]isaR1_12h_DFB_addition_1


title: PCC6803_WT_pVZ_6h_copper_addition_1


title: 534107A03 - Stress_1h_BR1 vs Stress_8h_BR1

hyb_protocol: Stress_8h_BR1 Cy5 / Stress_1h_BR1 Cy3 : 30pmol.


title: PCC6803_[delta]isaR1_12h_DFB_addition_2


title: PCC6803_WT_72h_DFB_addition_2

value: WT


title: 534331A04 - Stress_8h_BR2 vs Stress_1h_BR2

hyb_protocol: Stress_1h_BR2 Cy5 / Stress_8h_BR2 Cy3 : 30pmol.


title: PCC6803_[delta]isaR1_3h_DFB_addition_2


title: PCC6803_WT_48h_DFB_addition_1


title: PCC6803_[delta]isaR1_0h_DFB_addition_1


title: 9974366114_R04C01

type: genomic

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

hyb_protocol: Hybridization: 22 hr at 48 degrees C. (full protocol details for all steps can be found in Illumina Infinium HD Methylation Assay manual)

scan_protocol: iScan Scan Setting: Methylation  NXT

data_processing: β values are calculated using the formula:  β = Methylated / (Methylated + Unmethylated + 100). The file methyl_and_unmethylated_signal_Annotated_AA_vs_EA.txt is available on the series record and contains the non-normalized beta values, detection p-values and raw methylated and unmethylated signal in addition to probe annotation.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Naïve CD4+ T cell

label_protocol: Staining Protocol (Tecan Freedom Evo): XStain HD BeadChip

extract_protocol: Whole blood was collected at the time of enrollment and processed within 6 h of collection. Peripheral blood mononuclear cells were isolated using Ficoll density gradient centrifugation media (GE Healthcare Biosciences, USA) followed by indirect isolation of untouched naïve CD4+ T cells using the Naïve CD4+ T cell Isolation Kit II (Miltenyi Biotec Inc., USA). DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen, USA) and DNA concentration was determined by spectrophotometry on the NanoDrop 2000 (Thermo Scientific, USA). Flow cytometry was used to confirm purity of isolated naïve CD4+ T cells using CD4 and CD45RA fluorochromeconjugated antibodies (BioLegend, USA).

tag: disease state

value: Healthy Control

value: CD4+ T cell

tag: gender

value: Female

tag: race

value: African-American


title: PCC6803_WT_24h_DFB_addition_2

tag: genotype


title: Control unstressed VS Test acid-stressed bacterial cells_rep3.1

city: ottawa

first: ALAIN

last: STINTZI

state: ONTARIO

address: 451 SMYTH ROAD

department: BIOCHEMSISTRY, MICROBIOLOGY AND IMMUNOLOGY

institute: UOTTAWA

description: Unstressed contreol vs acid stressed test bacterial cells

hyb_protocol: not provided

scan_protocol: The signal intensities of each spot were collected using ScanArray software (PerkinElmer).

data_processing: The spot intensities were normalized via locally weighted linear regression (LOWESS) using MIDAS

organism: Campylobacter jejuni

source_name: US-C. jejuni bacterial cells

label_protocol: The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 350 μL of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 10000 X g, followed by washing with sterile ddH2O. Following concentration and resuspension into NaHCO3 pH 9.0, the aminoallyl-labeled cDNA was coupled to either Cy3 (used to label control samples) or Cy5 dye (used to label test samples) by adding 10 μL of Cy3  or Cy5 (GE Healthcare) in dimethyl sulfoxide followed by incubation in the dark for 1 h at room temperature. Next, the fluorescently labeled cDNA was purified using QIAquick PCR purification kit according to the manufacturer’s instructions (Qiagen). Fluorescent Cy3- and Cy5-labeled cDNAs were combined and the fluor-labeled cDNA mix was dried under vacuum with a SpeedVac and resuspended in 15.14 μL of water, to which the following was added: 2.5 μL of salmon sperm DNA (10 mg/mL), 9 μL of 20X SSC, 0.36 μL of 10% SDS, and 9 μL of formamide.

growth_protocol: C. jejuni 81-176 was grown to logarithmic phase in biphasic MH medium (pH 7.4) under microaerophilic conditions. Bacterial cells were exposed to acid stress at pH 4 for 8 min in HCl-adjusted MH broth

extract_protocol: 10 μg of total RNA samples from each control (unstressed C. jejuni) and test sample (acid-stressed C. jejuni) were converted to cDNA using Superscript II (Invitrogen); 10 µg of random hexamers (Amersham Biosciences); a dNTP mixture of 0.5 mM dGTP, dATP and dCTP each; 0.16 mM dTTP; and 0.34 mM aminoallyl-dUTP. Aminoallyl-dUTP was incorporated in the reaction to permit the labeling of the cDNA with the monoreactive fluors indocarbocyanine (Cy3) and indodicarbocyanine (Cy5) (GE Healthcare)

treatment_protocol: Total RNA was extracted using a hot phenol-chloroform method

tag: strain

value: Unstressed

tag: ph

value: pH 7 for 8 min

source_name: AS-C. jejuni bacterial cells

value: Acid-stressed

value: pH 4 for 8 min


title: Control unstressed VS Test acid-stressed bacterial cells_rep3.2

tag: treatment


title: Control unstressed VS Test acid-stressed bacterial cells_rep3.3


title: PCC6803_[delta]isaR1_3h_DFB_addition_1


title: PCC6803_WT_48h_DFB_addition_2


title: PCC6803_WT_72h_DFB_addition_1


title: PCC6803_[delta]isaR1_0h_DFB_addition_2


title: PCC6803_WT_12h_DFB_addition_1


title: 9974366114_R04C02


title: PCC6803_WT_12h_DFB_addition_2


title: Control unstressed VS Test acid-stressed bacterial cells_rep2.3


title: PCC6803_WT_3h_DFB_addition_2


title: PCC6803_WT_24h_DFB_addition_1


title: 9974366114_R06C02


title: 9974366114_R02C02


title: 9974366114_R06C01

value: European-American


title: Control unstressed VS Test acid-stressed bacterial cells_rep2.1


title: PCC6803_WT_0h_DFB_addition_2


title: 534107A09 - Control_8h+2h_BR1 vs Stress_8h+2h_BR1

hyb_protocol: Stress_8h+2h_BR1 Cy5 / Control_8h+2h_BR1 Cy3 : 30pmol.

tag: harvest date


title: Control unstressed VS Test acid-stressed bacterial cells_rep1.1


title: Control unstressed VS Test acid-stressed bacterial cells_rep2.2


title: HT29_siRNA_C_rep3

city: Stavanger

first: Oddmund

last: Nordgard

address: Gerd Ragna Bloch Thorsens gate 8

department: Dep. of Hematology and Oncology

country: Norway

institute: Stavanger University Hospital

hyb_protocol: Norwegian Microarray Consortium 2008

scan_protocol: Norwegian Microarray Consortium 2008

data_processing: The data were quantile normalized in R

source_name: HT29 cells, transfected with siRNA C (scramble)

label_protocol: Norwegian Microarray Consortium 2008

extract_protocol: Allprep DNA/RNA/protein Mini kit (Qiagen)

tag: transfection

value: siRNA C (scramble)


title: Control unstressed VS Test acid-stressed bacterial cells_rep1.2


title: Control unstressed VS Test acid-stressed bacterial cells_rep1.3


title: 9974366114_R02C01


title: PCC6803_WT_0h_DFB_addition_1


title: 9974366108_R02C02


title: 9974366111_R02C02


title: HT29_siRNA_C_rep2


title: 9974366111_R06C02


title: HT29_siRNA_C_rep1


title: HT29_siRNA_C_rep4


title: HT29_siRNA_B_rep4

source_name: HT29 cells, transfected with siRNA B (PHGR1)

value: siRNA B (PHGR1)


title: 9974366108_R02C01


title: HT29_siRNA_B_rep2


title: 9974366108_R06C01


title: 9974366111_R04C02


title: HT29_siRNA_B_rep1


title: HT29_siRNA_B_rep3


title: HT29_siRNA_A_rep3

source_name: HT29 cells, transfected with siRNA A (PHGR1)

value: siRNA A (PHGR1)


title: 9974366111_R04C01


title: HT29_siRNA_A_rep4


title: mdx TA replicate 2

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

description:
raw data file: SG12494259_252800520725_S001_GE2_1105_Oct12_1_2
Biological replicate 2 of 3. mdx TA muscle
mdx-2

hyb_protocol: 300 ng of cRNA from the control and test samples were combined and fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized on an Agilent SurePrint G3 mouse 8x60K microarray (028005) 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: Scanned on an Agilent SureScan Microarray scanner following manufacturer's protocol.

data_processing: Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Microarray analysis was completed with an ANOVA and a Tukey's post-hoc test when a significant ANOVA was observed. In addition, a mean absolute log2 expression ratio of at least 0.585 (50% increase or decrease in expression) must be satisfied.

source_name: mdx_tibialis anterior muscle

label_protocol: Cy3 (control samples) and Cy5 (test samples) labeled cRNA was prepared using the Agilent LowInput QuickAmp Labeling Kit according to 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: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Mice were all fed on regular chow diet

tag: strain background

tag: mouse model

value: mdx model

value: mdx

value: 9-month old

tag: tissue

value: Tibialis anterior muscle


title: HT29_siRNA_A_rep2


title: N1ICD-mdx TA replicate 3

description:
raw data file: SG12494259_252800520725_S001_GE2_1105_Oct12_1_3
Biological replicate 3 of 3. N1ICD-mdx TA muscle
N1ICD-mdx3

source_name: N1ICD-mdx_tibialis anterior muscle

tag: genotype/variation

tag: age


title: HT29_siRNA_A_rep1


title: N1ICD-mdx TA replicate 1

description:
raw data file: SG12494259_252800520725_S001_GE2_1105_Oct12_1_1
Biological replicate 1 of 3. N1ICD-mdx TA muscle
N1ICD-mdx1


title: 9974366089_R02C02

tag: cell type


title: N1ICD-mdx TA replicate 2

description:
raw data file: SG12494259_252800520725_S001_GE2_1105_Oct12_1_2
Biological replicate 2 of 3. N1ICD-mdx TA muscle
N1ICD-mdx2


title: 9974366089_R06C01


title: mdx TA replicate 3

description:
raw data file: SG12494259_252800520725_S001_GE2_1105_Oct12_1_3
Biological replicate 3 of 3. mdx TA muscle
mdx-3


title: PCC6803_WT_3h_DFB_addition_1

value: Desferrioxamine B (endconcentration 100µM)

value: WT