title: T87 protoplast, biological rep2

city: Ikoma

first: Arata

last: Yoneda

address: 8916-5 Takayama

department: Graduate school of Biological Science

institute: Nara Institute of Science and Technology

hyb_protocol: The biotin-tagged cRNA was fragmented and hybridized with Affymetrix ATH1 array at 45 °C for 16 h, followed by the standard post-hybridization washing and staining on an Affymetrix GeneChip Fluidics Station 400 (Affymetrix)

scan_protocol: Arrays were scanned on an Affymetrix GeneArray Scanner.

data_processing:
The raw data were normalized and analyzed by GeneSpring software version 7.3 (Agilent Technologies, Palo Alto, CA).
Algorithm: ExpressionStat 5.0

organism: Arabidopsis thaliana

source_name: protoplasts from Arabidopsis T87 cells

label_protocol: Biotinylated cRNA were prepared by GeneChip 3' IVT Express Kit from 750 ng total RNA

growth_protocol: Suspension cultures of a wild-type Arabidopsis T87 cells were maintained with a modified Linsmaier and Skoog medium, containing Murashige and Skoog plant salt mixture (Wako Pure Chemical Industries Ltd., Osaka, Japan). The cell suspensions were agitated on a rotary shaker at 130 rpm at 22 °C under light condition. The cells were diluted 20-fold at weekly intervals with fresh liquid medium.

extract_protocol: Total RNA was extracted from protoplasts, intact leaves or intact T87 by RNeasy plant mini kit (Quiagen, Hilden, Germany).

treatment_protocol: The 4-day-old T87 cells were treated with enzyme mixture containing 1% cellulase Onozuka RS and 0.5% pectolyase Y-23 in 0.35 M mannitol for 1.5 h on a shaker at 50 rpm at 22 °C to digest the primary cell wall completely. Then the cells were washed by 0.4M mannitol three times, and re-suspended into the medium containing 0.4M mannitol. After 3 hours incubation at 22 °C, the cell wall-digested cells were collected as the protoplast samples. Also, 4-day-old T87 cells were treated with the medium containing 0.4M mannitol for 3 hours, and were collected as the osmotic stress-treated samples.

value: Arabidopsis thaliana T87 suspension cells


title: Blood_pre_XB0094_rep1

status: Public on Feb 01 2017

type: RNA

city: London

first: Thalia

last: Eley

address: DeCrespigny Park, Denmark Hill

department: SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience

country: United Kingdom

institute: King's College London

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Stringent quality control processing of the data was conducted using standardised procedures from internal pipelines (available at https://github.com/snewhouse/BRC_MH_Bioinformatics). Expression data was background corrected using Module-based Background Correction for Beadarray (Ding et al., 2008). Probes were then filtered by selecting probes with expression levels >2SD greater than the mean intensity of the negative control (background) beads. Reported gender was compared to XIST gene expression (female specific) and Y chromosome gene expression (male specific). Each probe was then transformed and normalised using log2 transformation and Robust-Spline Normalisation (Schmid et al., 2010, Du et al., 2008). Sample relationships within the co-expression network were assessed and outliers were removed (Oldham et al., 2012).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human, Whole Blood, pre-therapy

label_protocol: Biotinylated, amplified cRNA was generated using the Illumina® TotalPrep™-96 RNA Amplification Kit for Illumina Sentrix Arrays.

extract_protocol: Blood RNA was isolated and purified using the PAXgene Blood miRNA Kit according to the manufacturer’s protocol using the Qiagen Qiacube. RNA quality and integrity were measured using both the Nanodrop 1000 spectrophotometer.

tag: gender

value: FEMALE

tag: tissue

value: Blood

tag: timepoint

value: pre


title: Blood_fu_XB0099_rep1

description: QC ok

source_name: Human, Whole Blood, follow-up-therapy

value: follow-up


title: X-ray_4Gy_day7_rep 1

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

country: USA

institute: Columbia University

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 µl 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 4x44k v.2 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 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or not significantly above background were excluded.

organism: Mus musculus

source_name: blood

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

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia at days 1, 3, and 7 post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: protocol

value: male


title: Blood_post_XB0094_rep1

description: QC ok

source_name: Human, Whole Blood, post-therapy

value: post


title: Neutrophils, Patient, JIA, ADM, Biological replicate 3 [RNA]

city: Buffalo

first: kaiyu

last: Jiang

address: 875 Ellicott Street

department: Pediatrics

institute: University at Buffalo

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr on Affymetrix human EXON 1.0 ST array or GeneChip™ miRNA 1.0 array following manufacturer's directions. GeneChips were washed and stained in an Affymetrix 450 Fluidics Station.

scan_protocol: GeneChips were scanned using an Affymetrix 3000 7G scanner.

data_processing: Expression summary values from Affymetrix Exon and miRNA arrays were generated using RMA software in the Affy package of Bioconductor in the R statistical computing environment.

label: Biotin

source_name: neutrophil RNA, JIA, ADM

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

tag: disease state

value: juvenile idiopathic arthritis (JIA)

tag: group

value: active disease, on therapy (ADM)

tag: cell type

value: neutrophils


title: Neutrophils, Patient, JIA, ADM, Biological replicate 23 [RNA]


title: X-ray_1Gy_day7_rep 4


title: X-ray_1Gy_day7_rep 5


title: T87 protoplast, biological rep1

country: Japan

tag: strain


title: Neutrophils, Patient, JIA, ADM, Biological replicate 14 [RNA]


title: T87 osmotic stress (0.4M mannitol)-treated, biological rep3

source_name: 4-day-old Arabidopsis T87 suspension cells treated with 0.4M mannitol


title: Neutrophils, Patient, JIA, ADM, Biological replicate 9 [RNA]


title: Blood_fu_XB0090_rep1

description: QC ok

value: MALE


title: Neutrophils, Patient, JIA, ADM, Biological replicate 5 [RNA]


title: X-ray_1Gy_day7_rep 3


title: Neutrophils, Patient, JIA, ADM, Biological replicate 6 [RNA]


title: Control_day3_rep 5

value: Control


title: Neutrophils, Patient, JIA, ADM, Biological replicate 2 [RNA]


title: Neutrophils, Patient, JIA, ADM, Biological replicate 18 [RNA]


title: Blood_post_XB0090_rep1

description: QC ok


title: X-ray_1Gy_day7_rep 2


title: Neutron_1Gy_day7_rep 6


title: T87 osmotic stress (0.4M mannitol)-treated, biological rep2


title: Blood_pre_XB0090_rep1

description: QC ok


title: T87 osmotic stress (0.4M mannitol)-treated, biological rep1


title: Neutron_1Gy_day7_rep 3


title: Neutron_1Gy_day7_rep 4


title: intact T87, biological rep2

source_name: 4-day-old Arabidopsis T87 suspension cells


title: intact T87, biological rep1


title: intact T87, biological rep3


title: X-ray_1Gy_day7_rep 1


title: Blood_pre_XB0087_rep1

description: QC ok


title: Blood_post_XB0087_rep1

description: QC ok


title: Neutron_1Gy_day7_rep 1


title: Neutrophils, Patient, JIA, ADM, Biological replicate 7 [RNA]


title: Control_day3_rep 4


title: Blood_fu_XB0087_rep1

description: QC ok


title: T87 protoplast, biological rep3


title: Neutrophils, Patient, JIA, ADM, Biological replicate 4 [RNA]


title: Neutron_1Gy_day7_rep 2


title: Blood_fu_XB0072_rep1

description: QC ok


title: CD4+ T cells, 2IU vitamin D, biological replicate 6

city: Solna

first: Manuel

last: Zeitelhofer

address: Biomedicum

department: MBB

country: Sweden

institute: Karolinska Institute

description: Gene expression data from CD4+ T cells isolated from lymph nodes 7 days post MOG immunization from DA rats treated with regular diet

hyb_protocol: GeneChip® ST Arrays (GeneChip® Gene 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

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

data_processing: The raw data were normalized using Robust Multi-array Average (RMA) method. Subsequent analysis of the gene expression, including Principal Component Analysis (PCA) and hierarchical clustering, was carried using Partek Genomics Suite v6.0 (Partek Incorporated, St.Louis, MO, USA) together with ANOVA model with a filter to select transcripts that show significant differential expression determined at a 1% False Discovery Rate (FDR).

organism: Rattus norvegicus

source_name: CD4+ T cells from lymph nodes of DA rats treated with regular diet

label_protocol: 250 ng of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit (P/N 4425209 Rev C 09/2009) and Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 6, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Qiqagen RNA purification kit was used according to manufactureres instructions

treatment_protocol: Age matched DA rats were treated with either vitamin D supplemented (10 IU), vitamin D deprived (0 IU) or regular diet (2 IU). The diet was given 5 weeks prior to MOG immunization and until the end of the experiment.

value: Dark agouti

value: female

value: CD4+ T cells from lymph node


title: CD4+ T cells, 2IU vitamin D, biological replicate 5


title: Neutron_0.25Gy_day7_rep 4


title: Blood_pre_XB0099_rep1

description: QC ok


title: Blood_pre_XB0072_rep1

description: QC ok


title: Blood_post_XB0072_rep1

description: QC ok


title: CD4+ T cells, 2IU vitamin D, biological replicate 4


title: Neutron_0.25Gy_day7_rep 5


title: Neutron_0.25Gy_day7_rep 3


title: Neutron_0.25Gy_day7_rep 2


title: Control_day7_rep 5


title: Neutron_0.25Gy_day7_rep 1


title: Neutrophils, Patient, JIA, ADM, Biological replicate 1 [RNA]


title: Control_day7_rep 6


title: CD4+ T cells, 2IU vitamin D, biological replicate 3


title: X-ray_4Gy_day1_rep 4


title: Blood_fu_XB0059_rep1

description: QC ok


title: Neutrophils, Patient, JIA, ADM, Biological replicate 10 [RNA]


title: X-ray_4Gy_day1_rep 3


title: CD4+ T cells, 10IU vitamin D, biological replicate 5

description: Gene expression data from CD4+ T cells isolated from lymph nodes 7 days post MOG immunization from DA rats treated with vitamin D supplemented diet

source_name: CD4+ T cells from lymph nodes of DA rats treated with vitamin D supplemented diet


title: Blood_post_XB0059_rep1

description: QC ok


title: Blood_fu_XB0055_rep1

description: QC ok


title: Blood_pre_XB0059_rep1

description: QC ok


title: Blood_fu_XB0071_rep1

description: QC ok


title: CD4+ T cells, 10IU vitamin D, biological replicate 6


title: Blood_post_XB0055_rep1

description: QC ok


title: X-ray_1Gy_day1_rep 6


title: CD4+ T cells, 10IU vitamin D, biological replicate 4


title: Neutron_1Gy_day7_rep 5


title: Control_day7_rep 1


title: Control_day3_rep 3


title: X-ray_1Gy_day1_rep 5


title: CD4+ T cells, 2IU vitamin D, biological replicate 1


title: CD4+ T cells, 10IU vitamin D, biological replicate 1


title: X-ray_4Gy_day1_rep 2


title: X-ray_4Gy_day1_rep 1


title: Control_day7_rep 3


title: Control_day7_rep 4


title: Blood_pre_XB0055_rep1

description: QC ok


title: CD4+ T cells, 10IU vitamin D, biological replicate 3


title: Blood_fu_XB0054_rep1

description: QC ok


title: Blood_post_XB0054_rep1

description: QC ok


title: CD4+ T cells, 10IU vitamin D, biological replicate 2


title: Blood_pre_XB0071_rep1

description: QC ok


title: CD4+ T cells, 2IU vitamin D, biological replicate 2


title: 254706910115_b4 - N657_303E1_2 vs Col_P2_2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What is the transcriptomic contrast between a TDNA-mutant and its respective wild-type from young rosette grown in precisely-controlled conditions on our phenotyping robot (Phenoscope)?

hyb_protocol: Col_P2_2 Cy5 / N657_303E1_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

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.

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: caulin leaf - Media: Peatmoss soil plugs. Hygrometry: 65%RH. Temperature: 21°C (D) / 18°C (N). Light: Short days (8h photoperiod) / 230µE.

extract_protocol: Col_P2_2:30mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: cultivar

value: columbia

value: rosette leaf

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

extract_protocol: N657_303E1_2:30mg. (Qiagen_RNeasy.pdf)

tag: mutant

value: t-dna mutant


title: Blood_fu_XB0046_rep1

description: QC ok

value: FEMALE


title: Blood_post_XB0046_rep1

description: QC ok

value: Blood


title: CD4+ T cells, 0IU vitamin D, biological replicate 6

description: Gene expression data from CD4+ T cells isolated from lymph nodes 7 days post MOG immunization from DA rats treated with vitamin D deprived diet

source_name: CD4+ T cells from lymph nodes of DA rats treated with vitamin D deprived diet


title: 254706910115_b2 - N657_303A1_1 vs Col_P1_1

hyb_protocol: Col_P1_1 Cy5 / N657_303A1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col_P1_1:30mg. (Qiagen_RNeasy.pdf)

extract_protocol: N657_303A1_1:30mg. (Qiagen_RNeasy.pdf)


title: Blood_pre_XB0046_rep1

description: QC ok

value: pre


title: Blood_fu_XB0040_rep1

description: QC ok

value: follow-up


title: Blood_post_XB0040_rep1

description: QC ok


title: Blood_pre_XB0054_rep1

description: QC ok


title: Blood_post_XB0071_rep1

description: QC ok


title: 254706910115_b3 - Col_P2_2 vs N657_303E1_2

hyb_protocol: N657_303E1_2 Cy5 / Col_P2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CD4+ T cells, 0IU vitamin D, biological replicate 2


title: 254706910042_b4 - 5_2WT12_2 vs 2_2WT0_2

description: Correlate clock-controlled diurnal gene expression changes with H2Bub chromatin mark changes on a genome-wide scale.

hyb_protocol: 2_2WT0_2 Cy5 / 5_2WT12_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: seedling - Media: MURASHIGE & SKOOG 1,5% Sucrose; Hygrometry: not controlled; Temperature: 19°C/23°C; Light: 80 µE/m²/sec.

extract_protocol: 2_2WT0_2:10ug. (Qiagen_RNeasy.pdf)

value: seedling

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

tag: zeitgeber time

value: 24 (dawn)

extract_protocol: 5_2WT12_2:10ug. (Qiagen_RNeasy.pdf)

value: 36 (dusk)


title: CD4+ T cells, 0IU vitamin D, biological replicate 5


title: 254706910042_b2 - 4_1WT12_1 vs 1_1WT0_1

hyb_protocol: 1_1WT0_1 Cy5 / 4_1WT12_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1_1WT0_1:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: 4_1WT12_1:10ug. (Qiagen_RNeasy.pdf)


title: CD4+ T cells, 0IU vitamin D, biological replicate 4


title: CD4+ T cells, 0IU vitamin D, biological replicate 3


title: 254706910115_b1 - Col_P1_1 vs N657_303A1_1

hyb_protocol: N657_303A1_1 Cy5 / Col_P1_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control_day7_rep 2

value: male


title: X-ray_1Gy_day1_rep 4


title: X-ray_1Gy_day1_rep 3


title: 254706910043_b1 - 3_3WT0_3 vs 6_3WT12_3

hyb_protocol: 6_3WT12_3 Cy5 / 3_3WT0_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 6_3WT12_3:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: 3_3WT0_3:10ug. (Qiagen_RNeasy.pdf)


title: 254706910043_b2 - 6_3WT12_3 vs 3_3WT0_3

hyb_protocol: 3_3WT0_3 Cy5 / 6_3WT12_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Blood_pre_XB0040_rep1

description: QC ok


title: X-ray_4Gy_day1_rep 5


title: Control_day3_rep 2


title: Neutron_1Gy_day1_rep 6


title: Neutron_1Gy_day1_rep 5


title: Blood_post_XB0037_rep1

description: QC ok

value: post


title: X-ray_1Gy_day1_rep 1


title: 254706910042_b3 - 2_2WT0_2 vs 5_2WT12_2

hyb_protocol: 5_2WT12_2 Cy5 / 2_2WT0_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Neutron_1Gy_day1_rep 4


title: X-ray_1Gy_day1_rep 2


title: Blood_pre_XB0037_rep1

description: QC ok

value: MALE


title: Neutron_1Gy_day1_rep 3


title: Neutron_1Gy_day1_rep 2


title: 254706910042_b1 - 1_1WT0_1 vs 4_1WT12_1

hyb_protocol: 4_1WT12_1 Cy5 / 1_1WT0_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Neutron_1Gy_day1_rep 1


title: Meningioma 13 [miRNA]

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

description:
Sample name: 13
miRNA expression data from fresh-frozen meningioma tumor sample.

hyb_protocol: Hybridization was done for 20 hours as described in FlashTag Biotin HSR RNA Labeling Kit (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner.

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software.

source_name: Fresh-frozen meningioma tumor sample

label_protocol: Poly-A tailed RNA molecules were labeled with Biotin labeled DNA.

growth_protocol: Meningial cells were cultured in T75 cell culture flasks in Meningeal Cell Medium.

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

treatment_protocol: Not Applicable.

value: Meningioma tumor

tag: location

value: Left Parietal Parasagital Meningioma

value: Female

tag: age


title: Meningial Cells [miRNA]

description:
Sample name: 15
miRNA expression data from human meningial cells grown under normal conditions.

source_name: Meningial cells grown under normal conditions

value: Meningial cell line


title: Blood_post_XB0035_rep1

description: QC ok


title: Blood_fu_XB0035_rep1

description: QC ok


title: 254706910108_b4 - 4_MYB92_OE_R2 vs 2_col0_R2

description: What are the genes over expressed or down regulated in seeds in response to a myb92 mutation or to MYB92 overexpression?

hyb_protocol: 2_col0_R2 Cy5 / 4_MYB92_OE_R2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: seed - Media:soil Hygrometry:65% Temperature: variable :19C°(2h)/21°C(12h)/20°C(2h)/18°C(8h) Light:16h light/8h dark

extract_protocol: 2_col0_R2:50mg. (Qiagen_RNeasy.pdf)

tag: ecotype

value: Columbia

tag: harvest date

extract_protocol: 4_MYB92_OE_R2:50mg. (Qiagen_RNeasy.pdf)

tag: mutant (oe mutant)


title: Blood_pre_XB0035_rep1

description: QC ok

extract_protocol: Blood RNA was isolated and purified using the PAXgene Blood miRNA Kit according to the manufacturer’s protocol using the Qiagen Qiacube. RNA quality and integrity were measured using both the Nanodrop 1000 spectrophotometer.

tag: gender

tag: tissue


title: Neutron_0.25Gy_day1_rep 5

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

tag: protocol


title: Blood_pre_XB0030_rep2

description: QC ok

tag: timepoint


title: Blood_fu_XB0030_rep2

description: QC ok


title: Neutron_0.25Gy_day1_rep 6


title: Blood_fu_XB0016_rep1

description: QC ok


title: Meningioma 14 [miRNA]

description:
Sample name: 14
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Tuberculum Sella meningioma

value: Male


title: 254706910108_b2 - 3_MYB92_OE_R1 vs 1_col0_R1

hyb_protocol: 1_col0_R1 Cy5 / 3_MYB92_OE_R1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1_col0_R1:50mg. (Qiagen_RNeasy.pdf)

extract_protocol: 3_MYB92_OE_R1:50mg. (Qiagen_RNeasy.pdf)


title: 254706910108_b1 - 1_col0_R1 vs 3_MYB92_OE_R1

hyb_protocol: 3_MYB92_OE_R1 Cy5 / 1_col0_R1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Meningioma 11 [miRNA]

description:
Sample name: 11
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Right parietal convexity Meningioma


title: Meningioma 12 [miRNA]

description:
Sample name: 12
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Left Clinoidal Meningioma


title: Neutron_0.25Gy_day1_rep 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl 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.


title: Neutron_0.25Gy_day1_rep 2


title: Neutron_0.25Gy_day1_rep 4


title: 254706910107_b4 - 6_myb92_R2 vs 2_col0_R2

hyb_protocol: 2_col0_R2 Cy5 / 6_myb92_R2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 6_myb92_R2:50mg. (Qiagen_RNeasy.pdf)

tag: mutant (ko mutant)


title: Blood_post_XB0016_rep1

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol

value: FEMALE

value: Blood


title: Meningioma 9 [miRNA]

description:
Sample name: 9
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Right frontobasal Meningioma


title: Neutron_0.25Gy_day1_rep 1


title: 254706910107_b3 - 2_col0_R2 vs 6_myb92_R2

hyb_protocol: 6_myb92_R2 Cy5 / 2_col0_R2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910107_b1 - 1_col0_R1 vs 5_myb92_R1

hyb_protocol: 5_myb92_R1 Cy5 / 1_col0_R1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 5_myb92_R1:50mg. (Qiagen_RNeasy.pdf)


title: Meningioma 8 [miRNA]

description:
Sample name: 8
miRNA expression data from fresh-frozen meningioma tumor sample.


title: Blood_pre_XB0016_rep1

description: QC ok

value: pre


title: Meningioma 7 [miRNA]

description:
Sample name: 7
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Left cavernous Sinus Meningioma


title: 254706910107_b2 - 5_myb92_R1 vs 1_col0_R1

hyb_protocol: 1_col0_R1 Cy5 / 5_myb92_R1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Meningioma 10 [miRNA]

description:
Sample name: 10
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Left sphenoid wing Meningioma


title: Blood_fu_XB0008_rep1

description: QC ok

value: follow-up


title: Meningioma 6 [miRNA]

description:
Sample name: 6
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Parietal Parasagital Meningioma


title: Blood_pre_XB0008_rep1

description: QC ok


title: Blood_post_XB0008_rep1

description: QC ok

value: post


title: Blood_fu_XB0052_rep1

description: QC ok


title: Control_day1_rep 4

value: Control

value: male


title: Control_day1_rep 3


title: 254706910092_b4 - Mut2_ftral.a2_2 vs SegWT(9sem)_2

description: Recherche nouvelles fonctions pour le système TRX plastidial.

hyb_protocol: SegWT(9sem)_2 Cy5 / Mut2_ftral.a2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: aerial - Media: soil Hygrometry: 65% Temperature: 20°C/22°C (night/day) Light: 70-80 µE/m2/s, 8 hours

extract_protocol: SegWT(9sem)_2:16ug. (Qiagen_RNeasy.pdf)

value: Columbia x wassilewskija

tag: genotype/variation

value: mutant


title: Control_day1_rep 1


title: 254706910092_b3 - SegWT(9sem)_2 vs Mut2_ftral.a2_2

hyb_protocol: Mut2_ftral.a2_2 Cy5 / SegWT(9sem)_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910092_b1 - SegWT(9sem)_1 vs Mut2_ftral.a2_1

hyb_protocol: Mut2_ftral.a2_1 Cy5 / SegWT(9sem)_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: SegWT(9sem)_1:5ug. (Qiagen_RNeasy.pdf)


title: Meningioma 5 [miRNA]

description:
Sample name: 5
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Meningioma tumor

value: Petroclival Meningioma

value: Female


title: Control_day3_rep 1


title: Control_day1_rep 2


title: Control_day1_rep 5


title: Meningioma 3 [miRNA]

description:
Sample name: 3
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Parietal Convexity Meningioma


title: 254706910091_b4 - Mut2_ftral.a2_2 vs SegWT(10F)_2

hyb_protocol: SegWT(10F)_2 Cy5 / Mut2_ftral.a2_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: SegWT(10F)_2:15ug. (Qiagen_RNeasy.pdf)


title: Meningioma 4 [miRNA]

description:
Sample name: 4
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Petrous Meningioma


title: X-ray_1Gy_day3_rep 5


title: Blood_post_XB0052_rep1

description: QC ok

value: FEMALE

value: Blood


title: 254706910091_b3 - SegWT(10F)_2 vs Mut2_ftral.a2_2

hyb_protocol: Mut2_ftral.a2_2 Cy5 / SegWT(10F)_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910091_b2 - Mut2_ftral.a2_1 vs SegWT(10F)_1

hyb_protocol: SegWT(10F)_1 Cy5 / Mut2_ftral.a2_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: SegWT(10F)_1:9.5ug. (Qiagen_RNeasy.pdf)


title: 254706910092_b2 - Mut2_ftral.a2_1 vs SegWT(9sem)_1

hyb_protocol: SegWT(9sem)_1 Cy5 / Mut2_ftral.a2_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910108_b3 - 2_col0_R2 vs 4_MYB92_OE_R2

hyb_protocol: 4_MYB92_OE_R2 Cy5 / 2_col0_R2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia


title: Blood_pre_XB0052_rep1

description: QC ok

value: pre


title: Meningioma 1 [miRNA]

description:
Sample name: 1
miRNA expression data from fresh-frozen meningioma tumor sample.

hyb_protocol: Hybridization was done for 20 hours as described in FlashTag Biotin HSR RNA Labeling Kit (Affymetrix).

value: Olfactor Groove Meningioma

value: Male


title: Childhood melanocytic tumor #1

type: genomic

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Copy number alterations and allelic imblances

hyb_protocol: Arrays were hybridized for 16-18 hours, then washed and stained in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000 Dx2, controlled by AMDS

data_processing: OncoScan SNP-array data were analyzed by the software couple of OncoScan Console (Affymetrix) and Nexus Express (BioDiscovery) using Affymetrix TuScan algorithm. All array data were also manually reviewed for subtle alterations not automatically called by the software.

molecule: genomic DNA

source_name: acral nevus in a 1-yr child with unusual features

label_protocol: 80 ng FFPE-DNA was subjected to Annealing - Gap fill --- Linearization - 1st PCR - 2nd PCR – HaeIII digestion, and the fragments from HaeIII digestion were hybridized to arrays with biotinylated oligos which were targets for labeling. Labeling occurs during hybridization.

extract_protocol: DNA was extracted from FFPE tumor tissue using QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer's instructions.

value: FFPE tumor tissue

tag: genotype

value: NTRK3 intragenic copy number change


title: Blood_post_XB0032_rep1

description: QC ok

value: post


title: Meningioma 2 [miRNA]

description:
Sample name: 2
miRNA expression data from fresh-frozen meningioma tumor sample.

value: Sphennopetroclival Meningioma


title: Blood_fu_XB0032_rep1

description: QC ok

value: follow-up


title: Blood_fu_XD0025_rep1

description: QC ok

value: MALE


title: X-ray_1Gy_day3_rep 4

value: male


title: X-ray_1Gy_day3_rep 1


title: 254706910091_b1 - SegWT(10F)_1 vs Mut2_ftral.a2_1

hyb_protocol: Mut2_ftral.a2_1 Cy5 / SegWT(10F)_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia x wassilewskija

value: mutant


title: X-ray_1Gy_day3_rep 2

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 µl 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.


title: Blood_pre_XD0025_rep1

description: QC ok


title: Neutron_0.25Gy_day3_rep 5


title: 254706910090_b3 - Col0(11sem)_2 vs Mut1_ftrb_2

hyb_protocol: Mut1_ftrb_2 Cy5 / Col0(11sem)_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Mut1_ftrb_2:15ug. (Qiagen_RNeasy.pdf)

extract_protocol: Col0(11sem)_2:18ug. (Qiagen_RNeasy.pdf)


title: 254706910090_b4 - Mut1_ftrb_2 vs Col0(11sem)_2

hyb_protocol: Col0(11sem)_2 Cy5 / Mut1_ftrb_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 558220A12 - FEWWA2_2 vs FEWSB2_2

description:
harvest date:03-02-13
harvest date:27-01-13
What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: FEWSB2_2 Cy5 / FEWWA2_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

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

organism: Lathyrus oleraceus

growth_protocol: caulin leaf - Growth conditions (1-2-3-4):1. Media: perlite:sand (vol:vol 3:1) - hygrometry: 50% - Temperature: 15°C night; 18°C day -  Light: 16h photoper

treatment_protocol: Name:Water stressed - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 50percent .

value: mutant (CAMEOR)

value: leaf

treatment_protocol: Name:Well Watered - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 100percent . Pea seeds were sown in 2L pots filled with a mixture (3:1, vol/vol) of perlite and sand and were inocculated with Rhizobium. Watering with a nutritve solution without nitrate (to allow nodulation) was unlimited (drainage conditions) until flowering. At flowering, plants were weighted three times a day in order to maintain a soil relative water content correspondong to the maximum (100%) water holding capacity of the substrate for all the plants. Twelve days after flowering irrigation was stopped for half of the plants (WS plants) until soil water relative content reached 50% of the maximum water-holding capaciy of the substrate. Once this target value was reached (24 hours), it was kept to 50% until samples harvest.


title: Blood_post_XD0025_rep1

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol


title: Neutron_0.25Gy_day3_rep 6


title: Neutron_0.25Gy_day3_rep 4


title: 558220A10 - FEWWA1_1 vs FEWSB1_1

hyb_protocol: FEWSB1_1 Cy5 / FEWWA1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_fu_XD0019_rep1

description: QC ok


title: X-ray_1Gy_day3_rep 3


title: 254706910089_b4 - Mut1_ftrb_2 vs Col0(10F)_2

hyb_protocol: Col0(10F)_2 Cy5 / Mut1_ftrb_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0(10F)_2:8ug. (Qiagen_RNeasy.pdf)


title: Blood_post_XD0019_rep1

description: QC ok


title: Blood_pre_XD0019_rep1

description: QC ok


title: E8.5_placenta_mRNA_KO_rep5

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

institute: BRC, RIKEN

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate4

hyb_protocol: For miRNA analysis, Cy3-labeled RNAs was hybridized with the miRNA Complete Labeling Reagent and Hyb Kit onto mouse miRNA Microarray rel.17.0 (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions. For mRNA analysis, 0.6ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized onto SurePrint G3 Mouse GE microarray 8x60K (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions.

scan_protocol: Scanning of microarray slides was performed with a DNA microarray scanner at 3 um resolution (Agilent Technologies).

data_processing: Scanned image files were processed to give signal intensities using Feature Extraction software (Agilent Technologies). All raw data were loaded into GeneSpring GX 12.5 software (Agilent Technologies) and normalized using default settings.

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, miRNA KO, replicate5

label_protocol: For miRNA analysis, total RNA from placentas was labeled with the miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies). For mRNA analysis, total RNAs were labeled with a Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: In vitro-fertilized embryos derived from wild-type and miRNA-deleted mice were cultured in KSOM medium at 37°C for 16 hours. Cultured embryos were transferred into pseudopregnant ICR females and E8.5 and 11.5 embryos were retrieved from the uterus.

extract_protocol: Placentas with deciduas removed were lysed and the total and miRNA isolated using a mirVana miRNA isolation kit (Themo Fisher Scientific).

value: placenta

tag: embryonic day

value: miRNA cluster knockout


title: 254706910090_b1 - Col0(11sem)_1 vs Mut1_ftrb_1

hyb_protocol: Mut1_ftrb_1 Cy5 / Col0(11sem)_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Mut1_ftrb_1:18ug. (Qiagen_RNeasy.pdf)

value: Columbia

extract_protocol: Col0(11sem)_1:10ug. (Qiagen_RNeasy.pdf)


title: 254706910089_b3 - Col0(10F)_2 vs Mut1_ftrb_2

hyb_protocol: Mut1_ftrb_2 Cy5 / Col0(10F)_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 558220A09 - FEWSB1_1 vs FEWWA1_1

description:
harvest date:27-01-13
harvest date:03-02-13
What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: FEWWA1_1 Cy5 / FEWSB1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: E8.5_placenta_mRNA_KO_rep4

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, miRNA KO, replicate4


title: 254706910089_b2 - Mut1_ftrb_1 vs Col0(10F)_1

hyb_protocol: Col0(10F)_1 Cy5 / Mut1_ftrb_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0(10F)_1:6ug. (Qiagen_RNeasy.pdf)


title: 558220A08 - FEWWA4_4 vs FEWWB4_4

hyb_protocol: FEWWB4_4 Cy5 / FEWWA4_4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 254706910089_b1 - Col0(10F)_1 vs Mut1_ftrb_1

hyb_protocol: Mut1_ftrb_1 Cy5 / Col0(10F)_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910074_b4 - SiO2-24h_1 vs T-24h_1

description: Understand and categorize plant mechanisms implicated in the interaction with nanoparticles, both in the phenomena responsible for toxicity as in accommodation, see detoxication.

hyb_protocol: T-24h_1 Cy5 / SiO2-24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: cell culture/primary cell - Media: Liquid growth medium (Axelos et al., 1992) Temperature: 24°C Light: 50 µE m–2 s–1

extract_protocol: T-24h_1:400mg. (Qiagen_RNeasy.pdf)

tag: treatment

value: no treatment

extract_protocol: SiO2-24h_1:400mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:SiO2 - compound based treatment - compound addition,nanoparticules (mg/l):quantity 92.5 time 24hour .  Cell cultures of Arabidopsis thaliana (ecotype Col-0) were maintained in 200 ml of culture medium (Axelos et al., 1992), under sterile conditions at 24 ° C under agitation (120 rpm). To study the impact of nanoparticles, this treatment was applied for 24h to A. thaliana cells 9 days after subculture: (ii) S: SiO2 nanoparticles at 92.5 mg / L.

value: S:SiO2 nanoparticles at 92.5 mg / L.


title: 558220A11 - FEWSB2_2 vs FEWWA2_2

hyb_protocol: FEWWA2_2 Cy5 / FEWSB2_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: E8.5_placenta_mRNA_KO_rep3

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate3

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, miRNA KO, replicate3


title: Blood_pre_XB0032_rep1

description: QC ok

extract_protocol: Blood RNA was isolated and purified using the PAXgene Blood miRNA Kit according to the manufacturer’s protocol using the Qiagen Qiacube. RNA quality and integrity were measured using both the Nanodrop 1000 spectrophotometer.

value: FEMALE

value: Blood

value: pre


title: Blood_fu_XD0008_rep1

description: QC ok


title: 558220A06 - FEWWA3_3 vs FEWWB3_3

hyb_protocol: FEWWB3_3 Cy5 / FEWWA3_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_pre_XD0008_rep1

description: QC ok


title: Blood_post_XD0008_rep1

description: QC ok

value: post


title: 558220A05 - FEWWB3_3 vs FEWWA3_3

hyb_protocol: FEWWA3_3 Cy5 / FEWWB3_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 558220A07 - FEWWB4_4 vs FEWWA4_4

hyb_protocol: FEWWA4_4 Cy5 / FEWWB4_4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 254706910090_b2 - Mut1_ftrb_1 vs Col0(11sem)_1

hyb_protocol: Col0(11sem)_1 Cy5 / Mut1_ftrb_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910074_b3 - T-24h_1 vs SiO2-24h_1

hyb_protocol: SiO2-24h_1 Cy5 / T-24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 558220A04 - FEWWA2_2 vs FEWWB2_2

hyb_protocol: FEWWB2_2 Cy5 / FEWWA2_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_post_XB0050_rep1

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol


title: Blood_fu_XB0050_rep1

description: QC ok


title: 558220A02 - FEWWA1_1 vs FEWWB1_1

hyb_protocol: FEWWB1_1 Cy5 / FEWWA1_1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: E8.5_placenta_mRNA_KO_rep1

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate1

hyb_protocol: For miRNA analysis, Cy3-labeled RNAs was hybridized with the miRNA Complete Labeling Reagent and Hyb Kit onto mouse miRNA Microarray rel.17.0 (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions. For mRNA analysis, 0.6ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized onto SurePrint G3 Mouse GE microarray 8x60K (Agilent Technologies) at 65°C for 17 hours according to manufacture's instructions.

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, miRNA KO, replicate1


title: E8.5_placenta_mRNA_KO_rep2

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate2

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, miRNA KO, replicate2


title: Blood_pre_XB0050_rep1

description: QC ok

source_name: Human, Whole Blood, pre-therapy


title: 558220A03 - FEWWB2_2 vs FEWWA2_2

hyb_protocol: FEWWA2_2 Cy5 / FEWWB2_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 254706910073_b1 - T-24h_1 vs CMB-24h_1

hyb_protocol: CMB-24h_1 Cy5 / T-24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: CMB-24h_1:400mg. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:CMB_clusters - compound based treatment - compound addition,nanoparticules (mg/l):quantity 7.5 time 24hour .  Cell cultures of Arabidopsis thaliana (ecotype Col-0) were maintained in 200 ml of culture medium (Axelos et al., 1992), under sterile conditions at 24 ° C under agitation (120 rpm). To study the impact of nanoparticles, this treatment was applied for 24h to A. thaliana cells 9 days after subculture: (i) CMB: Cs2[Mo6Br14] clusters at 7.5 mg / L.

value: CMB:Cs2[Mo6Br14] clusters at 7.5 mg / L.


title: E8.5_placenta_mRNA_WT_rep3

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate3

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, wildtype, replicate3

value: wildtype


title: 254706910074_b1 - T-24h_2 vs CMB-24h_2

hyb_protocol: CMB-24h_2 Cy5 / T-24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: CMB-24h_2:400mg. (Qiagen_RNeasy.pdf)

extract_protocol: T-24h_2:400mg. (Qiagen_RNeasy.pdf)


title: E8.5_placenta_mRNA_WT_rep4

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate4

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, wildtype, replicate4


title: Blood_post_XD0001_rep1

description: QC ok

source_name: Human, Whole Blood, post-therapy

value: MALE


title: Blood_fu_XD0001_rep1

description: QC ok

source_name: Human, Whole Blood, follow-up-therapy

value: follow-up


title: 549628A11 - FEWSB4_4 vs FEWWB4_4

description:
harvest date:03-02-13
harvest date:03-02-13
What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: FEWWB4_4 Cy5 / FEWSB4_4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: E8.5_placenta_mRNA_WT_rep2

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate2

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, wildtype, replicate2


title: 549628A12 - FEWWB4_4 vs FEWSB4_4

hyb_protocol: FEWSB4_4 Cy5 / FEWWB4_4 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 558220A01 - FEWWB1_1 vs FEWWA1_1

hyb_protocol: FEWWA1_1 Cy5 / FEWWB1_1 Cy3 : 30mmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_fu_XD0112_rep1

description: QC ok


title: 254706910072_b4 - SiO2-24h_2 vs T-24h_2

hyb_protocol: T-24h_2 Cy5 / SiO2-24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: SiO2-24h_2:400mg. (Qiagen_RNeasy.pdf)


title: 254706910073_b2 - CMB-24h_1 vs T-24h_1

hyb_protocol: T-24h_1 Cy5 / CMB-24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910072_b3 - T-24h_2 vs SiO2-24h_2

hyb_protocol: SiO2-24h_2 Cy5 / T-24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E8.5_placenta_mRNA_WT_rep1

description: embryonic day E8.5, mouse, placenta, in vitro fertilized embryo, mRNA, wildtype, replicate1

source_name: embryonic day 8.5, placenta, IVF derived, mRNA, wildtype, replicate1


title: 254706910074_b2 - CMB-24h_2 vs T-24h_2

hyb_protocol: T-24h_2 Cy5 / CMB-24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 549628A10 - FEWWB3_3 vs FEWSB3_3

hyb_protocol: FEWSB3_3 Cy5 / FEWWB3_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: E11.5_placenta_mRNA_KO_rep4

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate4

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, miRNA KO, replicate4

growth_protocol: In vitro-fertilized embryos derived from wild-type and miRNA-deleted mice were cultured in KSOM medium at 37°C for 16 hours. Cultured embryos were transferred into pseudopregnant ICR females and E11.5 embryos were retrieved from the uterus.


title: E11.5_placenta_mRNA_KO_rep3

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate3

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, miRNA KO, replicate3


title: Blood_post_XD0112_rep1

description: QC ok


title: 254706910071_b4 - CMB+SiO2-24h_2 vs T-24h_2

hyb_protocol: T-24h_2 Cy5 / CMB+SiO2-24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:CMB+SiO2 - compound based treatment - compound addition,nanoparticules (mg/l):time 24hour .  Cell cultures of Arabidopsis thaliana (ecotype Col-0) were maintained in 200 ml of culture medium (Axelos et al., 1992), under sterile conditions at 24 ° C under agitation (120 rpm). To study the impact of nanoparticles, this treatment was applied for 24h to A. thaliana cells 9 days after subculture: (iv) C+S: SiO2 nanoparticles at 92.5 mg / L plus CMB clusters at 7.5 mg / L.

value: C+S:SiO2 nanoparticles at 92.5 mg / L plus CMB clusters at 7.5 mg / L.


title: Blood_pre_XD0112_rep1

description: QC ok


title: E11.5_placenta_mRNA_KO_rep2

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate2

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, miRNA KO, replicate2


title: 549628A09 - FEWSB3_3 vs FEWWB3_3

hyb_protocol: FEWWB3_3 Cy5 / FEWSB3_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 254706910071_b2 - CMB+SiO2-24h_1 vs T-24h_1

hyb_protocol: T-24h_1 Cy5 / CMB+SiO2-24h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E11.5_placenta_mRNA_KO_rep1

description: embryonic day E11.5, mouse, placenta, in vitro fertilized embryo, mRNA, miRNA KO, replicate1

source_name: embryonic day 11.5, placenta, IVF derived, mRNA, miRNA KO, replicate1


title: 549628A08 - FEWWB2_2 vs FEWSB2_2

hyb_protocol: FEWSB2_2 Cy5 / FEWWB2_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_post_XD0106_rep1

description: QC ok

hyb_protocol: Standard Illumina hybridization protocol


title: Blood_fu_XD0106_rep1

description: QC ok


title: 254706910071_b3 - T-24h_2 vs CMB+SiO2-24h_2

hyb_protocol: CMB+SiO2-24h_2 Cy5 / T-24h_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 549628A07 - FEWSB2_2 vs FEWWB2_2

hyb_protocol: FEWWB2_2 Cy5 / FEWSB2_2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: Blood_post_XD0094_rep1

description: QC ok


title: Blood_pre_XD0106_rep1

description: QC ok


title: Blood_fu_XD0094_rep1

description: QC ok