title: KAN1-GR_60min_biorep2

first: Brenda

last: Reinhart

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

description: Collection day two

hyb_protocol: 20µg of cRNA was fragmented and hybridized on GeneChip Arabidopsis ATH1 Arrays for 16 hr at 45˚C. Chips were washed and stained in the Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Chips were scanned on an Agilent GeneArray Scanner G2500A and images were analyzed with Affymetrix GeneChip Operating Software.

data_processing: The data were analyzed with Genspring10 using GC-RMA and normalized to the mean of the Columbia 0 minute timepoints.

source_name: 35S::KAN1-GR seedlings, 60min DEX treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15µg total RNA.

growth_protocol: For each sample, 50 seeds were sterilized in 0.6 % bleach and 0.07% SDS, cold-treated at 4˚C for 48hrs, and grown at 22˚C in 50 ml of MS medium with 1% sucrose for 7 days before treatment. 35S::GR-REV and 35S::KAN1-GR samples were grown at different times, with simultaneously grown Columbia wild-type controls for each (wild-type biorep 1-3 were grown on the same day as 35S:GR-REV, wild-type biorep 4-6 were grown on the same day as 35S:KAN1-GR). A sample was prepared in a separate flask for each timepoint rather than sampling over time from a single treated flask.

extract_protocol: Total RNA was prepared using RNeasy columns from frozen, ground tissue according to the manufacturer (Qiagen). Qiashredder columns were used, with no more than 100mg of tissue per column. DNA was removed from the samples using the Ambion DNA-free kit according to the manufacturer's instructions.

treatment_protocol: Dexamethasone was added to the liquid medium for a final concentration of 50µM and the tissue was flash-frozen at 30min, 60min, or 120min post-treatment. For the 0min samples, tissue was flash-frozen just before dexamethasone addition to the other samples.

value: Columbia

value: whole seedling, 7 days old


title: Seedling_KUA1-IOX_mock_rep1

status: Public on Dec 31 2013

type: RNA

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

department: Plant Signaling

country: Germany

institute: MPIMP-golm

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 14-d-old seedling, control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: T3 seeds were stratified on plate for 72 h in the dark at 4°C and then transferred to 22°C with a 16-h light (100 μE m−2 s−1)/8-h dark period.

extract_protocol: Total RNA was extracted with the Plant RNAeasy kit (Qiagen)

treatment_protocol: 14-day-old seedlings were transferred to liquid MS medium and subsequently estradiol disolved in ethanol (treatment) or ethanol alone (mock) was added to each well. After 4 hours seedlings were collected and directly frozen in liquid nitrogen for storage.

tag: ecotype

tag: age

value: 14 days

tag: developmental stage

value: Seedling

tag: genotype/variation

value: control


title: H3K27me3, tumor #8

type: genomic

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

description:
K27.8T
H3K27me3 in colorectal tumor, patient#8

hyb_protocol: According to NimbleGen Kit.

scan_protocol: Follow NimbleScan's default using Agilent Scanner.

data_processing: For each array, Loess normalization was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio. Quantile normalization was then applied across all the arrays.

molecule: genomic DNA

organism: Homo sapiens

source_name: H3K27me3 ChIP DNA from tumor patient #8

label_protocol: According to standard NimbleGen Protocol.

extract_protocol: For chromatin immunoprecipitation, frozen tissues were homogenized in cold phosphate-buffered saline (PBS) and fixed for 10 min at room temperature in 1% formaldehyde. After adding of glycine to 0.125M final concentration, chromatin was sonicated and incubated with the following antibodies overnight: anti-H3K4me3 (39159, Active Motif), and anti-H3K27me3 (07-449, Millipore). For obtaining the H3K4me3 profile, the H3K4me3 antibodies were pre-blocked with an H3K9me3 peptide (Abcam) to remove minor cross-reactivity of this antibody. After genome amplification, immunoprecipitated DNA was hybridized versus input DNA on human CpG island/promoter microarrays (NimbleGen).

tag: disease status

value: colorectal cancer

tag: duke's stage

value: II

tag: tissue

value: colorectal tumor

tag: enrichment procedure

value: ChIP with H3K27me3 antibodies

tag: chip antibody

tag: patient identifier

source_name: Input DNA from colorectal tumor from patient #8 with colorectal cancer Duke's stage II


title: H3K27me3, mucosa #8

description:
K27.8N
H3K27me3 in colorectal mucosa, patient#8

source_name: H3K27me3 ChIP DNA from mucosa patient #8

value: matching normal colorectal mucosa

source_name: Input DNA from colorectal mucosa matched to tumor from patient #8 with colorectal cancer Duke's stage II


title: Cultured bacteria MA083850

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

hyb_protocol: Following the primer extension reaction, 80 µl of hybridization solution was added to each reaction. The total volume of 120 µl was then hybridized to a DNA microarray for 90 min at 42°C at high humidity. The tags on the extension primers hybridized to corresponding probes on the microarray. After hybridization, each chip was washed 5 times with 300 µl of 1X saline sodium citrate (SSC).

scan_protocol: Microarray were scanned using the confocal scanner integrated in the INFINITI analyzer

data_processing: Microarray results were controlled for background and negative control. For each probe a ratio between the mean of the background corrected signal of triplicate probes and background fluorescence was calculated. Positivity of the internal control probes (ratio > 3) confirmed the test validity for this sample. Serotypes were determined used the Pneumotyper software (https://github.com/fredericraymond/Pneumotyper)

organism: Streptococcus pneumoniae

source_name: LSPQ

label_protocol: Multiplex PCR was performed in a T1plus thermocycler (Biometra, Montreal Biotech, Montreal, Canada). Multiplex PCR was performed for each sample. The amplification solution was composed of 1X Platinum Taq buffer, 0.2 µM dNTPs, 1.5 mM MgCl2, 1µl multiplex PCR primer mix, 0.5 units of Platinum Taq DNA polymerase (Invitrogen, Burlington, ON, Canada), and 2.5 µl of cDNA, in a final volume of 20 µl. Prior to PCR, 107 copies of phage M13amp18 RF1 DNA (New England Biolabs, Pickering, ON, Canada) was added to each reaction as an internal control. The PCR program consisted in the following steps: 60 s at 94°C followed by 39 cycles of 30 s at 94°C, 30 s at 55°C and 90 s at 72°C. Finally, the reaction was incubated at 72°C for 3 min. Then, 3 units of shrimp alkaline phosphatase (Clontech, Mountain View, CA), 7.5 units of exonuclease (Clontech) and 0.25 µl of 50X titanium DNA polymerase (Clontech) were added to the solution, which was incubated at 37°C for 20 min and at 94°C for 10 min. This step allows for the degradation of remaining dNTPs and PCR primers that were not used in the multiplex PCR. The subsequent steps were automated by the INFINITI analyzer (AutoGenomics Inc., Carlsbad, CA). The primer extension solution was composed of 1X Platinum Taq buffer, 2.5µM MgCl2, 156 µM d(A/G/T)TP, 10µM Cy5-dCTP, 2µl primer extension primer mix completed with water to 20µl per reaction. A volume of 20µl of primer extension solution was added to each reaction. Primer extension reaction consisted in the following steps: 60 s at 94°C followed by 39 cycles of 15 s at 94°C and 15 s at 50°C. Primer extension was done in the presence of Cy5-dCTP.

growth_protocol: One hundred and sixty-six (166) isolates of S. pneumoniae, which had been previously serotyped using the Quellung method, were provided by the Laboratoire de santé publique du Québec (LSPQ), the Swiss National Reference Laboratory for S. pneumoniae and the Centre de recherche en Infectiologie de l’Université Laval strain collection.

extract_protocol: DNA was extracted from clinical samples using the Purelink viral RNA/DNA minikit (Invitrogen, Burlington, ON, Canada). Reference bacterial strains were grown in the appropriate medium until a turbidity of 0.5 McFarland was obtained. Bacteria were centrifuged and resuspended in 5X TE buffer. DNA was extracted using the BD GeneOhm™ Lysis Kit (BD GeneOhm, San Diego, CA). Purified DNA was quantified on a agarose gel and diluted to a concentration of 100 ng/µl and then to a concentration of 1 ng/µl. Genomic DNA was kept at 4°C.

treatment_protocol: No treatment

tag: serotype (quellung)


title: SJTALL032

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710878

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis.

source_name: RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia (non-ETP)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases

extract_protocol: Trizol

tag: disease state

value: non-ETP T-lineage ALL


title: SJTALL066

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710903


title: Cor +Cd_rep2

city: Tsukubashi

first: Yuko

last: Ogo

state: Ibaraki

address: 3-1-3 Kannondai

country: Japan

institute: NARO

description: Gene expression of cortex of root grown under Cd-stressed condition

hyb_protocol: Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4 • 44K microarray RAP-DB (G2519F#15241; Agilent Technologies) at 65°C for 17 h. Hybridization and washing of the hybridized slide were performed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanne.

data_processing: The scanned images were analyzed with FEATURE EXTRACTION 10.5.1.1 (Agilent Technologies) to obtain background correction of the Cy3 raw signals.

organism: Oryza sativa

label_protocol: One-color spikemix was added to the total RNA prior to the labeling reaction, and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP, according to the modified manufacturer’s protocol. The Cy3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen), and the quantity was examined with a NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop Technologies).

growth_protocol: Rice was grown hydroponically under 14-h/10-h light/dark cycles and at 30/25°C.

extract_protocol: The 0.5 cm to 1.5 cm of the root tip and DC were fixed in 75% ethanol/25% acetate and 100% acetone, respectively. Paraffin-embedding was followed by the microwave method. Serial paraffin sections were prepared at 10–20 μm in thickness, and they were put onto a glass slide. Laser Microdissection was performed using the Veritas Laser Microdissection System LCC1704 (Molecular Devices). Total RNA was extracted from cells prepared by Laser Microdissection with a Pico-PureTM RNA isolation kit (Molecular Devices) according to the manufacturer’s protocol. The extracted total RNA was quantified with a Quant-iTTM RiboGreen RNA reagent and kit (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. The quality of total RNA was assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA integrity was judged by RNA Integrity Number (RIN), which was calculated with 2100 Expert Software (Agilent, version B.02.02, eukaryote total RNA pico mode).

treatment_protocol: Fe deficiency was initiated at day 27 after germination by omitting Fe(III)–EDTA from the culture medium, and plants were harvested after 7 days. For Cd stress, 10 μM CdCl2 was added to the hydroponic culture on day 33 after germination and plants were harvested after 24 h.

value: cortex of root

tag: growth condition

value: Cd-stressed


title: Cultured bacteria MA083730


title: H3K27me3, mucosa #12

description:
K27.12N
H3K27me3 in colorectal mucosa, patient#12

source_name: H3K27me3 ChIP DNA from mucosa patient #12

source_name: Input DNA from colorectal mucosa matched to tumor from patient #12 with colorectal cancer Duke's stage II


title: Cultured bacteria MA083610


title: NGM [SL9]

city: Paterna

first: Patricia

last: Martorell

state: Valencia

address: Catedrático Agustín Escardino Benlloch, 9, Building 2

department: Agrifood Biotechnology

country: Spain

institute: Biópolis SL

description: Gene expression data from C. elegans (strain N2) at young adult stage

hyb_protocol: Hybridization was performed as described by the manufacturer (Affymetrix, SantaClara, CA). The complementary RNA hybridization cocktail was incubated overnight at 45C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the Affymetrix-recommended protocol

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA).

data_processing: GeneChip Operating Software supplied by Affymetrix was used to perform gene expression analysis. Four samples of control fed conditions and three samples of treated conditions were statistically analysed. Raw data obtained from Affymetrix arrays were background corrected using RMA methodology. Intensity signal was standardized across arrays via quantile normalization algorithm. The difference between treated samples and controls was statistically tested using limma moderate t-statistic. Aiming to control the false disocvery rate, p-values were corrected for multiple testing using Benjamini and Hochberg method

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans at young adult stage

label_protocol: Gene expression analysis was performed according to the Affymetrix-recommended protocol using Affymetrix C.Elegans Genome Array. GeneChips containing probes for over 22,500 transcripts. Total RNA (300 ng per sample) was biotin- labeled using the Affymetrix GeneChip 3' IVT express protocol

growth_protocol: C. elegans was cultured in Nematode Growth Medium (NGM) as estándar diet. Nematodes were age-synchronized by isolating eggs from gravid adults. Embryos were incubated in the corresponding agar plates at 20ºC for 3 days (until reach young adult stage)

extract_protocol: Worms from each fed condition (NGM or 13L peptide) were collected with M9 buffer and disrupted by sonication (3 pulses at 10W, 20s/pulse). RNA was isolated with a comercial kit (RNAsy Kit, Qiagen)

treatment_protocol: Treated nematodes were cultured in NGM plates supplemented with 1 µg/mL of peptide 13L and incubated at 20ºC from egg to young adult stage.

tag: strin

tag: protocol

value: Nematode Growth medium, control


title: EP Normal_rep3

description: Gene expression of epidermis plus exodermis of root grown under normal condition

value: epidermis plus exodermis of root

value: normal


title: KAN1-GR_30min_biorep3

city: Stanford

description: Collection day two

source_name: 35S::KAN1-GR seedlings, 30min DEX treatment


title: Cultured bacteria MA083248


title: KAN1-GR_60min_biorep1

description: Collection day two


title: Cultured bacteria MA083013


title: Cor +Cd_rep1

source_name: cortex of root grown under Cd-stressed condition


title: SJTALL020

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710856


title: SJTALL081

description:
RNA extracted from tumor cells obtained at diagnosis
Additional Array


title: Cultured bacteria MA082763


title: Cor -Fe_rep3

description: Gene expression of cortex of root grown under Fe-deficient condition

value: Fe-deficient


title: Cor -Fe_rep1

source_name: cortex of root grown under Fe-deficient condition


title: KAN1-GR_30min_biorep1

description: Collection day two

value: Columbia


title: Cultured bacteria MA082642


title: Cor -Fe_rep2


title: EP -Fe_rep2

description: Gene expression of epidermis plus exodermis of root grown under Fe-deficient condition


title: SJTALL024

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710861


title: KAN1-GR_30min_biorep2

description: Collection day two

value: whole seedling, 7 days old


title: Cor Normal_rep3

description: Gene expression of cortex of root grown under normal condition


title: Cor +Cd_rep3


title: SJTALL078

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710921


title: Cultured bacteria LSPQ-3677


title: SJTALL143

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710925


title: SJTALL067

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710904


title: SJTALL080


title: SJTALL070

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710910


title: KAN1-GR_0min_biorep1

description: Collection day two

source_name: 35S::KAN1-GR seedlings, 0min DEX treatment


title: Cor Normal_rep1

source_name: cortex of root grown under normal condition


title: GR-REV_120min_biorep2

description: Collection day one

source_name: 35S::GR-REV seedlings, 120min DEX treatment


title: Cultured bacteria MA053782


title: Cultured bacteria LSPQ-3646


title: KAN1-GR_0min_biorep2

description: Collection day two


title: SJTALL050

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710899


title: SJTALL048

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710897


title: Cultured bacteria LSPQ-3645


title: Cor Normal_rep2


title: KAN1-GR_0min_biorep3

description: Collection day two


title: SJTALL044

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710893


title: VB +Cd_rep3

description: Gene expression of vascular bundle of root grown under Cd-stressed condition

value: vascular bundle of root


title: Cultured bacteria LSPQ-3644


title: GR-REV_120min_biorep1

description: Collection day one


title: SJTALL047

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710895


title: GR-REV_60min_biorep2

description: Collection day one

source_name: 35S::GR-REV seedlings, 60min DEX treatment


title: VB +Cd_rep2

source_name: vascular bundle of root grown under Cd-stressed condition


title: Cultured bacteria LSPQ-3643


title: KAN1-GR_60min_biorep3

description: Collection day two

source_name: 35S::KAN1-GR seedlings, 60min DEX treatment


title: GR-REV_60min_biorep3

description: Collection day one


title: Cultured bacteria LSPQ-3162


title: Cultured bacteria LSPQ-3641


title: VB +Cd_rep1


title: VB -Fe_rep2

description: Gene expression of vascular bundle of root grown under Fe-deficient condition


title: GR-REV_60min_biorep1

description: Collection day one


title: Cultured bacteria LSPQ-3095


title: SJTALL027

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710868


title: GR-REV_30min_biorep3

description: Collection day one

source_name: 35S::GR-REV seedlings, 30min DEX treatment


title: Cultured bacteria LSPQ-3093


title: VB -Fe_rep1

source_name: vascular bundle of root grown under Fe-deficient condition


title: GR-REV_30min_biorep2

description: Collection day one


title: Cultured bacteria LSPQ-3092


title: VB -Fe_rep3


title: SJTALL038

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710889


title: VB Normal_rep2

description: Gene expression of vascular bundle of root grown under normal condition


title: VB Normal_rep1

source_name: vascular bundle of root grown under normal condition


title: SJTALL041

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710891


title: SJTALL036

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710884


title: SJTALL037

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710887


title: SJTALL031

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710876


title: GR-REV_30min_biorep1

description: Collection day one


title: GR-REV_0min_biorep1

description: Collection day one

source_name: 35S::GR-REV seedlings, 0min DEX treatment


title: GR-REV_0min_biorep3

description: Collection day one


title: VB Normal_rep3


title: SJTALL034

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710882

source_name: RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia (non-ETP)


title: SJTALL026

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710866


title: Cultured bacteria LSPQ-3081

source_name: LSPQ


title: Cultured bacteria LSPQ-3089


title: SJTALL029

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710872


title: Cultured bacteria LSPQ-3078


title: GR-REV_0min_biorep2

description: Collection day one


title: Rice mesocotyl d14-1_+GR24_rep3

city: Chikusa

first: Takaki

last: Yamauchi

address: Furo-cho

institute: Nagoya University

description: Gene expression data in rice mesocotyl

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent).  1650 ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2505C according to manufacturer's instructions.

data_processing: signal intensities were extracted by using Feature Extraction software (Version 10.5.1.1; Agilent Technologies).For inter-array normalization, a global median normalization was applied across all microarrays to achieve the same median signal intensities for each array. In the statistical analysis, SAM t-tests were performed to obtain P values using R software (http://www.r-project.org/). The fold change of each probe between one condition and another was calculated by using an average of three replicates.

organism: Oryza sativa Japonica Group

source_name: Rice mesocotyl, 4-d-old-d14-1 w/ GR24 treatment

label_protocol: Cy3-labeled cRNA were prepared from total RNA using Quick Amp Labeling Kit (Agilent) in accordance with the manufacturer's protocol with slight modification.

growth_protocol: Dehusked rice caryopses were sterilized in a 0.5% (v/v) sodium hypochlorite solution for 1 h. After washing with deionized water, seeds were kept in the water for 10 h at 4°C in darkness, and then seeds were sown on each 0.7% (w/v) agar plate. The agar plate was placed in a dark box made of black cardboard and then covered with black cloths. The boxes were put in the growth chamber, and the seeds were germinated and grown at 28°C under complete dark conditions.

extract_protocol: Dark-grown seedlings were fixed in 100% acetone (on ice) for 1 h in a dark room and vacuumed on ice for 5 min. This fixation was repeated twice with replacement of the fixative solution with fresh solution in darkness. The mesocotyls were then cut off under a stereo-microscope and frozen in liquid nitrogen. Total RNA was extracted from the frozen fixed tissues by using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: For GR24 treatment, 0.7% (w/v) agar was melted by autoclaving, and then GR24 (100 mM; dissolved in 100% acetone) was added to the melted agar (~50 °C) to prepare agar plates with 1 μM GR24 (final concentration) (0.001% acetone was contained in each plate). Desterilized seeds were placed on the agar plates with 0 μM or 1 μM GR24 and were germinated and grown at 28 °C under complete darkness. For negative controls, agar plates with 0.001% acetone were used.

tag: cultivar

value: Shiokari

value: dwarf mutant d14-1

value: mesocotyl - 4d after germination under darkness


title: Columbia_120min_biorep3

description: Collection day one

source_name: wild-type seedlings, 120min treatment


title: Cultured bacteria LSPQ-3073


title: Cultured bacteria LSPQ-3070


title: Cultured bacteria LSPQ-3077


title: Columbia_120min_biorep2

description: Collection day one


title: Cultured bacteria LSPQ-3064


title: Rice mesocotyl d14-1_+GR24_rep2

description: Gene expression data in rice mesocotyl


title: Columbia_120min_biorep1

description: Collection day one


title: Rice mesocotyl d14-1_-GR24_rep3

description: Gene expression data in rice mesocotyl

source_name: Rice mesocotyl, 4-d-old-d14-1 w/o GR24 treatment


title: WT_2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Replicate 2.

hyb_protocol: Hybridization was performed in the hybridization oven (Agilent Technologies, 17h, 10 rpm, 65˚C)

scan_protocol: Cy3 intensities were detected by a one-color microarray scanner (G2505C, Agilent Technologies) at 5 µm resolution

data_processing: Data were quantile normalized using R and Bioconductor package limma.

organism: Mus musculus

source_name: TAp73WT testis 2

label_protocol: For each array 200 ng RNA was processed and Cy3 labeled by the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: animals were housed at the mouse facility of the ENI, University Göttingen

extract_protocol: mRNA was isolated from murine testis. Tissue samples were transferred into trizol buffer, homogenized and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer´s instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf). RNA-precipitation was done with Ethanol. RNA was diluted in nuclease-free water and concentrations were determined using a Nanodrop spectrophotometer.

treatment_protocol: mice were euthanized with carbon dioxide and the whole testis was removed

tag: strain/background

value: TAp73 WT

value: 10 weeks

tag: proband sex

value: male

value: testis


title: SJTALL019

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710854

value: non-ETP T-lineage ALL


title: Rice mesocotyl d14-1_+GR24_rep1

description: Gene expression data in rice mesocotyl


title: Columbia_60min_biorep6

description: Collection day two

source_name: wild-type seedlings, 60min DEX treatment

tag: ecotype


title: Rice mesocotyl d10-1_+GR24_rep3

description: Gene expression data in rice mesocotyl

source_name: Rice mesocotyl, 4-d-old-d10-1 w/ GR24 treatment

value: dwarf mutant d10-1

tag: developmental stage


title: SJTALL025

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710864


title: Columbia_60min_biorep5

description: Collection day two

tag: genotype/variation


title: SJTALL016

description:
RNA extracted from tumor cells obtained at diagnosis
GSM710852


title: Rice mesocotyl d10-1_+GR24_rep2

description: Gene expression data in rice mesocotyl


title: Columbia_60min_biorep2

description: Collection day one


title: WT_1

description: Replicate 1.

source_name: TAp73WT testis 1

tag: age


title: Rice mesocotyl d14-1_-GR24_rep2

description: Gene expression data in rice mesocotyl


title: Columbia_60min_biorep4

description: Collection day two


title: TAp73KO_3

description: Replicate 3.

source_name: TAp73KO testis 3

value: TAp73 KO


title: Cultured bacteria HEMO8

source_name: Geneva


title: Cultured bacteria HEMO7


title: Cultured bacteria HEMO9


title: Rice mesocotyl d14-1_-GR24_rep1

description: Gene expression data in rice mesocotyl


title: Rice mesocotyl d10-1_-GR24_rep3

description: Gene expression data in rice mesocotyl

source_name: Rice mesocotyl, 4-d-old-d10-1 w/o GR24 treatment


title: Cultured bacteria LSPQ-3059


title: WT_3

description: Replicate 3.

source_name: TAp73WT testis 3


title: TAp73KO_2

description: Replicate 2.

source_name: TAp73KO testis 2


title: Cultured bacteria HEMO5


title: Columbia_60min_biorep3

description: Collection day one


title: Rice mesocotyl d10-1_+GR24_rep1

description: Gene expression data in rice mesocotyl


title: Columbia_60min_biorep1

description: Collection day one


title: GR-REV_120min_biorep3

description: Collection day one

source_name: 35S::GR-REV seedlings, 120min DEX treatment


title: Cultured bacteria HEMO3


title: Cultured bacteria HEMO4


title: Columbia_30min_biorep5

description: Collection day two

source_name: wild-type seedlings, 30min DEX treatment


title: TAp73KO_1

description: Replicate 1.

source_name: TAp73KO testis 1


title: Rice mesocotyl d10-1_-GR24_rep2

description: Gene expression data in rice mesocotyl


title: Cultured bacteria HEMO2


title: Columbia_30min_biorep2

description: Collection day one


title: Columbia_30min_biorep4

description: Collection day two


title: Rice mesocotyl d10-1_-GR24_rep1

description: Gene expression data in rice mesocotyl


title: Columbia_30min_biorep6

description: Collection day two


title: Rice mesocotyl WT_+GR24_rep1

description: Gene expression data in rice mesocotyl

source_name: Rice mesocotyl, 4-d-old-WT w/ GR24 treatment

value: WT


title: Rice mesocotyl WT_+GR24_rep2

description: Gene expression data in rice mesocotyl


title: Cultured bacteria HEMO10


title: Columbia_30min_biorep3

description: Collection day one


title: Cultured bacteria CTRLNEG2


title: Rice mesocotyl WT_+GR24_rep3

description: Gene expression data in rice mesocotyl


title: Rice mesocotyl WT_-GR24_rep3

description: Gene expression data in rice mesocotyl

source_name: Rice mesocotyl, 4-d-old-WT w/o GR24 treatment


title: Columbia_0min_biorep6

description: Collection day two

source_name: wild-type seedlings, 0min DEX treatment


title: Columbia_0min_biorep4

description: Collection day two


title: Cultured bacteria CTRLNEG1


title: Cultured bacteria 14762

source_name: CRI


title: Cultured bacteria 14748


title: Columbia_0min_biorep5

description: Collection day two


title: Rice mesocotyl WT_-GR24_rep2

description: Gene expression data in rice mesocotyl


title: SHSY5Y_K

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

institute: Keio University

description: SH-SY5Y cells Human Tiling 1.0R chip K

hyb_protocol: Approximately 6.0μg of DNA was hybridized per array using the Affymetrix hybridization kit. For these 14 array sets, 7 arrays were hybridized for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven. The hybridized solution was removed from these arrays and reused to hybridize the remaining seven arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G. Images were quantified using GCOS software (Affymetrix). Signal values ware exported to text files using GCOS Manager software (Affymetrix).

data_processing:
The ".CEL" files are raw data. The "normalized.txt" files (supplementary data linked to GSE18490) are data normalized as follows.

1) To exclude potential low quality probes, we excluded probes that corresponded to the following conditions: A) probes for which either the Perfect Match (PM) or Miss Match (MM) probe perfectly match more than once in the genome, B) probes which contain SNPs, C) probes located on sex chromosomes.
2) To reduce inter-chip differences, we equalized the mean and variance of probe intensities among all chips in each tissue. Note that the intensities were converted to a logarithmic scale (base 2).
3) To reduce background noise, we subtracted the intensity of each MM probe from the PM probe in each probe set. If the value was negative, zero was assigned as the value.
4) To adjust for GC content of probes, we calculated normalized intensities by each GC content.
5) To equalize the distribution of signals in each chip, we performed quantile normalization for each chip
6) To smooth the probe intensities with neighboring probes, we calculated Hodges-Lehmann statistics. The size of each sliding window was 101bp.
7) All probes that ranked higher than the top 15% signal threshold were selected and those with an inter-probe distance less than a maximum gap threshold of 25bp were concatenated. Then, the concatenated probes with length longer than a minimum run threshold of 101bp were defined as transfrags. Finally, we performed BLAST to exclude probes that mapped to multiple locations.

source_name: pooled Human SH-SY5Y cells total RNA

label_protocol: Reverse transcription, amplification, fragmentation and labeling steps were performed according to Affymetrix protocol using WT Amplified Double-Strand cDNA Synthesis Kit (Affymetrix) and WT Double-Strand DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.

tag: cell line


title: Columbia_30min_biorep1

description: Collection day one


title: Uterus_K

description: uterus Human Tiling 1.0R chip K

source_name: pooled Human uterus total RNA

tag: tissue

value: uterus

tag: race

value: caucasian


title: Rice mesocotyl WT_-GR24_rep1

description: Gene expression data in rice mesocotyl


title: Cultured bacteria 51916


title: Columbia_0min_biorep3

description: Collection day one


title: heart doxorubicin treated rep8

city: Little Rock

first: Valentina

last: Todorova

state: AR

address: 4301 W. Markham

institute: UAMS

description: left ventricle of heart was used

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The probe intensities were log2 transformed and averaged over samples. Within each sample the median of the log2-transformed intensities of the not expressed probes was subtracted from the log2 intensities to normalize the data

organism: Rattus norvegicus

source_name: heart

label_protocol: RNA was amplified using the Nugen PicoSL WTA system and labeled with the Encore Biotin IL module kit prior to hybridization of samples to beadchips

growth_protocol: Rats were subjected to 12 hour dark/light and ad libitum food and water

extract_protocol: Total RNA was extracted from PBMCs and left heart ventricle using the AllPrep DNA/RNA/protein mini kit from Qiagen. RNA quality and quantity were measured on the Agilent 2100 bioanalyzer

treatment_protocol: Seventeen rats were randomized to receive 12 mg/kg doxorubicin or saline and sacrificed after 48 hours.

value: left ventricle of heart

tag: strain

value: Sprague-Dawley

tag: treatment

value: doxorubicin treated


title: Cultured bacteria 9095

tag: serotype (quellung)


title: Cultured bacteria 14634


title: heart doxorubicin treated rep7

description: left ventricle of heart was used


title: Columbia_0min_biorep1

description: Collection day one

value: Columbia

value: whole seedling, 7 days old


title: HeLa_K

description: HeLa cells Human Tiling 1.0R chip K

source_name: Human HeLa cells total RNA

value: HeLa


title: Cultured bacteria 14587


title: Trachea_K

description: trachea Human Tiling 1.0R chip K

source_name: pooled Human trachea total RNA

value: trachea


title: MG6_replicated

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

hyb_protocol: Hybridization was performed as specified by Agilent for array CGH 8x15k arrays; after hybridization for 24 hours, the slide was washed in aCGH buffer 1 for 5 minutes, and buffer 2 for 1 minute. The slide was immediately scanned.

scan_protocol: Scanning was performed on a GenePix 4100A scanner using the supplied software.

data_processing: Data were extracted in GenePix 4100A scanning software and normalized using the lowess method implemented in TM4 MIDAS

organism: Escherichia coli BW25113

source_name: Plasmid DNA, post conjugation

label_protocol: 1 ug plasmid DNA was amplified using Exo-Klenow fragment and amino-allyl dUTP (Invitrogen) as specified by the manufacturer; the samples were then ethanol precipitated, resuspended in coupling buffer, and mixed with the appropriate CyDye (Cy3 or Cy5) according to the manufacturer's protocol. Uncoupled dye and other impurities were removed from each sample with size selective column. A NanoDrop spectrophotometer was used to assess labeling efficiency and DNA yield following this purification procedure

growth_protocol: Donor was transformed with a random genomic library made from E. coli and stored as glycerol stocks. The library was revived and transferred to four recipient strains using conjugation; the donor was miniprepped at this time, and the recipients were miniprepped after outgrowth under dual selection. Two recipient libraries in BWG and BWY were propagated under n-butanol stress for three days, and then miniprepped as well.

extract_protocol: Library minipreps were performed with the Zyppy Miniprep kit (Zymo Technologies) and quantified using the Qubit dsDNA BR kit (Invitrogen) and the Nanodrop spectrophotometer (Thermo Scientific)

tag: plasmid source

value: Initial Recipient Library

organism: Escherichia coli

source_name: Plasmid DNA, donor, XL1-Blue

tag: plasmid

value: Donor Library


title: Columbia_0min_biorep2

description: Collection day one


title: BWG_butanol_3passages

source_name: Plasmid DNA, after n-butanol selection

value: Post Selection Library

source_name: Plasmid DNA, BWG post conjugation

value: Initial Recipient Library (BWG)


title: Thymus_K

description: thymus Human Tiling 1.0R chip K

source_name: pooled Human thymus total RNA

value: thymus


title: BWY_butanol_3passages

source_name: Plasmid DNA, BWY post conjugation

value: Initial Recipient Library (BWY)


title: Cultured bacteria 1392


title: heart doxorubicin treated rep6

description: left ventricle of heart was used


title: Testes_K

description: testes Human Tiling 1.0R chip K

source_name: pooled Human testes total RNA

value: testes


title: heart doxorubicin treated rep9

description: left ventricle of heart was used


title: Stomach_K

description: stomach Human Tiling 1.0R chip K

source_name: pooled Human stomach total RNA

value: stomach


title: BWY_replicated


title: heart doxorubicin treated rep5

description: left ventricle of heart was used


title: Spleen_K

description: spleen Human Tiling 1.0R chip K

source_name: pooled Human spleen total RNA

value: spleen


title: BWG_replicated


title: Thyroid_K

description: thyroid Human Tiling 1.0R chip K

source_name: pooled Human thyroid total RNA

value: thyroid

value: caucasian


title: Cultured bacteria 9079


title: heart doxorubicin treated rep2

description: left ventricle of heart was used

value: left ventricle of heart

value: Sprague-Dawley


title: SpinalCord_K

description: spinal cord Human Tiling 1.0R chip K

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: heart doxorubicin treated rep3

description: left ventricle of heart was used

value: doxorubicin treated


title: Cultured bacteria 9078

source_name: CRI


title: heart doxorubicin treated rep1

description: left ventricle of heart was used


title: MY4_replicated


title: heart Saline control rep8

description: left ventricle of heart was used

value: saline control


title: heart doxorubicin treated rep4

description: left ventricle of heart was used


title: heart Saline control rep7

description: left ventricle of heart was used


title: heart Saline control rep5

description: left ventricle of heart was used


title: 168 h control replicate 3

city: Charlottetown

first: Fraser

last: Clark

state: PEI

address: 550 University Ave

department: Pathology and Microbiology

institute: University of Prince Edward Island

description:
Biological replicate 3 of 4 for 168 h infected
8--MC_6813 14954 Top April 14 2011aa

hyb_protocol: Labeled aRNA and cDNA were quantified spectrophotometrically (NanoDrop ND-1000) and 140 ng of cDNA and 100 pmol of labeled aRNA were used for microarray hybridization.  Prior to hybridization, labeled aRNA was fragmented using 1 µL 10x Fragmentation solution and incubation for 10 min at 70°C followed by 1 µL of Stop solution (Life Technologies Inc.).  Hybridizations were performed using A2 chambers on a Tecan 400 HS Pro hybridization system (Tecan, NC, USA).  Briefly, microarrays were incubated at 65°C for 10 min, washed twice with hybridization buffer 1 (5x SSC, 0.01% SDS, 0.2% BSA) for 20s at room temperature, incubated at 50°C for 13 min, washed once with buffer 1 for 20s, incubated at 48°C for 13 min, washed once with buffer 1 for 1 min and once with buffer 4 (5x SSC) for 1 min.  The sample was then injected and hybridized to the microarray with sample agitation at 48°C for 16 h.  The microarray was washed with buffer 2 (2x SSC, 0.2% SDS) at 40°C for 1 min and incubated at 40°C for 2 min, washed with buffer 2 at 30°C for 1 min and with buffer 5 at 30°C for 1 min, incubated at 30°C for 2 min, washed with buffer 5 at 23°C for 1 min, and buffer 3 (0.2x SSC) at 23°C for 1 min.  Finally the microarray was incubated at 23°C for 2 min followed by a wash with buffer 3 for 1 min and then dried with nitrogen gas for 3 min.

scan_protocol: Microarrays were imaged using a GenePix 4000B scanner (Molecular Devices, PA, USA) and features were extracted using SpotReader v 1.3.1 (Niles Scientific, CA, USA).

data_processing:
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.
Data was analyzed using TM4/MeV v4.8.1 (Saeed et al., 2003).  Two colour gene expression arrays were normalized by LOWESS and flagged using the MIDAS (Microarray Data Analysis Software) v2.2.2 software (Quackenbush, 2002).  The data was used to generate log2 ratios of sample to reference gene intensity so that all arrays could be compared.

label: Alexa Flour 555

organism: Homarus americanus

source_name: 168 h control

label_protocol: Alexa Fluor® 555 labeled single strand cDNA was generated from 20 µg high quality sample RNA using 20 µg of RNA using a SuperScript™ Plus Indirect cDNA Labeling System (Life Technologies Inc., Burlington, ON, Canada). Reference aRNA was generated from 5 µg of pooled lobster hepatopancreatic RNA using an Amino Allyl MessageAmp™ II aRNA Amplification kit (Life Technologies Inc.). Reference aRNA was Alexa Fluor® 647  labeled using 12 µg of aRNA and a Superscript™ Plus Indirect cDNA Labeling System (Life Technologies Inc.).

growth_protocol: H. americanus were individually housed in a recirculating artificial sea water system with UV and 1 µm filter.

extract_protocol: Total RNA was extracted using a phenol-chloroform extraction method with the aqueos phase cleaned up using an Rneasy kit following manufacturers instructions.

treatment_protocol: Infected lobster were injected with A. haemophila.

tag: moult status

value: Intermoult

tag: gender

value: male

value: Hepatopancreas

label: Alexa Flour 647

source_name: aRNA reference sample from pooled sample of Homarus americanus hepatopancreatic tissue

tag: sample complexity

value: standard reference pooled sample

value: hepatopancreas


title: heart Saline control rep6

description: left ventricle of heart was used

source_name: heart


title: SmallIntestine_K

description: small intestine Human Tiling 1.0R chip K

source_name: pooled Human small intestine total RNA

value: small intestine


title: heart Saline control rep4

description: left ventricle of heart was used


title: 168 h infected replicate 4

description:
Biological replicate 4 of 4 for 96 h infected
7--MI_6833 14358 Bottom May 4 2011fc

source_name: 168 h infected


title: heart Saline control rep1

description: left ventricle of heart was used


title: heart Saline control rep2

description: left ventricle of heart was used


title: 168 h control replicate 4

description:
Biological replicate 4 of 4 for 168 h infected
8--MC_6816 14960 Top April 15 2011fc


title: SkeletalMuscle_K

description: skeletal muscle Human Tiling 1.0R chip K

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: SalivaryGland_K

description: salivary gland Human Tiling 1.0R chip K

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Prostate_K

description: prostate Human Tiling 1.0R chip K

source_name: pooled Human prostate total RNA

value: prostate


title: PC3-4_2

city: Birmingham

first: Victor

middle: J

last: Thannickal

state: AL

address: BMR2 470, 901 19th Street S

department: Medicine

institute: University of Alabama at Birmingham

description: replicate 2

scan_protocol: BeadChips were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.2

source_name: PC3 growth in BMCM

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: Prostate carcinoma


title: Lung_K

description: lung Human Tiling 1.0R chip K

source_name: pooled Human lung total RNA

value: lung


title: 168 h control replicate 2

description:
Biological replicate 2 of 4 for 168 h infected
8--MC_6807 14974 Bottom March 25 2011fc


title: Pancreas_K

description: pancreas Human Tiling 1.0R chip K

source_name: pooled Human pancreas total RNA

value: pancreas

value: caucasian


title: 168 h infected replicate 2

description:
Biological replicate 2 of 4 for 96 h infected
7--MI_6817 14969 Bottom April 13 2011fc


title: PC3-5

description: replicate 1


title: PC3-5_2

description: replicate 2


title: 168 h infected replicate 3

description:
Biological replicate 3 of 4 for 96 h infected
7--MI_6830 14955 Bottom April 12 2011fc


title: PC3-1_2

description: replicate 2

source_name: PC3 Control in Regular Medium


title: heart Saline control rep3

description: left ventricle of heart was used

value: left ventricle of heart

value: Sprague-Dawley


title: PBMC doxorubicin treated rep9

description: left ventricle of heart was used

source_name: PBMC

value: PBMC

value: doxorubicin treated


title: PBMC doxorubicin treated rep8

description: left ventricle of heart was used


title: Liver_K

description: liver Human Tiling 1.0R chip K

source_name: pooled Human liver total RNA

value: liver


title: 168 h control replicate 1

description:
Biological replicate 1 of 4 for 168 h infected
8--MC_6806 14951 Top April 14 2011fc

value: Intermoult

value: male


title: PBMC doxorubicin treated rep6

description: left ventricle of heart was used


title: PC3-4

description: replicate 1


title: FetalBrain_K

description: fetal brain Human Tiling 1.0R chip K

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: PBMC doxorubicin treated rep7

description: left ventricle of heart was used


title: Heart_K

description: heart Human Tiling 1.0R chip K

source_name: pooled Human heart total RNA

value: heart


title: 96 h infected replicate 3

description:
Biological replicate 3 of 4 for 48 h infected
6--96I_6821 14971 Bottom April 13 2011fc

source_name: 96 h infected

value: Hepatopancreas

value: standard reference pooled sample

value: hepatopancreas


title: 168 h infected replicate 1

description:
Biological replicate 1 of 4 for 96 h infected
7--MI_6804 14366 Bottom May 4 2011fc


title: PC3-1

description: replicate 1


title: Colon_K

description: colon Human Tiling 1.0R chip K

source_name: pooled Human colon total RNA

value: colon


title: Cortex_K

description: cortex Human Tiling 1.0R chip K

source_name: pooled Human cortex total RNA

value: cortex


title: BoneMarrow_K

description: bone marrow Human Tiling 1.0R chip K

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: 96 h infected replicate 1

description:
Biological replicate 1 of 4 for 48 h infected
6--96I_6808 14966 Top April 12 2011fc

source_name: aRNA reference sample from pooled sample of Homarus americanus hepatopancreatic tissue


title: Cerebellum_K

description: cerebellum Human Tiling 1.0R chip K

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: Kidney_K

description: kidney Human Tiling 1.0R chip K

source_name: pooled Human kidney total RNA

value: kidney

value: caucasian


title: PBMC doxorubicin treated rep2

description: left ventricle of heart was used

value: Sprague-Dawley


title: SHSY5Y_H

description: SH-SY5Y cells Human Tiling 1.0R chip H

source_name: pooled Human SH-SY5Y cells total RNA


title: PBMC doxorubicin treated rep3

description: left ventricle of heart was used

value: PBMC


title: PBMC doxorubicin treated rep5

description: left ventricle of heart was used

value: doxorubicin treated


title: PBMC doxorubicin treated rep4

description: left ventricle of heart was used


title: 96 h infected replicate 4

description:
Biological replicate 4 of 4 for 48 h infected
6--96I_6825 14976  Bottom April 19 2011fc


title: 24 h infected replicate 4

description:
Biological replicate 4 of 4 for 12 h Infected
4--24I_6831 14951 Bottom April 14 2011fc

source_name: 24 h infected


title: PBMC doxorubicin treated rep1

description: left ventricle of heart was used


title: HeLa_H

description: HeLa cells Human Tiling 1.0R chip H

source_name: Human HeLa cells total RNA

value: HeLa


title: Uterus_H

description: uterus Human Tiling 1.0R chip H

source_name: pooled Human uterus total RNA

value: uterus


title: 48 h infected replicate 1

description:
Biological replicate 1 of 4 for 24 h Infected
5--48I_6810 14975 Bottom April 12 2011fc

source_name: 48 h infected

value: Intermoult

value: male


title: 48 h infected replicate 2

description:
Biological replicate 2 of 4 for 24 h Infected
5--48I_6815 14952 Bottom April 15 2011fc


title: 24 h infected replicate 3

description:
Biological replicate 3 of 4 for 12 h Infected
4--24I_6826 14961 Top March 25 2011fc


title: PBMC Saline control rep6

description: left ventricle of heart was used

value: saline control


title: Trachea_H

description: trachea Human Tiling 1.0R chip H

source_name: pooled Human trachea total RNA

value: trachea


title: PBMC Saline control rep8

description: left ventricle of heart was used

source_name: PBMC


title: 48 h infected replicate 4

description:
Biological replicate 4 of 4 for 24 h Infected
5--48I_6829 14977 Top April 19 2011fc

value: Hepatopancreas

value: standard reference pooled sample


title: PBMC Saline control rep7

description: left ventricle of heart was used


title: 24 h infected replicate 1

description:
Biological replicate 1 of 4 for 12 h Infected
4--24I_6802 14960 Bottom April 15 2011fc

value: hepatopancreas


title: Thymus_H

description: thymus Human Tiling 1.0R chip H

source_name: pooled Human thymus total RNA

value: thymus


title: 96 h infected replicate 2

description:
Biological replicate 2 of 4 for 48 h infected
6--96I_6811 14959 Top April 15 2011fc


title: PBMC Saline control rep3

description: left ventricle of heart was used


title: Granulosa_cells_30_days-Rep2

city: Québec City

first: Marc-André

last: Sirard

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

description: Biological replicats 2 of 3. Granulosa cells at 30 days after calving compare to the 120 days reference.

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

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

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Cows after 2 days (42 hours) from prostraglandin injection (PGF2alfa) have been submitted to Ovum Pick Up for granulosa cells isolation from dominant follicles.  Two consecutives centrifugations have been made for to separe the follicular liquid from the granulosa cells and for to wash, trough the PBS solution,  the granulosa cells before the nitrogen liquid conservation.

extract_protocol:
Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
Amplification protocol:
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: breed

value: Holstein-Friesian

tag: time

value: 30 days after calving

value: 120 days after calving


title: 24 h infected replicate 2

description:
Biological replicate 2 of 4 for 12 h Infected
4--24I_6812 14355 Bottom May 4 2011fc


title: Testes_H

description: testes Human Tiling 1.0R chip H

source_name: pooled Human testes total RNA

value: testes

value: caucasian


title: PBMC Saline control rep5

description: left ventricle of heart was used

value: PBMC

value: Sprague-Dawley


title: Thyroid_H

description: thyroid Human Tiling 1.0R chip H

source_name: pooled Human thyroid total RNA

value: thyroid


title: 12 h infected replicate 4

description:
Biological replicate 4 of 4 for 6 h infected
3--12I_6824 14963 Bottom April 13 2011fc

source_name: 12 h infected


title: PBMC Saline control rep4

description: left ventricle of heart was used


title: Stomach_H

description: stomach Human Tiling 1.0R chip H

source_name: pooled Human stomach total RNA

value: stomach


title: Granulosa_cells_30_days-Rep3

description: Biological replicats 3 of 3. Granulosa cells at 30 days after calving compare to the 120 days reference.


title: Spleen_H

description: spleen Human Tiling 1.0R chip H

source_name: pooled Human spleen total RNA

value: spleen


title: 12 h infected replicate 3

description:
Biological replicate 3 of 4 for 6 h infected
3--12I_6823 14956 Top April 19 2011fc

value: Intermoult

value: male


title: 12 h infected replicate 2

description:
Biological replicate 2 of 4 for 6 h infected
3--12I_6818 14366 Top May 4 2011fc


title: 12 h infected replicate 1

description:
Biological replicate 1 of 4 for 6 h infected
3--12I_6805 14979 Bottom March 25 2011fc


title: SpinalCord_H

description: spinal cord Human Tiling 1.0R chip H

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: Granulosa_cells_90_days-Rep3

description: Biological replicats 3 of 3. Granulosa cells at 90 days after calving compare to the 120 days reference.

value: 90 days after calving


title: PBMC Saline control rep1

description: left ventricle of heart was used

value: saline control


title: Granulosa_cells_60_days-Rep2

description: Biological replicats 2 of 3. Granulosa cells at 60 days after calving compare to the 120 days reference.

value: 60 days after calving


title: 6 h infected replicate 4

description:
Biological replicate 3 of 3 for 168 h control
2--6I_6832 14358 Top May 4 2011fc

source_name: 6 h infected

value: Hepatopancreas

source_name: aRNA reference sample from pooled sample of Homarus americanus hepatopancreatic tissue

value: standard reference pooled sample

value: hepatopancreas


title: Granulosa_cells_60_days-Rep1

description: Biological replicats 1 of 3. Granulosa cells at 60 days after calving compare to the 120 days reference.

value: Holstein-Friesian

value: 120 days after calving


title: 6 h infected replicate 2

description:
Biological replicate 2 of 3 for 168 h control
2--6I_6827 14954 Bottom April 14 2011fc


title: Granulosa_cells_60_days-Rep3

description: Biological replicats 3 of 3. Granulosa cells at 60 days after calving compare to the 120 days reference.


title: SmallIntestine_H

description: small intestine Human Tiling 1.0R chip H

source_name: pooled Human small intestine total RNA

value: small intestine

value: caucasian


title: 48 h infected replicate 3

description:
Biological replicate 3 of 4 for 24 h Infected
5--48I_6819 14958 Bottom April 14 2011fc


title: 6 h infected replicate 3

description:
Biological replicate 3 of 3 for 168 h control
2--6I_6828 14958 Top April 14 2011fc


title: Granulosa_cells_30_days-Rep1

description: Biological replicats 1 of 3. Granulosa cells at 30 days after calving compare to the 120 days reference.

value: 30 days after calving


title: PBMC Saline control rep2

description: left ventricle of heart was used

value: PBMC

value: Sprague-Dawley


title: 6 h infected replicate 1

description:
Biological replicate 1 of 3 for 168 h control
2--6I_6814_14952 Top April 15 2011fc


title: SkeletalMuscle_H

description: skeletal muscle Human Tiling 1.0R chip H

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: Granulosa_cells_90_days-Rep1

description: Biological replicats 1 of 3. Granulosa cells at 90 days after calving compare to the 120 days reference.


title: Treatment-24h-Rep 3

city: Hobart

first: Minghui Jessica

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description:
Replicate 3
5038770029_K

hyb_protocol: Standard Illumina hybridization protocol with a hybridization duration of 17h.

scan_protocol: Standard Illumina scanning protocol with a pmt value=503 and scan factor=0.74.

data_processing: The data were normalised using median normalisation with GeneSpring Ver 7.3

source_name: Right cortex

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

growth_protocol: All procedures performed in this study were approved by the Institutional Animal Care and Use Committee of the National University of Singapore.

extract_protocol: RNA was extracted using the conventional Trizol method and cleaned up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: Cerebral ischemia was induced by permanent occlusion of the left middle cerebral artery (MCA) using a subtemporal approach (Qu et al., 2006). Male Wistar rats (250 - 300 g) were anesthetized with ketamine (75mg/kg, intraperitoneal) and xylazine (10mg/kg, intraperitoneal). The MCA was exposed through a subtemporal craniectomy and cauterized from the point proximal to its origin to the point where it intersects the inferior cerebral vein. Sham group was operated in the same way as the experimental group without the occlusion of MCA.

value: Wistar

value: Male

tag: weight

value: Treatment

tag: treatment time-point


title: Vehicle-24h-Rep 4

description:
Replicate 2
5038770029_J

value: Vehicle


title: 6 h control replicate 3

description:
Biological replicate 3 of 3 for 6 h control
1--6C_6836 14969 Top April 13 2011fc

source_name: 6 h control

value: Intermoult

value: male


title: SalivaryGland_H

description: salivary gland Human Tiling 1.0R chip H

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Prostate_H

description: prostate Human Tiling 1.0R chip H

source_name: pooled Human prostate total RNA

value: prostate


title: 6 h control replicate 2

description:
Biological replicate 2 of 3 for 6 h control
1--6C_6835 14966 Bottom April 12 2011fc

value: Hepatopancreas

value: standard reference pooled sample

value: hepatopancreas


title: Sham-24h-Rep 4

description:
Replicate 4
5038770029_H

value: Sham


title: Granulosa_cells_90_days-Rep2

description: Biological replicats 2 of 3. Granulosa cells at 90 days after calving compare to the 120 days reference.

value: Holstein-Friesian

value: 90 days after calving

value: 120 days after calving


title: Lung_H

description: lung Human Tiling 1.0R chip H

source_name: pooled Human lung total RNA

value: lung

value: caucasian


title: Liver_H

description: liver Human Tiling 1.0R chip H

source_name: pooled Human liver total RNA

value: liver


title: Kidney_H

description: kidney Human Tiling 1.0R chip H

source_name: pooled Human kidney total RNA

value: kidney


title: Pancreas_H

description: pancreas Human Tiling 1.0R chip H

source_name: pooled Human pancreas total RNA

value: pancreas


title: Heart_H

description: heart Human Tiling 1.0R chip H

source_name: pooled Human heart total RNA

value: heart


title: Treatment-24h-Rep 4

description:
Replicate 4
5038770029_L

value: Wistar

value: Male

value: Treatment


title: Merkel cell carcinoma tumor 26

city: Stockholm

first: Hong

last: Xie

address: KUS-Solna, CCK R8:04

country: Sweden

institute: Karolinska Institutet

description: formalin-fixed paraffin-embedded tissue

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4470B) for 20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v2.0. Images obtained after scanning were processed with Feature Extraction Software 10.7.3.1 (Agilent, Santa Clara, CA)

data_processing: Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized and median centered. Only normalized miRNAs with less than 20% missing values across the samples were included in the further analysis.

source_name: Tumor Biopsies from Merkel Cell Carcinoma specimens

label_protocol: 200 ng of total RNA were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase.

extract_protocol: Total RNA was extracted using TRIzol Reagent as previously described (Ma et al. 2009).

tag: tissue type

value: tumor biopsy

value: Merkel Cell Carcinoma (MCC)

tag: follow up time (months)

tag: outcome

value: died of disease


title: 100µM VX 6hr neuron replicate 3

city: Aberdeen Proving Ground

first: E Chepchumba

middle: K

last: Yego

state: MD

address: 3100 Ricketts Point Road

department: Research

institute: US Army Medical Research Institute of Chemical Defense

description: Cells maintained in humidified incubator at 37 degres C during treatment

hyb_protocol: Labelled RNA was hybridized for 16 hrs at 48 degrees C on miRNA 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics script FS450_0003

scan_protocol: GeneChips were scanned using Affymetrix 7G GeneChip Scanner using Affymetrix GeneChip Command Console Scan Control 3.1.01228 (Affymetrix 2009)

data_processing: Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)

source_name: Neuron 100uM VX treatment for 6hr

label_protocol: 500ng total RNA was labeled using the RNA biotin labeling flashtag biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA) as per manufacturer’s instructions

growth_protocol: iPSC-derived neurons (Cellular Dynamics, WI) were seeded at a density of 2.0 X10E6 per well in 6-well plates and maintained according to manufucturer's specifications

extract_protocol: Following treatment, cells were gently rinsed five times with hanks buffered salt solution. Total RNA was isolated from exposed and control cells using miRNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: One week after plating, cells were treated with VX or saline control

value: iPSC-deived Neuron

value: 100µM VX


title: FetalBrain_H

description: fetal brain Human Tiling 1.0R chip H

source_name: pooled Human fetal brain total RNA

tag: tissue

value: fetal brain

tag: race


title: Merkel cell carcinoma tumor 5a

description: formalin-fixed paraffin-embedded tissue


title: Vehicle-24h-Rep 3

description:
Replicate 1
5038770029_I

tag: strain

tag: treatment

value: Vehicle


title: Merkel cell carcinoma tumor 24

description: formalin-fixed paraffin-embedded tissue


title: Merkel cell carcinoma tumor 16

description: formalin-fixed paraffin-embedded tissue


title: Merkel cell carcinoma tumor 5b

description: formalin-fixed paraffin-embedded tissue


title: 6 h control replicate 1

description:
Biological replicate 1 of 3 for 6 h control
1--6C_6822 14955 Top April 12 2011fc

value: Intermoult

value: male

value: Hepatopancreas

value: standard reference pooled sample

value: hepatopancreas


title: Cortex_H

description: cortex Human Tiling 1.0R chip H

source_name: pooled Human cortex total RNA

value: cortex

value: caucasian


title: Merkel cell carcinoma tumor 25

description: formalin-fixed paraffin-embedded tissue

value: dead


title: Merkel cell carcinoma tumor 17

description: formalin-fixed paraffin-embedded tissue


title: Colon_H

description: colon Human Tiling 1.0R chip H

source_name: pooled Human colon total RNA

value: colon


title: 100µM VX 6hr neuron replicate 2


title: Cerebellum_H

description: cerebellum Human Tiling 1.0R chip H

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: Merkel cell carcinoma tumor 13

description: formalin-fixed paraffin-embedded tissue

value: tumor biopsy


title: Merkel cell carcinoma tumor 3b

description: formalin-fixed paraffin-embedded tissue

value: Merkel Cell Carcinoma (MCC)


title: Merkel cell carcinoma tumor 3a

description: formalin-fixed paraffin-embedded tissue

value: died of disease


title: 100µM VX 6hr neuron replicate 1

value: iPSC-deived Neuron


title: Sham-24h-Rep 2

description:
Replicate 2
5038770021_H

value: Wistar

value: Male

value: Sham


title: Treatment-8h-Rep 3

description:
Replicate 3
5038770029_E

value: Treatment


title: Treatment-24h-Rep 1

description:
Replicate 1
5038770021_K


title: Merkel cell carcinoma tumor 12

description: formalin-fixed paraffin-embedded tissue


title: BoneMarrow_H

description: bone marrow Human Tiling 1.0R chip H

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: 0.1µM VX 1hr neuron replicate 2

source_name: Neuron 0.1uM VX treatment for 1hr

value: 0.1µM VX


title: 0.1µM VX 6hr neuron replicate 3

source_name: Neuron 0.1uM VX treatment for 6hr


title: Treatment-24h-Rep 2

description:
Replicate 2
5038770021_L

source_name: Right cortex


title: SHSY5Y_J

description: SH-SY5Y cells Human Tiling 1.0R chip J

source_name: pooled Human SH-SY5Y cells total RNA

tag: cell line


title: 100µM VX 1hr neuron replicate 2

source_name: Neuron 100uM VX treatment for 1hr

value: 100µM VX


title: 100µM VX 1hr neuron replicate 3


title: Treatment-8h-Rep 4

description:
Replicate 4
5038770029_F


title: Vehicle-24h-Rep 1

description:
Replicate 3
5038770021_I

value: Vehicle


title: 0.1µM VX 6hr neuron replicate 1


title: HeLa_J

description: HeLa cells Human Tiling 1.0R chip J

source_name: Human HeLa cells total RNA

value: HeLa


title: 100µM VX 6hr neuron replicate 4


title: 0.1µM VX 1hr neuron replicate 1


title: 0.1µM VX 6hr neuron replicate 4


title: Vehicle-8h-Rep 3

description:
Replicate 1
5038770029_C


title: Merkel cell carcinoma tumor 2b

description: formalin-fixed paraffin-embedded tissue


title: Treatment-8h-Rep 2

description:
Replicate 2
5038770021_F


title: Uterus_J

description: uterus Human Tiling 1.0R chip J

source_name: pooled Human uterus total RNA

value: uterus

value: caucasian


title: Sham-24h-Rep 1

description:
Replicate 1
5038770021_G


title: Sham-24h-Rep 3

description:
Replicate 3
5038770029_G


title: Merkel cell carcinoma tumor 2a

description: formalin-fixed paraffin-embedded tissue


title: Sham-8h-Rep 4

description:
Replicate 4
5038770029_B


title: Vehicle-8h-Rep 2

description:
Replicate 4
5038770021_D


title: Trachea_J

description: trachea Human Tiling 1.0R chip J

source_name: pooled Human trachea total RNA

value: trachea


title: Vehicle-24h-Rep 2

description:
Replicate 4
5038770021_J


title: 0.1µM VX 1hr neuron replicate 4


title: Merkel cell carcinoma tumor 8

description: formalin-fixed paraffin-embedded tissue

value: not available


title: 100µM VX 1hr neuron replicate 1


title: 0.1µM VX 1hr neuron replicate 3


title: Thymus_J

description: thymus Human Tiling 1.0R chip J

source_name: pooled Human thymus total RNA

value: thymus


title: Vehicle-8h-Rep 4

description:
Replicate 2
5038770029_D


title: 0µM VX 6hr neuron replicate 3

source_name: Neuron saline treatment for 6hr

value: 0µM VX


title: Testes_J

description: testes Human Tiling 1.0R chip J

source_name: pooled Human testes total RNA

value: testes


title: Treatment-8h-Rep 1

description:
Replicate 1
5038770021_E


title: Thyroid_J

description: thyroid Human Tiling 1.0R chip J

source_name: pooled Human thyroid total RNA

value: thyroid


title: 100µM VX 1hr neuron replicate 4

value: iPSC-deived Neuron


title: Merkel cell carcinoma tumor 1a

description: formalin-fixed paraffin-embedded tissue

source_name: Tumor Biopsies from Merkel Cell Carcinoma specimens

value: tumor biopsy

value: Merkel Cell Carcinoma (MCC)

value: dead


title: Vehicle-8h-Rep 1

description:
Replicate 3
5038770021_C

value: Wistar

value: Male


title: Merkel cell carcinoma tumor 1b

description: formalin-fixed paraffin-embedded tissue


title: Stomach_J

description: stomach Human Tiling 1.0R chip J

source_name: pooled Human stomach total RNA

value: stomach


title: Sham-8h-Rep 3

description:
Replicate 3
5038770029_A

value: Sham


title: 0.1µM VX 6hr neuron replicate 2

value: 0.1µM VX


title: 0µM VX 6hr neuron replicate 4


title: Sham-8h-Rep 2

description:
Replicate 2
5038770021_B


title: Spleen_J

description: spleen Human Tiling 1.0R chip J

source_name: pooled Human spleen total RNA

value: spleen


title: 0µM VX 6hr neuron replicate 2


title: 0µM VX 1hr neuron replicate 4

source_name: Neuron saline treatment for 1hr


title: Sham-8h-Rep 1

description:
Replicate 1
5038770021_A


title: SpinalCord_J

description: spinal cord Human Tiling 1.0R chip J

source_name: pooled Human spinal cord total RNA

value: spinal cord

value: caucasian


title: SmallIntestine_J

description: small intestine Human Tiling 1.0R chip J

source_name: pooled Human small intestine total RNA

value: small intestine


title: SkeletalMuscle_J

description: skeletal muscle Human Tiling 1.0R chip J

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: SalivaryGland_J

description: salivary gland Human Tiling 1.0R chip J

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: 0µM VX 6hr neuron replicate 1

value: 0µM VX


title: Prostate_J

description: prostate Human Tiling 1.0R chip J

source_name: pooled Human prostate total RNA

value: prostate


title: 100µM GD 6hr neuron replicate 3

source_name: Neuron 100uM GD treatment for 6hr

treatment_protocol: One week after plating, cells were treated with GD or saline control

value: iPSC-deived Neuron

value: 100µM GD


title: RNA-DHL4-R406-48H-3

city: Boston

first: Stefano

last: Monti

state: MA

address: 72 East Concord st. E-613B

institute: Boston University

description:
DHL4.R406.48h.c
DHL4 DLBCL cell line treated with R406 for 48h.

hyb_protocol: According to the manufacturer's protocol.

data_processing: The raw .CEL files were converted into probeset-specific expression values using the RMA summarization method as implemented in the BioConductor package 'affy' (Gentleman et al. 2004).

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

extract_protocol: Cell samples were homogenized in Trizol and RNA was extracted according to standard protocols.

treatment_protocol: DLBCL cell lines were grown in RPMI 1640 with 10% fetal calf serum and 2mM glutamine with R406 (1 micromolar) or  vehicle (DMSO) alone.

value: diffuse large B-cell lymphoma cells

tag: treatment duration


title: RNA-DHL6-R406-48H-3

description:
DHL6.R406.48h.c
DHL6 DLBCL cell line treated with R406 for 48h.

scan_protocol: According to the manufacturer's protocol.


title: RNA-DHL4-R406-48H-2

description:
DHL4.R406.48h.b
DHL4 DLBCL cell line treated with R406 for 48h.


title: 0µM VX 1hr neuron replicate 3


title: adult Hippocampus litter 1 Sumo2tg, biol. repl. 3

city: Munich

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

description: mRNA expression of adult hippocampus

hyb_protocol: According to standard settings given by the manufacturer (Affymetrix)

data_processing: CEL files were normalized applying the RMA altgorithm and analyzed with ANOVA for expression differences using the Genomics Suite (Partek)

source_name: adult hippocampus isolated at ZT4-17

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip®Whole Transcript (WT) Sense Target Labeling AssayP/N 701880 Rev. 5, Affymetrix).

growth_protocol: standard group housing until adulthood

extract_protocol: TRIZOL purification followed by RNAeasy column cleanup

treatment_protocol: no treatment applied

value: Hippocampus

tag: age

value: 8-12 weeks

tag: genotype

value: SUMO2 transgenic

tag: litter


title: 0µM VX 1hr neuron replicate 1

tag: cell type


title: RNA-DHL6-R406-48H-2

description:
DHL6.R406.48h.b
DHL6 DLBCL cell line treated with R406 for 48h.


title: 100µM GD 6hr neuron replicate 4


title: 0µM VX 1hr neuron replicate 2


title: 2 weeks after CBDL

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

description: CD31-positive pulmonary vascular endothelial cells at 2 weeks after CBDL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99°for 5 minutes, then 42°for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45°at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The robust multichip average (RMA) method was used background correction and normalization.
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na33.2.mm9.transcript.csv

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

growth_protocol: CD31-positive pulmonary vascular endothelial cells were obtaind at 2 and 3 weeks after surgery.

extract_protocol: Homogenized whole lungs were treated using a solution of type-1 collagenase (400 U/ml). CD31-positive cells, including pulmonary vascular endothelial cells, were collected with magnetic beads coated with anti-CD31 antibodies. The cellular digest was then filtered through sterile, 40-μm mesh and washed three times in 10% FBS-DMEM. One ml of the cell suspension was placed in a tube with the magnetic beads/CD31-antibody complex, and rotated for 20 min at 4℃. The bead-bound cells were then washed five times with 10% FBS-DMEM and the isolated cells were used in total RNA extraction by ISOGEN II.

treatment_protocol: not applicable

value: 8 weeks

value: Lung

value: Balb/c


title: RNA-DHL6-R406-48H-1

description:
DHL6.R406.48h.a
DHL6 DLBCL cell line treated with R406 for 48h.


title: Pancreas_J

description: pancreas Human Tiling 1.0R chip J

source_name: pooled Human pancreas total RNA

value: pancreas


title: adult Hippocampus litter 2 wt, biol. repl. 2

description: mRNA expression of adult hippocampus

scan_protocol: According to standard settings given by the manufacturer (Affymetrix)

source_name: adult hippocampus isolated at ZT4-13

value: wild type


title: 100µM GD 6hr neuron replicate 2


title: RNA-DHL6-R406-24H-2

description:
DHL6.R406.24h.b
DHL6 DLBCL cell line treated with R406 for 24h.


title: 100µM GD 6hr neuron replicate 1


title: 100µM GD 1hr neuron replicate 3

source_name: Neuron 100uM GD treatment for 1hr


title: 100µM GD 1hr neuron replicate 4


title: Lung_J

description: lung Human Tiling 1.0R chip J

source_name: pooled Human lung total RNA

value: lung

value: caucasian


title: adult Hippocampus litter 1 Sumo2tg, biol. repl. 1

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-15


title: adult Hippocampus litter 1 Sumo2tg, biol. repl. 2

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-16


title: 3 weeks after CBDL

description: CD31-positive pulmonary vascular endothelial cells at 3 weeks after CBDL


title: Liver_J

description: liver Human Tiling 1.0R chip J

source_name: pooled Human liver total RNA

value: liver


title: adult Hippocampus litter 2 wt, biol. repl. 3

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-14


title: Kidney_J

description: kidney Human Tiling 1.0R chip J

source_name: pooled Human kidney total RNA

value: kidney


title: 100µM GD 1hr neuron replicate 2


title: 2 weeks after sham operation

description: CD31-positive pulmonary vascular endothelial cells at 2 weeks after sham operation


title: Heart_J

description: heart Human Tiling 1.0R chip J

source_name: pooled Human heart total RNA

value: heart


title: RNA-DHL6-R406-24H-3

description:
DHL6.R406.24h.c
DHL6 DLBCL cell line treated with R406 for 24h.


title: adult Hippocampus litter 1 Sumo1tg, biol. repl. 3

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-11

value: SUMO1 transgenic


title: FetalBrain_J

description: fetal brain Human Tiling 1.0R chip J

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: RNA-DHL4-R406-48H-1

description:
DHL4.R406.48h.a
DHL4 DLBCL cell line treated with R406 for 48h.


title: Cortex_J

description: cortex Human Tiling 1.0R chip J

source_name: pooled Human cortex total RNA

value: cortex


title: 100µM GD 1hr neuron replicate 1

value: iPSC-deived Neuron

value: 100µM GD


title: RNA-DHL6-R406-24H-1

description:
DHL6.R406.24h.a
DHL6 DLBCL cell line treated with R406 for 24h.

value: diffuse large B-cell lymphoma cells


title: RNA-DHL4-R406-24H-3

description:
DHL4.R406.24h.c
DHL4 DLBCL cell line treated with R406 for 24h.


title: RNA-DHL4-R406-24H-2

description:
DHL4.R406.24h.b
DHL4 DLBCL cell line treated with R406 for 24h.


title: adult Hippocampus litter 2 wt, biol. repl. 1

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-12

value: Hippocampus

value: 8-12 weeks


title: Colon_J

description: colon Human Tiling 1.0R chip J

source_name: pooled Human colon total RNA

value: colon


title: 0.1µM GD 6hr neuron replicate 4

description: Cells maintained in humidified incubator at 37 degres C during treatment

source_name: Neuron 0.1uM GD treatment for 6hr

value: 0.1µM GD


title: Cerebellum_J

description: cerebellum Human Tiling 1.0R chip J

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: 0.1µM GD 6hr neuron replicate 2


title: adult Hippocampus litter 1 Sumo1tg, biol. repl. 1

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-9


title: adult Hippocampus litter 1 wt, biol. repl. 2

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-7

value: wild type


title: 0.1µM GD 6hr neuron replicate 3


title: adult Hippocampus litter 1 Sumo1tg, biol. repl. 2

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-10


title: RNA-DHL4-R406-24H-1

description:
DHL4.R406.24h.a
DHL4 DLBCL cell line treated with R406 for 24h.


title: RNA-DHL4-R406-6H-3

description:
DHL4.R406.6h.c
DHL4 DLBCL cell line treated with R406 for 6h.


title: adult Hippocampus litter 1 wt, biol. repl. 3

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-8


title: SHSY5Y_I

description: SH-SY5Y cells Human Tiling 1.0R chip I

source_name: pooled Human SH-SY5Y cells total RNA


title: RNA-DHL4-R406-6H-2

description:
DHL4.R406.6h.b
DHL4 DLBCL cell line treated with R406 for 6h.


title: RNA-DHL6-R406-6H-3

description:
DHL6.R406.6h.c
DHL6 DLBCL cell line treated with R406 for 6h.


title: 0.1µM GD 1hr neuron replicate 4

source_name: Neuron 0.1uM GD treatment for 1hr


title: 0.1µM GD 6hr neuron replicate 1


title: adult Hippocampus litter 1 wt, biol. repl. 1

description: mRNA expression of adult hippocampus

source_name: adult hippocampus isolated at ZT4-6


title: RNA-DHL6-R406-6H-2

description:
DHL6.R406.6h.b
DHL6 DLBCL cell line treated with R406 for 6h.


title: BoneMarrow_J

description: bone marrow Human Tiling 1.0R chip J

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: HeLa_I

description: HeLa cells Human Tiling 1.0R chip I

source_name: Human HeLa cells total RNA

value: HeLa


title: 0.1µM GD 1hr neuron replicate 3


title: 0.1µM GD 1hr neuron replicate 1


title: 0.1µM GD 1hr neuron replicate 2


title: 0µM GD 6hr neuron replicate 4

source_name: Neuron saline treatment for 6hr

value: 0µM GD


title: Trachea_I

description: trachea Human Tiling 1.0R chip I

source_name: pooled Human trachea total RNA

value: trachea

value: caucasian


title: RNA-DHL6-R406-2H-2

description:
DHL6.R406.2h.b
DHL6 DLBCL cell line treated with R406 for 2h.


title: Thyroid_I

description: thyroid Human Tiling 1.0R chip I

source_name: pooled Human thyroid total RNA

value: thyroid


title: RNA-DHL6-R406-6H-1

description:
DHL6.R406.6h.a
DHL6 DLBCL cell line treated with R406 for 6h.


title: 0µM GD 6hr neuron replicate 2


title: Thymus_I

description: thymus Human Tiling 1.0R chip I

source_name: pooled Human thymus total RNA

value: thymus


title: RNA-DHL6-R406-2H-3

description:
DHL6.R406.2h.c
DHL6 DLBCL cell line treated with R406 for 2h.


title: 0µM GD 6hr neuron replicate 3


title: RNA-DHL4-R406-6H-1

description:
DHL4.R406.6h.a
DHL4 DLBCL cell line treated with R406 for 6h.


title: lymph nodes sorted FRCs rep2

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

description: gene expression data from FRCs

hyb_protocol: Following fragmentation and end-labeling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix).The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2. CEL files were further processed with affy Bioconductor package (release 2.9) to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithm with default settings.

source_name: lymph nodes sorted FRCs

label_protocol: Biotinylated double strand cDNA targets were prepared, starting from 0.3 to 3 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) and the NuGEN Encore Biotin Module Kit (Cat # 4200) according to NuGEN recommendations.

growth_protocol: Lymphoid stromal cells were sorted as following: VSCs as CD45-CD21-CD31-Podoplanin+RFP+ and FRCs as CD45-CD21-CD31-Podoplanin+RFP-.

extract_protocol: Total RNA was extracted from sorted stromal cells using column‐based system RNAeasy micro kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: Pooled Lymph Nodes from chimeric double transgenic Cd21crexRosaRFP mice were digested at 37°C in a digestion buffer (DMEM, 10 mM HEPES, penicillin/streptomycin,1.2 mM CaCl2, 2% FCS) containing 1 mg/ml collagenase IV  and 10 mg/ml DNase I for 30min. Aggregates were further digested (15 min) in a digestion buffer containing 3 mg/ml collagenase D  and 10 mg/ml DNase I. EDTA was added to a final concentration of 5mM (pH 7.2) and cells were filtered through a 70 μm cell strainer.

tag: strain background

tag: genotype/variation

value: between 15 to 20 weeks

value: lymph nodes

value: Lymph node (LN) stromal cells

tag: cell subtype

value: FRCs as CD45-CD21-CD31-Podoplanin+RFP-


title: lymph nodes sorted FRCs rep3

description: gene expression data from FRCs

value: chimeric double transgenic Cd21crexRosaRFP


title: lymph nodes sorted VSCs rep3

description: gene expression data from VSCs

source_name: lymph nodes sorted VSCs

value: VSCs as CD45-CD21-CD31-Podoplanin+RFP+


title: RNA-DHL4-R406-2H-3

description:
DHL4.R406.2h.c
DHL4 DLBCL cell line treated with R406 for 2h.

value: diffuse large B-cell lymphoma cells


title: lymph nodes sorted FRCs rep1

description: gene expression data from FRCs


title: 0µM GD 1hr neuron replicate 3

source_name: Neuron saline treatment for 1hr

value: iPSC-deived Neuron

tag: time


title: lymph nodes sorted VSCs rep1

description: gene expression data from VSCs


title: Testes_I

description: testes Human Tiling 1.0R chip I

source_name: pooled Human testes total RNA

value: testes


title: Stomach_I

description: stomach Human Tiling 1.0R chip I

source_name: pooled Human stomach total RNA

value: stomach


title: RNA-DHL6-R406-2H-1

description:
DHL6.R406.2h.a
DHL6 DLBCL cell line treated with R406 for 2h.


title: WT6

city: BETHESDA

first: Scott

last: Canna

department: MIIB

institute: NIAMS

hyb_protocol: As suggested in the NuGen labeling protocol, we used 80uL of hybridization cocktail at a concentration of 23-27 ng/uL of labeled cDNA, hybridized at 45degrees C for 40 hours. Chips were washed on an Affymetrix 450 was station using fluidics protocol FS450-00007.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G

data_processing: Affymetrix Expression Console software (v.1.1) was used to perform quality control, which resulted in the exclusion of two chips from each group, leaving four biological replicates in each group for analysis. Microarrays were preprocessed using robust multiarray analysis [PMID 12925520]. Probe sets lacking gene symbol annotation or with a mean log2 intensity less than five among HPC samples were filtered out. This left 21861 probe sets for analysis out of 29010. Log2 transformed expression data were analyzed using the R statistical computing language Differentially expressed genes (DEGs) were defined as those with at least 1.5-fold difference in expression in HPCs as compared to resting macrophages. DEGs were tested for statistical significance using Student’s t test with multiple testing correction using false discovery rate (FDR)

label: Biotin

source_name: resting macrophages

label_protocol: We used the NuGen Encore Biotin Module according to manufacturer's specifications

growth_protocol: specific pathogen-free conditions, water and standard chow ad libitum

extract_protocol: Spleens were touched to a PEN-coated, RNAse-free slide and 20 target cells/mouse (resting macrophages from PBS-treated mice or HPCs from CpG/1B1.3a-treated mice) were isolated and pooled by laser capture microdissection.  RNA was isolated by WT-Ovation One-Direct Amplification System (NuGen systems) according to manufacturer's instructions

treatment_protocol: 200 uL PBS IP every other day for 4 doses, or 37.5 ug CpG1826 + 200ug antibody clone 1B1.3A IP every other day for 4 doses.

value: wild type

tag: gender

value: male

value: 8 wks

tag: treated with

value: resting splenic macrophages


title: Spleen_I

description: spleen Human Tiling 1.0R chip I

source_name: pooled Human spleen total RNA

value: spleen

value: caucasian


title: RNA-DHL4-R406-2H-2

description:
DHL4.R406.2h.b
DHL4 DLBCL cell line treated with R406 for 2h.


title: WT5

value: 200 uL PBS IP every other day for 4 doses


title: 0µM GD 6hr neuron replicate 1

value: 0µM GD


title: 0µM GD 1hr neuron replicate 4


title: lymph nodes sorted VSCs rep2

description: gene expression data from VSCs

value: between 15 to 20 weeks

value: lymph nodes


title: 0µM GD 1hr neuron replicate 2


title: 0µM GD 1hr neuron replicate 1


title: SmallIntestine_I

description: small intestine Human Tiling 1.0R chip I

source_name: pooled Human small intestine total RNA

value: small intestine


title: WT3


title: WT4


title: SkeletalMuscle_I

description: skeletal muscle Human Tiling 1.0R chip I

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: SalivaryGland_I

description: salivary gland Human Tiling 1.0R chip I

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: SpinalCord_I

description: spinal cord Human Tiling 1.0R chip I

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: RNA-DHL4-DMSO-2

description:
DHL4.b
DHL4 DLBCL cell line treated with vehicle (DMSO) alone.

source_name: DHL4, DMSO

value: diffuse large B-cell lymphoma cells

value: DMSO


title: RNA-DHL6-DMSO-3

description:
DHL6.c
DHL6 DLBCL cell line treated with vehicle (DMSO) alone.

source_name: DHL6, DMSO


title: RNA-DHL6-DMSO-2

description:
DHL6.b
DHL6 DLBCL cell line treated with vehicle (DMSO) alone.


title: RNA-DHL6-DMSO-1

description:
DHL6.a
DHL6 DLBCL cell line treated with vehicle (DMSO) alone.


title: Prostate_I

description: prostate Human Tiling 1.0R chip I

source_name: pooled Human prostate total RNA

value: prostate


title: RNA-DHL4-R406-2H-1

description:
DHL4.R406.2h.a
DHL4 DLBCL cell line treated with R406 for 2h.


title: Pancreas_I

description: pancreas Human Tiling 1.0R chip I

source_name: pooled Human pancreas total RNA

value: pancreas


title: wild type 5 day-rep3

city: Hangzhou

first: haichun

last: gao

address: 388 Yuhangtang Rd.

country: China

institute: Zhejiang University

description: Biological replicate 3 of 3

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

organism: Shewanella oneidensis

source_name: 5 day cells

growth_protocol: Grow in M1 for 24 h and then transfer 1% to fresh M1 media for 24 h. Repeat 5 times

treatment_protocol: A library of mutants were inoculated

value: Wild type

value: 5 day

source_name: 0 day cells

value: 0 day


title: Lung_I

description: lung Human Tiling 1.0R chip I

source_name: pooled Human lung total RNA

value: lung


title: CpG6

source_name: hemophagocytes

value: wild type

value: male

value: 8 wks

value: 37.5 ug CpG1826 + 200ug antibody clone 1B1.3A IP every other day for 4 doses

value: hemophagocytes (HPCs)


title: CpG3


title: 100µM VX 6hr cardiomyocyte replicate 1

description: Cells maintained in humidified incubator at 37 degres C during treatment

source_name: Cardiomyocyte 100uM VX treatment for 6hr

growth_protocol: iPSC-derived cardiomyocytes (Cellular Dynamics, WI) were seeded at a density of 1.0 X10E6 per well in 6-well plates and maintained according to manufucturer's specifications

treatment_protocol: One week after plating cells were treated with VX  or saline control

value: iPSC-deived Cardiomyocyte

value: 100µM VX


title: Liver_I

description: liver Human Tiling 1.0R chip I

source_name: pooled Human liver total RNA

value: liver

value: caucasian


title: CpG5


title: Male 8weekBL6 shamrep2

city: Baltimore

first: Susan

middle: G

last: Dorsey

address: 655 West Lombard Street

department: School of Nursing

institute: University of Maryland Baltimore

description: Gene expression data from jejunum

hyb_protocol: 10ug of cRNA were hybridized for 16 hours at 45degrees on Mouse Gene 1.0 ST Arrays.

scan_protocol: Scanned on an Affymetrix scanner.

data_processing: The data were normalized by Affymetrix Expression Console using RMA method.

label_protocol: Biotinylated cRNA was prepared per standard Affymetrix protocol from 1ug total RNA.

growth_protocol: 7 days following CBDL or sham surgery, the animals were euthanized and the jejunum was harvested under sterile conditions.

extract_protocol: Trizol extraction of total RNA performed per manufacturer instructions.

treatment_protocol: Either CBDL surgery or sham surgery.

tag: strain/background

value: jejunum

value: 8 weeks

value: sham surgery


title: 100µM VX 6hr cardiomyocyte replicate 3


title: 100µM VX 6hr cardiomyocyte replicate 4


title: 100µM VX 6hr cardiomyocyte replicate 2


title: wild type 1 day-rep2

description: Biological replicate 2 of 3

source_name: 1 day cells

value: 1 day


title: wild type 1 day-rep3

description: Biological replicate 3 of 3

value: Wild type


title: CpG2


title: Male 8weekBL6 shamrep1

description: Gene expression data from jejunum

tag: tissue


title: wild type 5 day-rep1

description: Biological replicate 1 of 3

value: 5 day


title: 100µM VX 1hr cardiomyocyte replicate 3

source_name: Cardiomyocyte 100uM VX treatment for 1hr


title: 100µM VX 1hr cardiomyocyte replicate 2


title: wild type 5 day-rep2

description: Biological replicate 2 of 3

value: 0 day


title: 100µM VX 1hr cardiomyocyte replicate 4


title: Male 8weekBL6 shamrep3

description: Gene expression data from jejunum


title: RNA-DHL4-DMSO-1

description:
DHL4.a
DHL4 DLBCL cell line treated with vehicle (DMSO) alone.

value: diffuse large B-cell lymphoma cells

value: DMSO


title: Male 8week AJ CBDLrep2

description: Gene expression data from jejunum

source_name: AJCBDL

value: A/J

value: male

value: cholestatic intestinal injury


title: Kidney_I

description: kidney Human Tiling 1.0R chip I

source_name: pooled Human kidney total RNA

value: kidney

tag: race


title: Male 8week AJ CBDLrep3

description: Gene expression data from jejunum


title: Heart_I

description: heart Human Tiling 1.0R chip I

source_name: pooled Human heart total RNA

value: heart


title: FetalBrain_I

description: fetal brain Human Tiling 1.0R chip I

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: Cortex_I

description: cortex Human Tiling 1.0R chip I

source_name: pooled Human cortex total RNA

value: cortex


title: Male 8week AJ CBDLrep1

description: Gene expression data from jejunum


title: Colon_I

description: colon Human Tiling 1.0R chip I

source_name: pooled Human colon total RNA

value: colon

value: caucasian


title: wild type 1 day-rep1

description: Biological replicate 1 of 3

tag: strain


title: Cerebellum_I

description: cerebellum Human Tiling 1.0R chip I

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: Male 8week AJ sham rep2

description: Gene expression data from jejunum

source_name: AJSHAM

value: jejunum

value: 8 weeks

tag: treatment

value: sham surgery


title: BoneMarrow_I

description: bone marrow Human Tiling 1.0R chip I

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: MLN3

city: Barcelona

first: Alba

last: Dalmases

address: Dr.Aiguader 88

institute: IMIM

description: Gene expression data from MDA-MB-231 breast cancer cell line

hyb_protocol: Sample was hybridized to Affymetrix Human Exon 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from MDA-MB-231 breast cancer cell line

label_protocol: 100ng of total RNA from each sample, isolated from MDA-MB-231 breast cancer cells under different experimental conditions was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

extract_protocol: RNA was extracted following Qiagen protocol

value: MLN

tag: cell line


title: 0.1µM VX 6hr cardiomyocyte replicate 3

source_name: Cardiomyocyte 0.1uM VX treatment for 6hr

value: iPSC-deived Cardiomyocyte

value: 0.1µM VX