title: mALK2-iPSCs-2

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent-026652 Human Whole Genome 44K, Agilent Technologies) containing approximately 44,000 probes (~26,600 unique genes) in accordance with the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner. The raw signal intensities were extracted from the arrays using Agilent Feature Extraction Software (Agilent Technologies).

data_processing: Only those array elements with signal intensities 1.4-fold higher than the local background were selected and normalized using the quantile method in R. The ratios from duplicated spots were averaged.

label_protocol: The pooled RNA was amplified and labeled using Agilent’s Low RNA Input Linear Amplification kit PLUS (Agilent Technologies, USA).

extract_protocol: Total RNA was prepared using the Easy-SpinTM total RNA extraction kit (iNtRON Biotechnology, Seoul, Republic of Korea) following the manufacturer’s instructions. RNA quality was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only samples with an RNA integrity number (RIN) greater than 7.0 were included in the microarray analysis. RNAs from triplicate experiments were pooled to exclude experimental bias.

tag: originating cell line

value: ALK2 R206H-human dermal fibroblasts (GM00513)

tag: cell type

value: ACVR1 p.R206H mutation


title: cALK2-iPSCs-1

status: Public on May 12 2015

type: RNA

description: Gene-corrected ALK2-iPSCs

molecule: total RNA

organism: Homo sapiens

tag: genotype/variation

value: gene corrected


title: CHL-742

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

country: USA

institute: Baylor Institute for Immunology Research

hyb_protocol: Hybridize Hu-6 V3

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analysed using BeadStudio version 1.5.1.3 using the average chip normalization method.

label: biotin

source_name: Pediatric influenza patient

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions.

tag: disease status

value: FLU

tag: race

value: Other

tag: age

tag: gender

value: Female

tag: tissue

value: Whole Blood


title: CHL-731

value: Black

value: Male


title: TICNX_48h_rep3

city: Philadelphia

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

hyb_protocol: Affymetrix Generic Hybridization

scan_protocol: Arrays were scanned using the Affymetrix GeneArray Scanner

data_processing: RMA

label: Biotin

organism: Mus musculus

source_name: TICNX inguinal mammary gland

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

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

treatment_protocol: 48h or 96h induction with 2mg/mL doxycycline + 5% sucrose starting at 6 weeks of age

tag: strain

value: FVB

value: 6 weeks

value: Mammary gland

tag: genotype

value: TetO-NICD1 (control)

tag: treatment

value: Doxycycline

tag: time


title: abHtz1vsabH2B_WTyFR117_rep2

type: genomic

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description: Biological replicate 2 of 2. H2A.Z occupancy in WT (S288C) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

hyb_protocol: Hybridization: Resuspend colored pellet in 110uL hybridization buffer (100uL DIGEasy Buffer, 5uL 10mg/mL Salmon Sperm DNA, 5uL 8mg/mL yeast tRNA). Put at 95°C for 5 minutes. Put at 42°C for 10 min (Keep samples at 42°C while waiting for hybridization). Follow standard Agilent chamber hybridization protocols. Incubate overnight (16-24h) at 42°C in Agilent hybridization oven at 20 rpm rotation speed.Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash slides in Wash buffer #2 preheated at 31°C for 5 minutes at room temperature on an orbital shaker. Take slides out of the buffer slowly to dry them. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE. Stripping: Stripping is done in 1L of 5 mM Potassium phosphate buffer pH 6.6 after scanning of the slides. 1. Use a crystallization dish, and a metallic slide rack (use weighing spatulas to lift the rack from the bottom of the dish and avoid direct contact with the hot surface). Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly on heating plate until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 5 ml of this 1M solution in 1L Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Standard_Innopsys_Yeast4x180. Set the scan as follow: Pixel Size = 2µm; Speed = 20; Scan Mode = Normal; Acquisition Mode = Simultaneous; Focus = Auto.  Adjust manually the detection gain for 635 and 532 wavelengths in order to have less than 5% spot saturation.

data_processing: Correction = Foreground-Background; Normalisation = limma loess (subgrid)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly.Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice. Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C.    Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.    Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O).  PCR cycling conditions:  1) 5:00 at 55C  2) 5:00 at 72C  3) 2:00 at 95C  4) 0:30 at 95C  5) 0:30 at 55C  6) 1:00 at 72C  7) Repeat steps 4-6 31 more times.  8) 4:00 at 72C  9) Forever at 4C    Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness.    Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour.    Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to dryness.      Phosphate Wash Buffer (100mL):  0.5mL 1M KPO4, pH 8.5  15.25mL ddH2O  84.25mL 95% EtOH  Solution will be cloudy upon mixing.    Phosphate Elution Buffer (10mL):  0.04mL 1M KPO4, pH 8.5  9.96mL ddH2O    1M KPO4, pH 8.5 (10mL):  9.5mL 1M K2HPO4  0.5mL 1M KH2PO4    1M Sodium Carbonate Buffer, pH 9.0 (100mL):  10.8g Na2CO3  80mL ddH2O  pH to 9.0 with concentrated HCl  Adjust volume to 100mL with ddH2O  DILUTE 1:10 WHEN USING!  Solution will change composition over time. Use only if less than a month old.

growth_protocol: Standard_YEPD_50mL. 50mL of YEP+2% Glucose is inoculated at OD600= 0.1 from an overnight preculture in the appropriate media and allowed to grow until it reach OD600= 0.6-1.0. Culture is poured in 50mL Falcon tube containing 1.4mL 37% formaldehyde for crosslinking, and incubate on rotating wheel for 30 min. Crosslinking is stopped by addition of 2.5mL 2.5M Glycine to quench formaldehyde (optional). Crosslinked cells are pelleted at 4'C, 3000 rpm, resuspended in 40mL ice cold TBS and pelleted again. This wash is repeated a second time. Cell pellets are resuspended in the remaining liquid (~1mL) and transfered to 1.5mL screw cap tubes. Cells are pelleted by centrifugation, the supernatant removed by pipetting, and the cells pellet snap-freeze in liquid nitrogen and stock at -80'C.

extract_protocol:
Cells are thawed on ice, and resuspended in 700uL lysis buffer with protease inhibitors (solution composition detailed at the end). 500uL of acid-washed glass beads (Sigma) are added, and the cells are lysed using the bead-beater (4x5min cycles, with 5min breaks on ice). The tubes are pierced with a 18-gauge syringe needle to allow transfer of lysate, but not beads. The pierced tubes are put in 2mL collection tubes and spun briefly. The lysate is then homogenized by pipetting and sonicated 4x 20sec at output 7 Watts, with a 1 minute break between sonication cycles. The sonicated lysates is centrifuge for 5 min at 4'C max speed and supernatant used immediately for ChIP (or saved and frozen at -80'C). Lysis buffer: 50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL Pepstatin.
The following amounts of antibody per immunoprecipitation were used: HA (Santa Cruz, F7, 3µg), Myc (9E11, a gift from A. Verreault, 5μg), H2A.Z (Active Motif, 39647, 2µL), H2B (Abcam, ab1790, 5µg), H4 (a gift from A. Verreault, 2µl), Spt16 (a gift from T. Formosa, 1μL), FRB (mTor, human FRB domain from Enzo Life Sciences, ALX-215-065, 5μL), rabbit IgG (Cell Signaling Technology, 2729, 5µg). All comercial antibodies have been validated for ChIP (see manufacturers’ web sites). The Myc, H4 and Spt16 antibodies have been described before (Drouin et al., 2010; Duina et al., 2007).

tag: spike dna

tag: antibody

value: Htz1 (Active Motif_39647)

value: H2B (Abcam ab1790)


title: abHtz1vsabH2B_WTyFR116_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in WT (W303) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: mALK2-iPSCs-1


title: abHtz1vsabH2B_WTyFR117_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT (S288C) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: TICNX_48h_rep4


title: TICNX_48h_rep2


title: abHtz1vsabH2B_snf2DyFR283_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in snf2D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATa, his3^1, leu2^0, met15^0, ura3^0, snf2::KanMx4


title: CHL-749

value: White


title: abHtz1vsabH2B_rsc7DyFR932_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in rsc7D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: Lowcount3

city: Petach Tikva

first: Uri

last: Rozovski

address: Jabotinsky

department: Leukemia

country: Israel

institute: Beilinson

hyb_protocol: Hybridization was performed with Human Gene 2.0 ST arrays (Affymetrix, Inc, Santa Clara, CA) according to the manufacturer’s instructions. Briefly, 100 ng of total RNA from each sample was reverse transcribed to cDNA, followed by overnight in vitro transcription to generate cRNA, which was also reverse transcribed. The quality of cDNA and fragmented cDNA was assessed using an Agilent Bioanalyzer system. Microarrays were hybridized, washed, stained, and images were scanned using the Affymetrix GeneChip Command Console and analyzed with the Affymetrix Expression Console.

scan_protocol: standard Affymetrix protocol

data_processing:
RMA
The t-test with Welch correction (variance not assumed equal) was used to compare gene expression levels and the analysis was done using Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO). Network analysis was performed on 1001 genes whose levels were upregulated (P <0.01 in samples with at least a 1.5-fold increase in lymphocyte counts) using the Ingenuity pathway analysis (Ingenuity Systems, www.ingenuity.com).

source_name: Plasma

label_protocol: standard Affymetrix protocol

growth_protocol: Not relevant

extract_protocol: Total RNA

treatment_protocol: PB cells were fractionated using Ficoll Hypaque 1077 (Sigma, St. Louis, MO). The low-density cellular fraction was used immediately or frozen for additional studies.

value: CLL cells from plasma

tag: phenotype

value: low CLL cell count


title: cALK2-iPSCs-2

description: Gene-corrected ALK2-iPSCs

value: ALK2 R206H-human dermal fibroblasts (GM00513)

value: gene corrected


title: Lowcount4


title: abHtz1vsabH2B_snf2DyFR283_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in snf2D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: CHL-730

value: FLU


title: WT-iPSCs

description: Wild type iPSCs

source_name: WT-iPSCs

value: human foreskin fibroblasts (PC501A-HFF)

value: WT-iPSCs

value: WT


title: EXP-550: TCGA-AV-A03D-20A-01D-A00B-05

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Control Cell Line

tag: disease state

value: NOT SPECIFIED

tag: disease staging

tag: Sex

tag: organism part

tag: sample name


title: TICNX_48h_rep1

value: FVB

value: Female

value: 6 weeks


title: CHL-748

tag: disease status

value: Hispanic

value: Whole Blood


title: EXP-550: TCGA-AG-A032-01A-01D-A00B-05

scan_protocol: See mage-tab files linked to series entry for additional details

source_name: Primary solid_tumor

value: Rectal Adenocarcinoma

value: Stage IIIB

value: MALE

value: rectal

value: Rectum


title: CHL-760

tag: race

value: Male


title: CHL-1035

tag: age


title: CHL-1022

value: White

tag: gender


title: young age (YA; <36 years old) 3

city: Valencia

first: Juan

middle: M

last: Moreno-Moya

address: Catedrático Agustín Escardino

country: Spain

institute: FIVI

description:
each sample was previous tested for miRNAs using Small RNA Labchip in an agilent bioanalyzer
YA3

hyb_protocol: After H2O resuspended, samples were mixed with another Spike, mixed with blocking agent and Hi-RPM hybridization buffer and heated at 100C for 5' and cooled at 4ºC. Then samples were loaded onto gaskets slides and microarrays slides were put on them. Finally Samples were hybridized for 20h at 55C.

scan_protocol: Microarrays slides were washed and scanned in Genepix Personal 4100A Scanner and scanned in Genepix Pro Software with a spot resolution of 5um in the green channel

data_processing: Median intensity value of each spot data was normalized and log2 transformed using R software and libraries from bioconductor database. The intensity values were logarithmically and quartile normalized using R software and the Bioconductor libraries ‘limma’ and ‘tkrplot’. Next, replicated probes were further merged by mean using GEPAS.

source_name: young age_follicular fluid

label_protocol: 100ng of total RNA were mixed with spike and treated with phosphatase for 30' at 37º then cooled at 4C. Next DMSO was added and heated at 100ºC for 7.5' then cooled at 4ºC. Next mixed with Cy3-pCp and T4 RNA Ligase for 2 hours at 16C and cooled at 4ºC. Samples were dried in a vacuum for 3h at 45C. Then H2O added.

extract_protocol: To ensure that miRNA fraction will be recovered we performed RNA extraction using the miRNeasy Kit (Qiagen, Valencia, CA, USA). RNA extracted was quantified using a NanoDrop (Thermo Fisher Scientific Inc, MA, USA) spectrophotometer and the proportion of miRNAs was evaluated using the Small RNA LabChip BioAnalyzer 2100,  (Agilent Technologies Inc, DE, USA)

treatment_protocol:
Ovarian stimulation and egg retrieval: A control ovarian hyperstimulation (COH) protocol with human recombinant FSH (Gonal-F, Merck Serono S.A., Madrid, Spain) and hMG-HP (Menopur, Ferring S.A., Madrid, Spain) was initiated on menstrual cycle day 2 or 3 at a variable dose depending of age, body mass index (BMI) and antral follicular count (AFC). Pituitary suppression was achieved by daily s.c. administration of 0.25 mg of cetrorelix acetate (Cetrotide, Merck Serono, S.A., Madrid, Spain) when at least one follicle exceeded a mean diameter of 14 mm or estradiol was >400pg/mL. Ovulation was triggered by s.c administration of 6500U of hCG (Ovitrelle®, Merk-Serono, S.A., Madrid, Spain). Transvaginal oocyte retrieval was performed 36 hours after hMG trigger administration and ICSI was performed in all cases. Embryo quality was recorded according to ASEBIR criteria [27].  Luteal phase was supported by 400 mg/day of vaginal micronized progesterone (Progeffik, Lab. Effik, Madrid, Spain) starting at the day of embryo transfer. Pregnancy was defined as a positive pregnancy test; clinical pregnancy was defined as intrauterine sac visualization in transvaginal ecography.
Collection of follicular fluid and granulosa cells: Follicular fluid (FF) were collected individually, after independent follicular puncture. FF and cumulus oophorus-oocyte complexes (COC) were subsequently separated after oocyte retrieval. Follicular fluid-derived cells were separated from erythrocytes by density gradient centrifugation on equal v/v of Histopaque (Sigma-Aldrich, St. Louis, USA) for 30min at 600g. Following centrifugation, three layers could be distinguished: a top layer containing the follicular fluid, a bottom layer containing erythrocytes and, in the middle, a ring-like layer containing the cells-derived from the follicular fluid. This middle layer was collected, washed by centrifugation for 10 min at 600g and resuspended in 1-ml phosphate-buffered saline (PBS). We use the cell strainer methodology to separate granulose cells, based on the fact that GCs form large cell aggregates in such a way that clusters can be retained by 40-µm pore cell strainers while erythrocytes and other blood contaminants (such as single cells and aggregates of a smaller size) pass through the strainer. Following the cell strainer methodology but with some modifications [PMID 10831550; 19001513; 22454458] the aspirates were first filtered through a 40-µm cell strainer (BD Biosciences) and the clusters of GCs were retained. The strainer was rinsed with 12-ml PBS in order to remove the last traces of blood contaminants and the strainer was then back washed with PBS to collect the ‘hypothetical’ GCs. The acquired suspension was incubated for several minutes and repeatedly aspirated through Pasteur pipettes stretched to different diameters to break up aggregates mechanically. The suspension was then filtered through a 70-µm cell strainer (BD Biosciences) to remove unwanted undispersed material, which was retained in the filter. The cell suspension, collected after filtering the sample, was subsequently washed by centrifugation for 5min at 600g, after which the supernatant was removed and the pellet was resuspended in 1 ml PBS.

value: young; <36 yrs

tag: oocyte maturation stage

value: metaphase II

tag: tissue

value: follicular fluid


title: Lowcount2

tag: cell type

value: CLL cells from plasma

value: low CLL cell count


title: abHtz1vsabH2B_rsc14DyFR940_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in rsc14D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

tag: strain

tag: genotype/variation

value: Htz1 (Active Motif_39647)

value: H2B (Abcam ab1790)


title: abHtz1vsabH2B_WTyFR116_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in WT (W303) cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

tag: spike dna


title: ACC-921

source_name: healthy control

value: healthy control

value: Female


title: abHtz1vsabH2B_rsc14DyFR940_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in rsc14D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

tag: antibody


title: Highcount3

tag: phenotype

value: high CLL cell count


title: Lowcount1


title: abHtz1vsabH2B_rsc7DyFR932_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in rsc7D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: abHtz1vsabH2B_ino80DyFR933_rep2

description: Biological replicate 2 of 2. H2A.Z occupancy in ino80D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.

value: MATalpha ura3 leu2 trp1 his3 can1 ino80::kanMX4


title: abHtz1vsabH2B_ino80DyFR933_rep1

description: Biological replicate 1 of 2. H2A.Z occupancy in ino80D mutant cells. H2A.Z ChIP sample (Cy5-labeled) was performed using a polyclonal antibody against H2A.Z and hybridized against H2B ChIP sample (Cy3-labeled), also performed on the some extract using a polyclonal antibody anti-H2B.


title: CHL-868

value: Hispanic

value: Whole Blood


title: Highcount2


title: ACC-2005


title: Highcount4


title: CHL-645

value: Black


title: EXP-550: TCGA-AG-A026-01A-01D-A00B-05

data_processing: See mage-tab files linked to series entry for additional details

tag: disease state

value: Rectal Adenocarcinoma

value: [Not Available]

value: MALE

value: rectal

value: Rectum


title: ACC-1108


title: SS2 NHDF cells infected with Borrelia afzeliiburgdorferi sensu stricto

city: Sosnowiec

first: Sławomir

last: Dudek

address: Jagiellonska 4

country: Poland

institute: Medical University of Silesia

hyb_protocol: 15μg of fragmented cRNA were hybridized on HG-U133A microarray (Affymetrix). Hybrydization was performed for 16h at 45°C. Gene chip was washed and stained with use  GeneChip® Fluidics Station 450 - protocol EukGE-WS2v4 .

scan_protocol: Scan was made with use of GeneArray Scanner G2500A (Affymetrix).

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).
Data were normalizated using RMA Express. Fluorescence intensity values of all 22 238 mRNA transcripts for HG-U133A chips were simultaneously normalized using RMA algorithm (log2).

label_protocol: Biotinylated cRNA were prepared according to Affymetrix protocol  from 5-8μg of total RNA (Gene Expression Analysis Technical Manual, Affymertix).

growth_protocol: The bacterial culture was carried out in BSK-H medium (Barbour'a, Stoenner'a, Kelly'ego; Sigma-Aldrich, St. Louis, MO, USA) at 37˚C in microaerophilic conditions. Normal human dermal fibroblasts were routinely maintained in the FBM medium (Fibroblast Basal Medium; Lonza, Basel, Switzerland), supplemented with a human fibroblast growth factor-basic (hFGF-B), insulin and gentamicin (FGMTM SingleQuotsTM; Lonza, Basel, Switzerland).

extract_protocol: Total RNA was extracted with Trizol Reagent according to the manufacturer's instructions.

treatment_protocol: For experiment, NHDF cells were washed with phosphate buffered saline (PBS; Lonza, Basel, Switzerland) and seeded into culture dishes (Nunc, Wiesbaden, Germany). After reaching subconfluence, three genospecies of Borrelia spirochetes: Borrelia afzelii, Borrelia garinii and Borrelia burgdorferi sensu stricto were added to the NHDF cells in a ratio of 10:1 bacteria to fibroblasts. For further analysis, the study and control fibroblasts were harvested after 24 hours.

tag: infection


title: Highcount1


title: ACC-1101

value: Male


title: EXP-550: TCGA-AG-A02X-01A-01D-A00B-05

label_protocol: See mage-tab files linked to series entry for additional details

tag: disease staging

value: Stage I

tag: Sex


title: EXP-550: TCGA-AG-A01J-01A-01D-A00B-05

extract_protocol: See mage-tab files linked to series entry for additional details

value: Stage IIA

value: FEMALE

tag: organism part

tag: sample name


title: SS3 NHDF cells infected with Borrelia afzeliiburgdorferi sensu stricto


title: EXP-550: TCGA-AG-A023-01A-01D-A00B-05


title: EXP-550: TCGA-AG-A02G-01A-01D-A00B-05


title: EXP-550: TCGA-AG-A01N-01A-01D-A00B-05


title: EXP-550: TCGA-AG-A00H-01A-01D-A00B-05


title: EXP-550: TCGA-AG-A025-01A-01D-A00B-05


title: ACC-2003.1

tag: disease status

tag: race


title: SS1 NHDF cells infected with Borrelia afzeliiburgdorferi sensu stricto


title: K3 NHDF cells

source_name: NHDF cells


title: EXP-550: TCGA-AV-A03E-20A-01D-A004-05

value: NOT SPECIFIED

tag: age


title: K2 NHDF cells


title: K1 NHDF cells


title: EXP-550: TCGA-AG-A016-01A-01D-A004-05


title: CHL-1044

value: healthy control

value: White

tag: gender


title: ACC-1054

value: Female

tag: tissue


title: EXP-550: TCGA-AG-A01L-01A-01D-A004-05

value: Stage IIIB


title: A2 NHDF cells infected with Borrelia afzelii

value: Borrelia afzelii


title: ACC-1098.1

value: Hispanic

value: Whole Blood


title: EXP-550: TCGA-AG-A015-01A-01D-A004-05

value: Rectal Adenocarcinoma


title: G2 NHDF cells infected with Borrelia garinii

value: Borrelia garinii


title: EXP-550: TCGA-AG-A00Y-01A-02D-A004-05

value: MALE


title: G3 NHDF cells infected with Borrelia garinii


title: ACC-1097


title: EXP-550: TCGA-AG-A008-01A-01D-A004-05

value: Rectal Mucinous Adenocarcinoma

value: rectal


title: EXP-550: TCGA-AG-A014-01A-02D-A004-05

value: Rectum


title: DRG_RTX_100nM_Rep3

city: Cologne

first: Joerg

last: Isensee

address: Robert Koch Str. 10

department: Department of Anesthesiology and Intensive Care Medicine

country: Germany

institute: University Hospital of Cologne

description: Method to eliminate TRPV1-positive neurons

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Raw fluorescence intensities were background corrected and exported from the Illumina Genome studio software. Background corrected data were log2 transformed and normalized (quantile method) using the R package lummi. The data were filtered for expressed genes (detection p < 0.01) and differentially expressed transcripts were identified with the R package limma. P-values were adjusted for multiple testing with Benjamini and Hochberg's method.

organism: Rattus norvegicus

source_name: Dissociated dorsal root ganglia treated for 30 min with RTX

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

growth_protocol: Lumbar dorsal root ganglia were isolated from 8 weeks old Spargue Dawley rats

extract_protocol: RNA isolation was performed with NucleoSpin RNA/Protein kits from Macherey-Nagel including on column DNase treatment. The RNA concentration and quality was measured with spectroscopy (Nanodrop, Thermo Fisher Scientific) and capillary electrophoresis (Agilent 2100 Bioanalyzer, 28S:18S rRNA ratio > 1.7, RNA integrity number (RIN) > 8.2).

treatment_protocol: Dorsal root ganglia were incubated in 5 ml MEM containing collagenase P (Roche, Penzberg, DE) (0.1 U/ml, 1 h, 37°C, 5% CO2), dissociated by trituration with fire-polished Pasteur pipettes, and then treated with the solvent DMSO (0.1%) or RTX (100 nM). The cells were spun down (100 g, 5 min), resuspended in 1 ml Hanks buffered salt solution (pH 8.0) containing 0.025% EDTA and 245 U/ml trypsin (Worthington, Lakewood, NJ), and incubated for 4 min at 37°C in a water bath. Trypsination was stopped by the addition MgSO4 (400 µM final conc.). The cell suspension was then loaded onto BSA gradients (15% BSA in Hanks buffered salt solution) and centrifuged (120 g, 8 min). The pellet was frozen in liquid nitrogen and stored at -80°C for RNA isolation.

value: male

value: 8 weeks

value: Sprague Dawley rats

value: lumbar dorsal root ganglia


title: EXP-550: TCGA-AG-A00C-01A-01D-A004-05

value: FEMALE


title: DRG_RTX_100nM_Rep1


title: EXP-550: TCGA-AG-3611-01A-01D-0825-05

value: Stage IIA


title: A1 NHDF cells infected with Borrelia afzelii


title: ACC-1055

value: healthy control

value: Black

value: Male


title: DRG_RTX_100nM_Rep4


title: EXP-550: TCGA-AG-A002-01A-01D-A004-05

value: Stage I


title: DRG_RTX_100nM_Rep2


title: EXP-550: TCGA-AV-A03D-20A-01D-0825-05

value: NOT SPECIFIED


title: EXP-550: TCGA-AG-3609-01A-02D-0825-05

value: Rectal Adenocarcinoma

value: Stage IIIC


title: EXP-550: TCGA-AG-3612-01A-01D-0825-05

value: Stage IIIB


title: DRG_Capsaicin_10microM_Rep3

source_name: Dissociated dorsal root ganglia treated for 30 min with capsaicin


title: DRG_Capsaicin_10microM_Rep4


title: EXP-550: TCGA-AG-3605-01A-01D-0825-05

value: Stage IV


title: DRG_Capsaicin_10microM_Rep1


title: DRG_DMSO_0.1%_Rep4

source_name: Dissociated dorsal root ganglia treated for 30 min with DMSO


title: EXP-550: TCGA-AG-3608-01A-01D-0825-05

value: rectal


title: DRG_Capsaicin_10microM_Rep2


title: EXP-550: TCGA-AG-3602-01A-02D-0825-05

value: Rectum


title: DRG_DMSO_0.1%_Rep2

value: male


title: C. elegans exposed to M. aeruginosa batch culture, biol. repl.3

city: Berlin

first: Nadine

last: Saul

address: Philippstr. 13, House 22

department: Department of Biology

institute: Humboldt-Universitaet zu Berlin

hyb_protocol: Chip hybridization was conducted according to the GeneChip® 3’ IVT Express Kit (Affymetrix) manual

scan_protocol: Scanning was performed according to the manuals of the Affymetrix GCS3000 microarray system and Affymetrix Expression Console 1.2.0.20

data_processing: The transcription expression values were pre-processed with the MAS5 algorithm (Affymetrix Expression Console 1.2.0.20). After background correction, probe set summarization and CHP file generation, the expression signals were normalized using the relative median over all genes algorithm (BRB-ArrayTools 4.3.0). Spots with spot intensities below the minimum signal value of 10 were excluded. Differentially expressed genes (DEGs) were identified with a random-variance t-test and a SAM (Significance Analysis of Microarrays) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3 and the fold change compared to control at least ≤0.67 or ≥1.5. To perform the GO Term analysis, the DEGs were processed with the Database for Annotation, Visualization and Integrated Discovery (DAVID 6.7)

organism: Caenorhabditis elegans

source_name: Nematodes at first day of adulthood, grown at 20°C on NGM agar plates and fed with OP50 and constant sample-exposure

label_protocol: Biotin-Modified RNA was prepared according to the GeneChip® 3’ IVT Express Kit (Affymetrix) manual

growth_protocol: Grown at 20 °C on NGM agar fed with OP50 bacteria until 1st day of adulthood

extract_protocol: At the first day of adulthood the animals were harvested by rinsing off with M9 buffer, washed at least three times, shock frozen in liquid nitrogen and stored at -80 ̊C. For each condition, samples were cultivated in triplicate. The samples were milled with 0.5 mm glass beads in a homogenizer (SpeedMill Plus, Analytik Jena, Germany) and thereafter the RNA was extracted using the innuSPEED Tissue RNA kit (Analytik Jena, Germany). The quality of the extracted RNA was examined by gel electrophoresis and the quantity with a Spectrophotometer (NanoDrop 2000, Thermo Scientific, USA). The RNA was stored at -80 °C.

treatment_protocol: After filtration (and lyophilisation) of the lake water and batch culture samples, they were added to the bacteria and agar in a concentration of 200% (compared to original AOBr-content in lake samples) or 40% (compared to original AOBr-content in the batch culture), respectively. Nematodes were exposed their whole life and harvested at the 1st day of adulthood.

value: N2 wildtype

tag: exposure concentration

value: 40% of original batch culture filtrate


title: C. elegans exposed to M. aeruginosa batch culture, biol. repl.2

tag: strain


title: EXP-550: TCGA-AG-3600-01A-01D-0825-05

value: MALE


title: C. elegans exposed to M. aeruginosa batch culture, biol. repl.1


title: C. elegans exposed to Lake Stößensee sample October, biol. repl.3

value: 200% of original lake sample filtrate


title: EXP-550: TCGA-AG-3599-01A-02D-0825-05

value: [Not Available]


title: @51154500794163031610407023251303

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Affy-169 : 200.0 ng at 45 degree_C during 17 hours

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Expression console (v1.1.1) data processing, RMA signal intensity calculation

label_protocol:
Affy-FS450-0007
Affy-WT_sense_target

extract_protocol: Qiagen RNeasy mini kit

tag: cell line

tag: cell type

value: Chronic Myeloid Leukemia (CML) cells

tag: genotype/variation

value: containing inducible shBmi1

tag: incubated with

value: doxycycline for 96h

tag: amount of rna used for labeling (µg)

tag: rin number


title: DRG_DMSO_0.1%_Rep1

value: 8 weeks

value: Sprague Dawley rats

value: lumbar dorsal root ganglia


title: C. elegans exposed to Lake Stößensee sample October, biol. repl.2


title: @51154500794166031610407023251960

value: none (control)


title: C. elegans exposed to Lake Stößensee sample August, biol. repl.3


title: C. elegans exposed to Lake Stößensee sample October, biol. repl.1


title: EXP-550: TCGA-AG-3601-01A-01D-0825-05

tag: disease state

value: Rectal Adenocarcinoma

tag: disease staging

value: Stage IIIB


title: DRG_DMSO_0.1%_Rep3


title: EXP-550: TCGA-AG-3593-01A-01D-0820-05

value: Stage IIA

tag: Sex

value: FEMALE

tag: organism part

value: rectal


title: EXP-550: TCGA-AG-A011-01A-01D-A004-05

tag: sample name

value: Rectum


title: EXP-550: TCGA-AG-3598-01A-01D-0825-05


title: Liver_100COSEFM10CMdiet_fish8

city: St. John's

first: Xi

last: Xue

state: NL

address: 1 Marine Lab Road

department: Department of Ocean Sciences

institute: Memorial University of Newfoundland

hyb_protocol: Equal quantities (825 ng) of each labeled aRNA (refer to label protocol) from one experimental sample and the common reference were pooled, fragmented following the manufacturer's instructions and co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299) as per the manufacturer’s instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: Each microarray was scanned at 5 µm resolution and 90% of laser power using a ScanArray Gx Plus scanner and ScanArray Express software (v4.0; Perkin Elmer, Woodbridge, ON) with photomultiplier tube (PMT) set to balance fluorescence signal between channels.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 2 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene.

organism: Salmo salar

source_name: Liver tissue, 100COSEFM10CM diet, individual fish

label_protocol: Nine individual fish each from the 100COSEFM10CM and control diet groups were used in the microarray analysis using a common reference design. An equal quantity of each DNase I-treated, column-purified liver total RNA sample involved in the microarray experiment was pooled to make a common reference for the microarray hybridizations. Anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 µg of each experimental RNA or reference pooled RNA using Ambion's Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies), following the manufacturers' instructions. The quality and quantity of aRNA were assessed using UV spectrophotometry and agarose gel electrophoresis. Twenty µg of aRNA was precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer; the resulting solution was used in a labeling reaction following the manufacturer's protocol. Resulting aRNA was labeled with either Cy3 (for the common reference) or Cy5 (for the experimental individuals) fluor (GE HealthCare, Mississauga, ON) through a dye-coupling reaction, following the manufacturer's instructions. The labeling efficiency was measured using the microarray function of the NanoDrop spectrophotometer.

growth_protocol: Atlantic salmon post-smolts (average weight 24201 g) were randomly distributed among fifteen tanks (500 L) with flow-through seawater  (~14°C, dissolved oxygen ≥ 10 mg L-1), and all fish were kept on a photoperiod of 12 hours light / 12 hours dark. Triplicate tanks of fish were fed experimental or control diets to apparent satiety, twice each day for a period of 16 weeks. At week 0 (the day before experimental diets were fed), week 1 (3 days of acclimation to the experimental diets plus a full week of feeding experimental diets), week 8 and week 16 of the feeding trial, seven fish from each tank at each time point were euthanized with 400 mg L-1 of tricaine-methane-sulfonate (TMS; Syndel Laboratories, Vancouver, BC) after 24 h of fasting. Body weight and fork length of fish were measured and recorded. Liver tissues (50-100 mg sample-1) were rapidly dissected from fish, placed in RNase-free 1.5 mL tubes, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extractions were performed.

extract_protocol: Liver samples collected from the feeding experiment were homogenized individually in 2.0 mL tubes containing TRIzol reagent (Invitrogen, Carlsbad, CA) with a volume of 0.8 mL per sample and a stainless steel bead (2.5mm; QIAGEN, Mississauga, ON) using a TissueLyser (QIAGEN) at 25 Hz for 3 min, and further disrupted using QIAshredder spin columns (QIAGEN) and subjected to RNA extration according to the manufacturers’ instructions. After extraction, the quality of total RNA was examined by 1% agarose/ethidium bromide gel electrophoresis, and RNA quantity and purity were measured by NanoDrop spectrophotometry (ThermoFisher, Mississauga, ON). However, due to low 260/230 ratios (i.e. less than 1.2) following TRIzol extraction, all RNA samples were re-extracted using the following phenol-chloroform phase separation method. Thirty µL of each crude RNA were diluted 10 times using nuclease-free water (Invitrogen), an equal volume of Acid Phenol:Chloroform:IAA (25:24:1, v/v; pH 6.6; Ambion, Burlington, ON) was added, and after mixing, phases were separated by centrifugation at 15,000 × g at 4°C for 20 min. The RNA was then precipitated from the aqueous phase with a mixture of 20 µL 3M sodium acetate (pH 5.2; Ambion) and 400 µL 95% ethanol (Greenfield, Toronto, ON) and incubated at -80°C for one hour, followed by centrifugation at 15,000 × g at 4°C for 30 min. The resulting RNA pellet was washed by adding 500 µL of 70% ethanol and centrifuging at 15,000 × g at 4°C for 20 min followed by removal of the supernatant, and then air-dried at room temperature for 10 min and dissolved in 40 µL of nuclease-free water (Invitrogen). Total RNA of each sample was then treated with DNase I (QIAGEN) to degrade residual genomic DNA, and all samples were purified from salts, proteins and nucleotides using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s protocols.

value: Liver

tag: life stage

value: Juvenile

source_name: pool of RNAs from liver tissues invovled in the microarray experiment (i.e. FO, 100COSEFM10CM)


title: EXP-550: TCGA-AG-3587-01A-01D-0820-05

tag: age

value: Stage I

value: MALE


title: Liver_100COSEFM10CMdiet_fish9


title: C. elegans exposed to Lake Stößensee sample August, biol. repl.1

value: N2 wildtype

value: 200% of original lake sample filtrate


title: EXP-550: TCGA-AG-3586-01A-02D-0820-05

value: [Not Available]

value: Stage III


title: Liver_100COSEFM10CMdiet_fish4


title: EXP-550: TCGA-AG-3594-01A-02D-0820-05

value: Rectal Mucinous Adenocarcinoma


title: Liver_100COSEFM10CMdiet_fish5


title: C. elegans exposed to Z-Medium (Control), biol. repl.3


title: C. elegans exposed to Z-Medium (Control), biol. repl.2


title: C. elegans exposed to Lake Stößensee sample August, biol. repl.2


title: Liver_100COSEFM10CMdiet_fish7


title: Liver_100COSEFM10CMdiet_fish3


title: EXP-550: TCGA-AG-3581-01A-01D-0820-05


title: Liver_100COSEFM10CMdiet_fish2


title: C. elegans exposed to Water (Control), biol. repl.3


title: C. elegans exposed to Water (Control), biol. repl.1


title: Liver_100COSEFM10CMdiet_fish1


title: EXP-550: TCGA-AG-3580-01A-01D-0820-05


title: Liver_FOdiet_fish8

source_name: Liver tissue, fish oil diet, individual fish


title: IBA_ibr3_6h_rep3

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Arabidopsis thaliana seeds were surface sterilized with 95% (v/v) ethanol for 5 min and 20% (v/v) bleach for 12 min. After 5 times rinsing with sterile water, seeds were imbibed and stratified at 4°C for 3 days before being sown on Petri dishes containing sterile ½ Murashige and Skoog mediums (0.5X MS salts, 0.8% sucrose, 0.5g/L MES, pH 5.7 and 1% agar). Seeds were germinated on vertically positioned Petri dishes in a growth chamber with continuous light at a temperature of 21ºC. Three-days-old Col-0 and ibr1ibr3ibr10 seedlings (five days post-imbibition) were transferred from ½ MS medium to a fresh ½ MS medium supplemented with or without 10 μM indole-3-buytric acid (IBA) for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction. For each treatment, at least 120 individual Col-0 or ibr1ibr3ibr10 mutant root tip segments were sampled and three independent biological replicates were performed. Hormone and DMSO solution were filer-sterilized before being added to the medium.

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix' Arabidopsis ATH1 Genome arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.40.0) of Bioconductor. Expression values are represented on a log2-scale.

organism: Arabidopsis thaliana

source_name: Root tip segment (~4mm) of ibr1ibr3ibr10 mutant (Col0 background) seedlings grown 3 days after germination on ½MS medium and transferred for 6 hours on IBA supplemented medium (10 μM).

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

extract_protocol: The material was extracted using the Rneasy® Plant Mini Kit according to the manufacturer's instructions

treatment_protocol: Three-days-old ibr1ibr3ibr10 seedlings (five days post-imbibition) were transferred from ½ MS medium to a fresh ½ MS medium supplemented with 10 μM indole-3-buytric acid (IBA) for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction.

tag: background ecotype

tag: genotype

value: 3 days after germination

value: root tip segment (~4mm)

tag: treatment

value: IBA 10 μM


title: Liver_FOdiet_fish9

tag: tissue


title: IBA_Col_6h_rep3

source_name: Root tip segment (~4mm) of wild type Col0 seedlings grown 3 days after germination on DMSO ½MS medium and transferred for 6 hours on IBA supplemented medium (10 μM).

growth_protocol: Arabidopsis thaliana seeds were surface sterilized with 95% (v/v) ethanol for 5 min and 20% (v/v) bleach for 12 min. After 5 times rinsing with sterile water, seeds were imbibed and stratified at 4°C for 3 days before being sown on Petri dishes containing sterile ½ Murashige and Skoog mediums (0.5X MS salts, 0.8% sucrose, 0.5g/L MES, pH 5.7 and 1% agar). Seeds were germinated on vertically positioned Petri dishes in a growth chamber with continuous light at a temperature of 21ºC.

treatment_protocol: Three-days-old Col-0 (five days post-imbibition) were transferred from ½ MS medium to a fresh ½ MS medium supplemented with 10 μM indole-3-buytric acid (IBA) for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction.

value: wild type


title: Liver_FOdiet_fish7


title: EXP-550: TCGA-AG-3574-01A-01D-0820-05

value: Rectal Adenocarcinoma

value: Stage II


title: EXP-550: TCGA-AG-3578-01A-01D-0820-05

value: Stage IIA

value: FEMALE

value: rectal


title: EXP-550: TCGA-AG-3582-01A-01D-0820-05

value: Stage IV

value: Rectum


title: C. elegans exposed to Z-Medium (Control), biol. repl.1

tag: strain

tag: exposure concentration

value: none (control)


title: Liver_FOdiet_fish5

value: Liver

value: Juvenile


title: Liver_FOdiet_fish6


title: EXP-550: TCGA-AF-3400-11A-01D-1552-05

source_name: Solid normal_tissue

value: MALE

value: Rectosigmoid Junction


title: EXP-550: TCGA-AG-3575-01A-01D-0820-05


title: DMSO_ibr3_0h_rep3

source_name: Root tip segment (~4mm) of ibr1ibr3ibr10 mutant (Col0 background) seedlings grown 3 days after germination on ½MS medium and transferred for 6 hours on DMSO supplemented medium.

treatment_protocol: Three-days-old ibr1ibr3ibr10 seedlings (five days post-imbibition) were transferred from ½ MS medium to a fresh ½ MS medium for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction.

value: none (control DMSO)


title: Liver_FOdiet_fish3


title: Liver_FOdiet_fish4


title: EXP-550: TCGA-AF-2692-01A-01D-0820-05

value: [Not Available]


title: Liver_FOdiet_fish2


title: IBA_ibr3_6h_rep2

value: 3 days after germination

value: root tip segment (~4mm)


title: EXP-550: TCGA-AF-3400-01A-01D-0820-05

value: Rectal Mucinous Adenocarcinoma


title: EXP-550: TCGA-AF-2689-01A-01D-0820-05

value: Rectal Adenocarcinoma


title: DMSO_Col_0h_rep3

source_name: Root tip segment (~4mm) of wild type Col0 seedlings grown 3 days after germination on ½MS medium and transferred for 6 hours on DMSO supplemented medium (control).

treatment_protocol: Three-days-old Col-0 seedlings (five days post-imbibition) were transferred from ½ MS medium to a fresh ½ MS medium for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction.

value: wild type


title: EXP-550: TCGA-AF-2691-01A-01D-0820-05

value: Stage I


title: Control 2 H011-3100506365

city: Houston

first: Todd

middle: Ryan

last: Heallen

state: Texas

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

hyb_protocol: Phalanx Hybridization Protocol (http://www.phalanxbiotech.com/)

scan_protocol: Scanned by Phalanx Biotech Group (http://www.phalanxbiotech.com/)

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve. Data was normalized using R Bioconductor software package (v.2.15.2).

source_name: murine embryonic heart tissue

label_protocol: AminoAllyl aRNA labeling. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA with the NHS-CyDye.

extract_protocol: Dissected P8 hearts were placed in RNAlater for tissue stabilization. Total RNA was then extracted using the RNeasy Micro Kit (Qiagen) and optical density was measured by NanoDrop ND-1000, Agilent RNA 6000 Nano Assay and agarose electrophoresis.

tag: strain background

value: C57bl/6 X 129 hybrid

tag: genotype/variation

value: wild-type

tag: developmental stage

value: whole heart


title: DMSO_Col_0h_rep2


title: EXP-550: TCGA-AG-3885-01A-01D-0904-05

source_name: Primary solid_tumor

value: Stage IIIB

value: FEMALE

value: rectal

value: Rectum


title: IBA_ibr3_6h_rep1

value: IBA 10 μM


title: C. elegans exposed to Water (Control), biol. repl.2

value: N2 wildtype

value: none (control)


title: DMSO_Col_0h_rep1

value: none (control DMSO)


title: IBA_Col_6h_rep1

value: 3 days after germination


title: DMSO_ibr3_0h_rep2

value: root tip segment (~4mm)


title: EXP-550: TCGA-AF-2691-11A-01D-1552-05


title: EXP-550: TCGA-07-0227-20A-01D-0820-05

source_name: Control Cell Line

value: NOT SPECIFIED


title: DMSO_ibr3_0h_rep1


title: IBA_Col_6h_rep2


title: Control 2 H012-3100506366


title: EXP-550: TCGA-AF-2692-11A-01D-1552-05

value: [Not Available]

value: Stage IIA


title: EXP-550: TCGA-AG-3883-01A-02D-0904-05

value: Rectal Adenocarcinoma

value: Stage I

value: MALE


title: EXP-550: TCGA-AG-3583-01A-01D-0820-05

value: Rectal Mucinous Adenocarcinoma

value: Stage IV


title: EXP-550: TCGA-AG-3584-01A-01D-0820-05


title: EXP-550: TCGA-AF-2689-11A-01D-1552-05

value: FEMALE

value: Rectosigmoid Junction


title: Bacillus cereus_water_30 min_3

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

country: Japan

institute: Tokyo University of Agriculture

description: Gene expression at 30 min after EEC exposure

hyb_protocol: Cy3-labeled cRNA (1.65 μg) was fragmented to an average size of about 50–100 nucleotides and then hybridized for 17 h at 65°C to an soybean oligonucleotide microarray slide. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned in Cy3 channel with the Agilent DNA Microarray Scanner (Agilent).

data_processing: Signal intensity per spot was generated from the scanned image with Agilent scan control 8.0 software according to Agilent Technologies standard operation procedures. Spots that did not pass quality control procedures were flagged as Not Detected. The scanned images were analyzed using commercial software (Gene spring GX11.5) as follows: (i) Gene expression more than seven of eight samples were Not detect, the gene was excluded, (ii) threshold raw signals were set at unify, and (iii) submitted to 75th percentile normalization.

organism: Bacillus cereus

source_name: Bacillus cereus_water_30 min_replicate3

label_protocol: Total RNAs of each samples were amplified with a FairPlay Microarray Labeling Kit and Gene Expression Hybridization Kit (Agilent Technologies).

growth_protocol: B. cereus ATCC 14579 was cultured in liquid LB medium for overnight. Then, 20 mL of LB medium were inoculated with 0.1% of overnight culture.

extract_protocol: Total RNA (2 or 3 samples/stage) was extracted using an RNeasy kit (Qiagen, Tokyo, Japan) and purified using the same kit. RNA quality and quantification were checked using the Agilent 2100 bioanalyzer (Agilent Technologies) and NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: 0.02mg/ml  of  EEC was added to the culture with OD. at 600 nm reached 0.5. Water was added instead of EEC for control. After 30 min later, total RNA was isolated.


title: Bacillus cereus_water_30 min_1

description: Gene expression at 30 min after water addition

source_name: Bacillus cereus_water_30 min_replicate1


title: EXP-550: TCGA-AG-3882-01A-01D-0904-05

value: rectal

value: Rectum


title: Control 2 H010-3100506364

value: C57bl/6 X 129 hybrid

value: wild-type

value: whole heart


title: Liver_FOdiet_fish1

value: Liver

value: Juvenile


title: Bacillus cereus_EEC expose_30 min_2

source_name: Bacillus cereus_EEC expose_30 min_replicate2


title: Liver_100COSEFM10CMdiet_fish6


title: Bacillus cereus_EEC expose_30 min_1

source_name: Bacillus cereus_EEC expose_30 min_replicate1


title: Bacillus cereus_EEC expose_30 min_3

source_name: Bacillus cereus_EEC expose_30 min_replicate3


title: Salv CKO 2 H009-3100506362

value: Salvador mutant (Salv CKO)


title: EXP-550: TCGA-AG-3881-01A-01D-0904-05

value: [Not Available]


title: Salv CKO 1 H003-3100506353


title: Bacillus cereus_water_30 min_2

source_name: Bacillus cereus_water_30 min_replicate2


title: Bacillus cereus_before EEC expose_1

description: Gene expression before EEC exposure

source_name: Bacillus cereus_EEC expose_0 min_replicate1


title: EXP-550: TCGA-AG-4015-01A-01D-1116-05

value: Stage IIA


title: Salv CKO 2 H008-3100506361


title: Bacillus cereus_before EEC expose_2

description: Gene expression before EEC exposure

source_name: Bacillus cereus_EEC expose_0 min_replicate2


title: EXP-550: TCGA-07-0227-20A-01D-0904-05

value: NOT SPECIFIED


title: Salv CKO 1 H002-3100506352


title: EXP-550: TCGA-AG-3728-01A-01D-0904-05

value: Rectal Adenocarcinoma

value: Stage IIIB


title: EXP-550: TCGA-AG-3726-01A-02D-0904-05

value: Stage I


title: Salv CKO 2 H007-3100506360


title: Patient 5

type: protein

city: Guangzhou

first: Liangru

last: Ke

state: Guangdong

address: 651 Dongfeng Road East

department: Department of Nasopharyngeal Carcinoma

country: China

institute: Sun Yat-sen University

description: The Explorer Antibody Array is a comprehensive array consisting of 656 highly specific and well-characterized antibodies covering more than nine pathways

hyb_protocol: Incubate the slides with blocking buffer on an orbital shaker rotating at 55 rpm for 30 to 45 minutes at room temperature .Rinse the slide extensively with Milli-Q grade water for 10 seconds by ten times. Then incubate the slides with Protein Coupling Mix on an orbital shaker rotating at 35 rpm for 1 – 2 hours at room temperature. Then wash the slides with wash sollution on  shaker for 10 minutes at room temperature by twice and rinse the slide extensively with Milli-Q grade water as above. Add 60 ul of Cy3-streptavidin at 0.5 mg/ml (or 30 ul at 1 mg/ml) to 60 ml of Detection Buffer. Submerge the slide in the Cy3-streptavidin solution. Incubate on an orbital shaker rotating at 35 rpm for 20 minutes at room temperature in the dark or covered with aluminum foil. And then wash  and dry the slides by centrifugation.

scan_protocol: The signals were collected by GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) and the Genepix software package was subjected to primary analysis.

data_processing:
The data were viewed as a scatter plot of Cy3 intensities after plotting on a grid, and then, the images of scanned microarrays were linked to a protein print list.
Normalized values of individual proteins were determined by calculating the ratio of each spot value to the average median for all of the spots in the same array.

molecule: protein

source_name: serum from NPC patients without distant metastasis after treatment

label_protocol: Add Labeling Buffer to 4 ul of serum to bring the volume to 75 ul,then add 3 ul of the Biotin/DMF solution to the sample. Incubate the mixture at room temperature for 1 – 2 hours with vortexing every 10 minutes. Then, add 35 ul of Stop Reagent. Mix by vortexing, then quickly spin down. Incubate for 30 minutes at room temperature with mixing.

extract_protocol: Centrifuge the serum/plasma sample at 18,000 x g for 10 – 15 minutes at 4°C,and transfer 2 – 3 uL of the clear, pale yellow liquid to a new tube and proceed directly to protein labeling step.

value: serum

tag: diagnosis

value: NPC

tag: status after 5 years

value: Alive

tag: histology

value: 59 years

value: Female

tag: Stage

value: ⅣA


title: Control 1 H006-3100506359

value: C57bl/6 X 129 hybrid

value: wild-type


title: Control 1 H004-3100506356

value: whole heart


title: Patient 8

value: 49 years

tag: Sex

value: Male

value: ⅣB


title: EXP-550: TCGA-AG-3878-01A-02D-0904-05

tag: disease state

tag: disease staging

value: MALE

tag: organism part

value: rectal

tag: sample name

value: Rectum


title: Patient 4

source_name: serum from NPC patients with distant metastasis after treatment

value: Dead

tag: age

value: 60 years


title: Control 1 H005-3100506357


title: EXP-550: TCGA-AG-3727-01A-01D-0904-05

value: Rectal Adenocarcinoma

value: Stage III

value: FEMALE


title: EXP-550: TCGA-AG-4007-01A-01D-1116-05

value: Stage IV


title: Patient 7

value: serum

value: NPC

value: Alive

value: Ⅲ


title: Patient 3

value: 25 years

value: Female


title: Patient 6

value: 36 years

value: Male

value: ⅣA


title: EXP-550: TCGA-AG-4008-01A-01D-1116-05

value: Stage IIA

value: MALE

value: rectal


title: EXP-550: TCGA-AG-3999-01A-01D-1116-05

value: Stage IIIC

value: Rectum


title: EXP-550: TCGA-AG-4001-01A-02D-1116-05

value: Rectal Adenocarcinoma


title: Patient 2

source_name: serum from NPC patients with distant metastasis before treatment

value: Dead

value: 63 years

value: ⅣC


title: Salv CKO 1 H001-3100506351

value: C57bl/6 X 129 hybrid

value: Salvador mutant (Salv CKO)

value: whole heart


title: Patient 1

value: serum

value: NPC

value: 48 years


title: EXP-550: TCGA-AG-4005-01A-01D-1116-05

value: Stage IV


title: EXP-550: TCGA-AG-3909-01A-01D-1116-05

value: Stage IIIB

value: FEMALE


title: EXP-550: TCGA-AG-3898-01A-01D-1116-05

value: Stage IIA

value: MALE


title: 24h-PB 3.2

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

institute: Health Canada

description:
Sample 4
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

hyb_protocol: Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A, Agilent Microarray Design ID: 028004; Agilent Technologies, Mississauga, ON, Canada) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R. After normalization, the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control [the sample-dye assignment information for each of the raw data files is included in the 'readme.txt' (available as Series supplementary file)].

source_name: TK6 lymphoblastoid cell line, 3.2 mM phenobarbital for 4h, 24h

label_protocol: Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on all time points from the definitive studies (n=3 per concentration and time point), along with the corresponding pooled vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 10^5 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that BaP requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 1% 5,6 benzoflavone-/phenobarbital-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.

extract_protocol: Following PB cellular exposures, total RNA was isolated from treated and control TK6 cells at the 8 and 24h time points. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high-quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0, were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to phenobarbital for 4 hours followed by recovery times of 4h and 20h in fresh media (8h and 24h time points, respectively) at 3 different concentrations, including a low (1 mM), a medium (3.2 mM), and a high (10 mM) concentration.

tag: cell line

tag: cell type

value: lymphoblastoid cells

tag: treatment

value: 3.2 mM phenobarbital (PB) for 4h

tag: time point

source_name: TK6 lymphoblastoid cell line, negative vehicle control, 24h

value: DMSO +S9


title: EXP-550: TCGA-AG-3902-01A-01D-1116-05

value: Rectal Adenocarcinoma

value: rectal

value: Rectum


title: EXP-550: TCGA-AG-3894-01A-01D-1116-05


title: 24h-PB 1

description:
Sample 3
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 1 mM phenobarbital for 4h, 24h

value: 1 mM phenobarbital (PB) for 4h


title: triple_negative_breast_cancer_FFPE_3233

city: Lyon

first: Magali

last: Olivier

address: 150 cours Albert Thomas

institute: IARC

hyb_protocol: The cDNA was then amplified with universal primers and hybridized to Illumina Human WG DASL HT Expression BeadChip arrays.

scan_protocol: Arrays were read in a Illumina BeadStation 500GX following to the Illumina protocol

data_processing: The Illumina Genome Studio V2010.2 was used to obtain the signal values (AVG-Signal), with no normalization and no background subtraction.The performance of hybridizations was evaluated by assessing the presence of outliers and the noise-to-signal ratios by calculating the ratio of centiles P95/P05 prior to normalisation for each sample. We defined outliers as samples with P95/P05 ratio <9.5. All samples were found to show a correct noise-to-signal ratio (P95/P05>9.6).

source_name: Tumor FFPE tissue

label_protocol: Biotinylated cRNA were prepared with the Illumina Whole Genome Gene Expression DASL kit

extract_protocol: Total RNA was extracted from FFPE tumor tissues using the RNeasy FFPE Kit (Qiagen)

tag: sample type

value: FFPE tissue

tag: tissue

value: breast

tag: gender

value: female

tag: patient country

value: Mexico

tag: age at diagnosis


title: 8h-PB 1

description:
Sample 1
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 1 mM phenobarbital for 4h, 8h

source_name: TK6 lymphoblastoid cell line, negative vehicle control, 8h


title: EXP-550: TCGA-AG-3896-01A-01D-1116-05

source_name: Primary solid_tumor

value: Stage I


title: triple_negative_breast_cancer_FFPE_11905


title: triple_negative_breast_cancer_FFPE_10512


title: 24h-PB 10

description:
Sample 5
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 10 mM phenobarbital for 4h, 24h

value: 10 mM phenobarbital (PB) for 4h


title: 8h-PB 10

description:
Sample 2
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 10 mM phenobarbital for 4h, 8h


title: EXP-550: TCGA-AG-3890-01A-01D-1116-05


title: EXP-550: TCGA-AG-3892-01A-01D-1116-05


title: 8h-PB 3.2

description:
Sample 6
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 3.2 mM phenobarbital for 4h, 8h


title: EXP-550: TCGA-AG-3901-01A-01D-1116-05

value: Rectal Mucinous Adenocarcinoma

value: Stage IIIB


title: triple_negative_breast_cancer_FFPE_11932


title: triple_negative_breast_cancer_FFPE_157


title: EXP-550: TCGA-AG-3728-01A-01D-1116-05


title: triple_negative_breast_cancer_FFPE_3192


title: EXP-550: TCGA-AG-3887-01A-01D-1116-05

value: Stage IIA


title: triple_negative_breast_cancer_FFPE_1619


title: EXP-550: TCGA-AG-3893-01A-01D-1116-05

value: MALE


title: triple_negative_breast_cancer_FFPE_324


title: EXP-550: TCGA-AF-3913-01A-02D-1116-05

value: [Not Available]

value: Rectosigmoid Junction


title: triple_negative_breast_cancer_FFPE_6916


title: EXP-550: TCGA-07-0227-20A-01D-1116-05

source_name: Control Cell Line

value: NOT SPECIFIED


title: PPGL_HS_087

status: Public on May 11 2015

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: standard Illumina protocol. Illumina Beadstudio software.

label: Cy5 and Cy3

source_name: Malignant Pheochromocytoma

label_protocol: Standard Illumina protocol.

growth_protocol: All samples were stored at -80C

extract_protocol: DNA was extracted from frozen tissue samples using a QIAamp DNA mini kit or an AllPrep kit (Qiagen).

value: M

tag: malignancy

value: Malignant

tag: tumor site

value: Right adrenal

tag: metastatic event

value: Yes

tag: metastasis delay (months)

tag: deceased

value: yes

tag: overall survival delay (months)


title: PPGL_HS_046

source_name: Malignant paraganglioma

tag: Sex

value: F

value: Abdominal paraganglioma


title: PPGL_HS_209

source_name: Malignant metastasis paraganglioma

value: Meta


title: PPGL_HS_208


title: triple_negative_breast_cancer_FFPE_8119

value: FFPE tissue

value: breast

value: female

value: Mexico


title: PPGL_HS_018


title: EXP-550: TCGA-AF-3913-11A-01D-1116-05

source_name: Solid normal_tissue

tag: disease state

value: Rectal Adenocarcinoma

tag: age

tag: disease staging

tag: organism part

value: rectal

tag: sample name


title: PPGL_HS_073


title: triple_negative_breast_cancer_FFPE_4864

tag: sample type


title: triple_negative_breast_cancer_FFPE_5463

tag: tissue


title: PPGL_HS_145

value: Left adrenal

value: no


title: PPGL_HS_015

value: Abdominal paraganglioma or meta


title: MARV PBMC, Mky 078115 Day 9

city: Boston

first: Ignacio S.

last: Caballero

state: MA

address: 620 Albany St., NEIDL 401V

department: NEIDL/Microbiology

institute: Boston University School of Medicine

description: commercially available human reference RNA from Agilent (Stratagene), used as a consistent control in dataset comparisons

hyb_protocol: Labeled reference RNA was added to each experimental sample, then samples were hybridized to arrays in Agilent SureHyb-enabled hybridization chambers.  After a 17-hour hybridization, arrays were washed with the Agilent gene expression wash buffers and then placed in Agilent scanner slide holders with ozone-barrier covers.

scan_protocol: Arrays were scanned using the Agilent High-Resolution Microarray Scanner and raw microarray images were processed using Agilent's Feature Extraction software

data_processing: Data were first background-corrected to remove noise from background intensity levels, and then normalized within the arrays using the Limma package in R (R development core team 2010). Following normalization, the reference and experimental samples were compared to generate log fold-change values that represent a change in mRNA expression (either positive or negative).  Data were further processed by zero-transformation, where the normalized values of the pre-infection samples were subtracted from the subsequent timepoints of each monkey, in order to remove animal-intrinsic variables and focus on gene expression changes due to infection only.

organism: Macaca fascicularis

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient

label_protocol: RNA samples were amplified and labeled with Cy dyes using the Agilent Low-Input Quick Amp Labeling kits

extract_protocol: Total RNA was extracted using TRIzol reagent following the manufacturer's instructions

tag: animal id

tag: cell type

value: PBMC

tag: time point (days post-infection)

source_name: Universal Human Reference RNA (Stratagene), commercially available

tag: vendor

value: Agilent Technologies

tag: catalog #

tag: rna source

value: 10 different human cell lines


title: MARV PBMC, Mky 0705043 Day 9


title: MARV PBMC, Mky 08R0200 Day 7


title: MARV PBMC, Mky 0802013 Day 5


title: MARV PBMC, Mky 07R0010 Day 7


title: MARV PBMC, Mky 0803063 Day 5


title: MARV PBMC, Mky 0806042 Day 3


title: MARV PBMC, Mky 0802039 Day 3


title: MARV PBMC, Mky 0806035 Day 7


title: MARV PBMC, Mky 0706018 Day 3


title: MARV PBMC, Mky 08R0038 Day 9


title: MARV PBMC, Mky 0807043 Day 1


title: MARV PBMC, Mky 07R0189 Day 1


title: MARV PBMC, Mky 0806025 Day 5


title: PPGL_HS_074

tag: age at diagnosis

tag: malignancy

value: Malignant

tag: tumor site

tag: metastatic event

value: Yes

tag: metastasis delay (months)


title: MARV PBMC, Mky 07R0189 Day 0


title: MARV PBMC, Mky 0705043 Day 0


title: MARV PBMC, Mky 071840 Day 1


title: MARV PBMC, Mky 0802013 Day 0


title: MARV PBMC, Mky 08R0200 Day 0


title: MARV PBMC, Mky 0806025 Day 0


title: PPGL_HS_140

tag: Sex

value: M

value: Left adrenal or Right adrenal or meta

tag: deceased

tag: overall survival delay (months)


title: MARV PBMC, Mky 07R0010 Day 0


title: MARV PBMC, Mky 078115 Day 0


title: MARV PBMC, Mky 0803063 Day 0


title: Biofilm+12hrtobra_rep3

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

description: Cells grown 72 hours in a drip flow reactor and then treated with 10.0 μg/ml tobramycin for 12 hours in the reactor

hyb_protocol: For each Pseudomonas genome array (#900339, Affymetrix), labeled fragmented cDNA (4.5 µg from antibiotic treated biofilms, or 3 µg from planktonic cultures), was hybridized to the arrays at 50oC for 16 h with constant rotational mixing at 60 rpm.  Washing and staining of the arrays was performed using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 7G and GCOS software version 1.4.

data_processing: Affymetrix CEL files were imported into FlexArray v1.6.1 for quality control, normalization, and data analysis. Microarray data was background corrected and normalized using the GC-RMA algorithm. Gene expression in 72 hour and 84 hour biofilms were pooled and compared to gene expression in antibiotic treated biofilms with an analysis of variance (ANOVA). Genes with expression changes greater than 4 fold at p ≤ 0.01 in response to ciprofloxacin or tobramycin (when compared to untreated biofilms) were selected for further analysis.

organism: Pseudomonas aeruginosa

label_protocol: Biotinylated fragmented cDNA was prepared according to Affymetrix's Prokaryotic Target Labeling Protocol  (GeneChip Expression Analysis Technical Manual; November, 2004).

growth_protocol: biofilm_samples: Biofilms were formed in the continuous flow drip-flow biofilm reactor at 37 ºC using PBM supplemented with 0.2 g l-1 at a flow rate of 60 ml h-1 onto the stainless steel slides (8.5cm x 1.3cm). The reactors were inoculated by adding 1 ml of an overnight culture to 15 ml of fresh PBM to cover the slides (inoculum OD600 ≈ 0.3) in PBM (1 g l-1 glucose) for 18-24 h on a level surface. After the inoculation period, the reactor was inclined at 10º from horizontal and medium flow was initiated. The biofilms were cultured in the drip-flow reactors for 72 h (n=3) or 84 h (n=3) after the static inoculation phase for no treatment controls. After 72 h of growth in the absence of antibiotic, antibiotics were added to the growth medium, and the flow with medium containing antibiotic was continued for an additional 12 h.  Tobramycin was applied at 10 μg ml-1 and ciprofloxacin at 1.0 μg ml-1.

extract_protocol: Cells were collected into 1ml of RNAlater® (Ambion) and stored at 4ºC for one day prior to removal of the RNAlater® by centrifugation and freezing at -70 ºC. Cells were thawed on ice and re-suspended in 300 µl of 1 mg lysozyme ml-1 in Tris-EDTA buffer, sonicated for 15 seconds, incubated at room temperature for 15 minutes, and then RNA was extracted with an RNeasy® mini kit (Qiagen Sciences) with on-column DNA digestion.

tag: antibiotic treatment

value: Tobramycin


title: MARV PBMC, Mky 0706018 Day 0


title: Biofilm+12hrtobra_rep2

source_name: Cells grown 72 hours in a drip flow reactor and then treated with 10.0 μg/ml tobramycin for 12 hours in the reactor

treatment_protocol: After 72 h of growth in the absence of antibiotic, antibiotics were added to the growth medium, and the flow with medium containing antibiotic was continued for an additional 12 h.  Tobramycin was applied at 10 μg ml-1 and ciprofloxacin at 1.0 μg ml-1.


title: MARV PBMC, Mky 0802039 Day 0


title: Biofilm+12hrcipro_rep2

description: Cells grown 72 hours in a drip flow reactor and then treated with 1.0 μg/ml ciprofloxacin for 12 hours in the reactor

value: Ciprofloxacin


title: Biofilm+12hrcipro_rep3

source_name: Cells grown 72 hours in a drip flow reactor and then treated with 1.0 μg/ml ciprofloxacin for 12 hours in the reactor


title: Biofilm+12hrtobra_rep1


title: MARV PBMC, Mky 0807043 Day 0


title: Biofilm+12hrcipro_rep1


title: Planktonic_rep4

description: Exponential phase planktonic cells

data_processing: Affymetrix CEL files were imported into FlexArray v1.6.1 for quality control, normalization, and data analysis. Microarray data was background corrected and normalized using the GC-RMA algorithm. Gene expression in 72 hour and 84 hour biofilms were pooled and compared to gene expression in planktonic cells with an analysis of variance (ANOVA). FDR correction was performed using the Benjamini Hochberg algorithm to generate a list of genes with expression changes greater than 4 fold at an adjusted p value ≤ 0.01.

source_name: Exponential phase planktonic cells

growth_protocol:
biofilm_samples: Biofilms were formed in the continuous flow drip-flow biofilm reactor at 37 ºC using PBM supplemented with 0.2 g l-1 at a flow rate of 60 ml h-1 onto the stainless steel slides (8.5cm x 1.3cm). The reactors were inoculated by adding 1 ml of an overnight culture to 15 ml of fresh PBM to cover the slides (inoculum OD600 ≈ 0.3) in PBM (1 g l-1 glucose) for 18-24 h on a level surface. After the inoculation period, the reactor was inclined at 10º from horizontal and medium flow was initiated. The biofilms were cultured in the drip-flow reactors for 72 h or 84 h after the static inoculation phase.
planktonic_samples: Planktonic cultures were grown from frozen stocks in Pseudomonas basal medium containing 1.0 g l-1 glucose overnight. 30 μl of each of these cultures was used to inoculate 30 ml of PBM (1 g l-1 glucose).  Cultures were allowed to incubate at 37°C for 5 hours until exponential phase with orbital shaking at 200 rpm.

extract_protocol: Cells were collected into 1ml of RNAlater® (Ambion) and stored at 4ºC for one day prior to removal of the RNAlater® by centrifugation and freezing at -70 ºC. Cells were thawed on ice and re-suspended in 300 µl of 1 mg lysozyme ml-1 in Tris-EDTA buffer, sonicated for 15 seconds (biofilm samples only), incubated at room temperature for 15 minutes, and then RNA was extracted with an RNeasy® mini kit (Qiagen Sciences) with on-column DNA digestion.

tag: mode of growth

value: Planktonic

tag: strain


title: Planktonic_rep3

description: Exponential phase planktonic cells


title: MARV PBMC, Mky 0806042 Day 0

tag: animal id


title: Planktonic_rep2

description: Exponential phase planktonic cells


title: MARV PBMC, Mky 0806035 Day 0

tag: cell type


title: MARV PBMC, Mky 071840 Day 0

tag: time point (days post-infection)


title: Planktonic_rep1

description: Exponential phase planktonic cells


title: MARV PBMC, Mky 08R0038 Day 0

tag: vendor


title: R30

city: Sao Paulo

first: Glauber

middle: Costa

last: Brito

state: Sao Paulo

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

hyb_protocol: cRNA was hybridized onto CodeLink –R whole genome microarray slides, washed and hybridized cRNA species were detected using Cy5-Streptavidin (Amersham, UK).

scan_protocol: GenePix Personal 4100A Microarray Scanner (Axon Instruments)

data_processing: Statistical analysis of the CodeLink–R microarray slides was performed using the publicly available R statistical environment (http://www.r-project.org). The normalization and background correction were performed using the LIMMA package (Linear Models for microarray Analysis); a part of the Bioconductor Microarray Suite (www.bioconductor.org). The background noise was corrected using the normEXP algorithm and the values were normalized by a cyclic LOESS smooth function with a hundred of interactions using the adjusting parameter of 1.0. The normalized data was organized locally and using a Perl (www.perl.org) script we determined the minimum variation (fold change) threshold accepted as been significant.

source_name: Renal cell cancer

label_protocol: BioArray HighYeld RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY)

growth_protocol: snap frozen tissue mantained at -80ºC until the experiment

extract_protocol: Trizol - according to a pre-established protocol (Invitrogen Life Technologies, Carlsbad, CA)

treatment_protocol: patients received neoadjuvant treatment with Sunitinib and were compared with samples from patients treated with surgery only

tag: gender

value: male

tag: group

value: surgery, no neodjuvant


title: R167

value: female

value: neoadjuvant


title: R110


title: R28


title: R209

value: surgery, no adjuvant


title: R34


title: R33


title: R177


title: OvCa78-S

first: Yuriko

last: Uehara

institute: Tokyo University

hyb_protocol: 10 micrograms of fragmented cRNA were hybridized (45 deg C, 16 hours). Hybridization was controlled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining were performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip Scanner 3000 7G.

data_processing: GeneChip analysis was performed using the Affymetrix GeneChip Operating Software v1.4. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: ovarian cancer

label_protocol: In vitro transcription was performed on all of cDNA using the GeneChip IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by metal-induced hydrolysis.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen). 1 microgram of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol Rev.3 recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned by Sample Cleanup Module (Affymetrix).

tag: histology

value: Serous

tag: age

tag: Stage

tag: pfs

tag: prognosis

value: NED


title: OvCa77-S


title: OvCa79-S


title: OvCa80-S

value: AWD


title: R191


title: R204


title: OvCa76-S


title: OvCa74-S


title: OvCa60-S


title: OvCa58-S

value: DOD


title: OvCa64-S


title: OvCa57-E

value: Endometrioid


title: OvCa56-E


title: OvCa73-S


title: OvCa59-S


title: OvCa63-S


title: OvCa61-S


title: OvCa54-E


title: OvCa53-E


title: OvCa75-S


title: OvCa55-E


title: OvCa65-S


title: OvCa50-E


title: OvCa49-E


title: OvCa51-E


title: OvCa40-E


title: OvCa38-E


title: OvCa37-E


title: OvCa39-E


title: OvCa32-C

value: Clear


title: OvCa34-C


title: OvCa41-E


title: OvCa15-C


title: OvCa14-C


title: OvCa33-C


title: OvCa35-C


title: OvCa62-S


title: OvCa18-C


title: OvCa20-C


title: OvCa52-E


title: OvCa36-C


title: OvCa17-C


title: OvCa11-C


title: OvCa16-C


title: OvCa12-C


title: OvCa13-C


title: OvCa19-C


title: OvCa09-C


title: OvCa10-C


title: OvCa08-C


title: Adult-Derived Human Liver Stem/progenitor Cell sample 4

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.12)  under Linux R.3.0.0

source_name: ADHLSC 4

label_protocol: Standard Affymetrix protocol

extract_protocol: Four donors were used in the current study. ADHLSC were obtained subsequently to primary culture of the liver parenchymal fraction previously obtained after a two-step collagenase perfusion, filtration and low speed centrifugation. HSCs were isolated from the corresponding non-parenchymal fraction using a Nycodenz gradient centrifugation step (Myegaard, Oslo, Norway).


title: Adult-Derived Human Liver Stem/progenitor Cell sample 5

source_name: ADHLSC 5


title: OvCa07-C


title: OvCa06-C


title: Adult-Derived Human Liver Stem/progenitor Cell sample 3

source_name: ADHLSC 3


title: Clone 211, Multipotent BMSCs

city: Bethesda

first: Prasun

middle: J.

last: Mishra

address: 37 Convent Drive

department: United States Department of Health and Human Services

institute: National Cancer Institute, National Institutes of Health

description: Gene expression data from 'multipotent' clonal BMSC cultures.

hyb_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

data_processing: The data was analyzed using GeneSpringGX software.  Signal intensity values were normalized using RMA (Robust Multi-array Analysis) summarization and baseline transformation to median of all samples was performed.  Entities were filtered based on their signal intensity values.  A list of top genes under/over represented genes between the groups was generated using Filtered signal intensity (>20.0), non-averaged, fold change >2, 5 and 10 with Mann-Whitney unpaired statistical test (p> 0.05).

source_name: Single colony-derived strains (SCDSs) of human bone marrow stromal cells (BMSCs)

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

growth_protocol: Cell lines were cultured and maintained in growth medium (alphaMEM, 2 mM glutamine, 100 U/ml penicillin, 100 ug/ml streptomycin sulfate, 20% lot-selected fetal bovine, non-heat inactivated serum, 10-8 M dexamethasone and 10-4 M ascorbic acid-2-phosphate)

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

treatment_protocol: BMNCs were plated at low density (2x103 nucleated cells/cm2) into 150mm2 tissue culture-treated dishes (Becton Dickinson), and cultured in growth medium at 37C for 14d without any media replacements. After 14d, single colonies with >50 cells were randomly selected and individually isolated. Only colonies with a round morphology and obvious separation from surrounding colonies were chosen. Colonies were isolated by attaching a cloning cylinder (Bel-Art Products) to the dish using sterile vacuum grease (Baxter Healthcare Corp). Cells were detached with 0.05% Trypsin/EDTA (Invitrogen), and transferred to 1 well of a 6-well dish (Becton Dickinson) with growth medium.  Once the cells approached confluency, they were passaged consecutively into one 75cm2 flask (Becton Dickinson), and then into two 75cm2 flasks.  Once these flasks became confluent, the cells were detached and used for RNA isolation and in vivo transplantation.

tag: cell line

value: clonal BMSC cultures

tag: differential potential

value: multipotent


title: OvCa03-C


title: Clone 302, Multipotent BMSCs

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)


title: Resto_C_PN

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix 3000

data_processing: The data were normalized by the RMA algorithm using GC content from the Partek Genomics Suite software (Partek, St Louis, MO). Background noise was decreased by eliminating PS with a low standard deviation to mean ratio.

source_name: tonsil-derived MSC primed with PN

label_protocol: Biotinylated cRNA were amplified according to the small sample labelling protocol (TwoCycle amplification kit, Affymetrix, Santa Clara, CA)

growth_protocol: BM-MSCs and tonsil-derived stromal cells (Resto) were obtained as previously described (Guilloton F, Blood 2012). Peripheral blood neutrophils were purified using whole blood CD15 microbeads from healthy donors. MSCs were cocultured with PN (ratio 1/1.5) for 1 day in RPMI1640-10% FBS.

extract_protocol: RNA extraction was  performed using RNEasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Stromal cells were extensively washed to remove PN before RNA extraction.

tag: status

value: healthy donor

tag: tissue for msc establishment

value: tonsil

tag: source of pn

value: peripheral blood

tag: treatment

value: primed with PN


title: Resto_C_woPN

source_name: tonsil-derived control (no PN)

value: control (no PN)


title: human hepatic stellate cell sample 5

description: human hepatic stellate cell sample 5

source_name: HSC 5

value: human hepatic stellate cell


title: OvCa02-C


title: Adult-Derived Human Liver Stem/progenitor Cell sample 6

source_name: ADHLSC 6


title: OvCa05-C


title: Adult-Derived Human Liver Stem/progenitor Cell sample 7

source_name: ADHLSC 7


title: Adult-Derived Human Liver Stem/progenitor Cell sample 2

source_name: ADHLSC 2


title: Clone 61, Multipotent BMSCs


title: OvCa01-C


title: Clone 107, Unipotent BMSCs

description: Gene expression data from 'unipotent' clonal BMSC cultures.

value: unipotent


title: human hepatic stellate cell sample 6

description: human hepatic stellate cell sample 6

source_name: HSC 6


title: Clone 109, Unipotent BMSCs


title: human hepatic stellate cell sample 7

description: human hepatic stellate cell sample 7

source_name: HSC 7


title: Clone 99, Unipotent BMSCs


title: OvCa04-C


title: Resto_B_woPN


title: Resto_B_PN


title: human hepatic stellate cell sample 3

description: human hepatic stellate cell sample 3

source_name: HSC 3


title: MSC_C_woPN

source_name: BM-MSC control (no PN)

value: bone marrow


title: human hepatic stellate cell sample 1

description: human hepatic stellate cell sample 1

source_name: HSC 1


title: Resto_A_PN


title: human hepatic stellate cell sample 2

description: human hepatic stellate cell sample 2

source_name: HSC 2


title: MSC_C_PN

source_name: BM-MSC primed with PN


title: Adult-Derived Human Liver Stem/progenitor Cell sample 1

source_name: ADHLSC 1


title: MSC_B_woPN


title: Resto_A_woPN


title: MSC_B_PN


title: wt(AB)_control_rep2

status: Public on May 10 2015

city: Madrid

first: Julio

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

institute: INIA

description:
7 rag +/+ NOI
3 wt zebrafish control biological replicate 2

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC and washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information

organism: Danio rerio

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: Wild-type (family AB) founder zebrafish were originally obtained from David Raible’s fish facility at the University of Washington. Heterozygous rag1 mutant zebrafish  (family Tubingen) obtained from Artemis Pharmaceuticals (Koln, Germany) were spawned to produce isogenic siblings that were predicted to be approximately one-quarter mutant:one-half heterozygous:one-quarter wild type for rag1. Their genotype was determined at 3 to 6 months of age using DNA obtained from a tail clip procedure.Zebrafish were maintained at 24-28 ºC in 30 l aquaria with tap-dechlorinated carbon-filtered water with 1 g of CaCl2, 1 g of NaHCO3 and 0.5 g of Instant Ocean sea salts added to water resulting in a conductivity of 200-300 µS and pH of 7.8-8.2. The aquaria were provided with biological filters and fish fed with a commercial feed diet.

extract_protocol: RNA was extracted using the RNAeasyPlus kit (Qiagen, Hilden, Germany).

treatment_protocol: For each infection experiment, groups of young zebrafish were moved to 2 l aquaria provided with biological filters. To infect zebrafish with SVCV, cell culture medium containing  SVCV was added to 2 l water tanks and fish exposed to the virus for 90 minutes. Mock-infected zebrafish were incubated with cell culture medium in parallel experiments. Fish were then separated in two groups (infected and non-infected). After 2-days zebrafish were sacrified by an overdosage of anesthetics (methanesulfonate 3-aminobenzoic acid ethyl ester, MSS2) and used for the experiments

tag: strain background

value: AB

tag: genotype/variation

value: wild type

tag: developmental stage

value: young adult (6 months)

tag: infected with

value: culture medium (mock control)

tag: tissue

value: head kidney and spleen


title: R29

source_name: Renal cell cancer

tag: gender

value: male

tag: group

value: surgery, no neodjuvant


title: rag1_control_rep2

description:
5 rag -/- NOI
3 rag1 zebrafish control biological replicate 2

value: rag1 -/- mutant


title: rag1_infected_rep1

description:
2 rag -/- I
3 rag1 zebrafish infected biological replicate 1

value: 10^5 pfu/ml of SVCV


title: IGR37 (Expression Human Genome U133 Plus 2.0)

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

description: Lymph node metastasis

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized

scan_protocol: GeneChips were scanned using Gene Chip Operating Software (GCOS 1.2, Affymetrix)

data_processing: The data were analyzed with Bioconductor affy package under statistical R software, computing the RMA (Robust Multichip Average) expression measure in log2 base scale described in Irizarry et al Biostatistics (2003).

source_name: Metastatic tumor cell line (MELANOMA)

growth_protocol: Cell were growth in DMEM complemented with FBS 10% and a combination of antibiotics and antimicotics

extract_protocol: RNA was extracted using TRIZOL methodology

value: lymph node metastasis


title: rag1_infected_rep2

description:
6 rag -/- I
3 rag1 zebrafish infected biological replicate 2


title: wt(AB)_control_rep1

description:
3 rag +/+ NOI
3 wt zebrafish control biological replicate 1


title: MSC_A_woPN

value: healthy donor


title: MSC_A_PN

value: peripheral blood


title: wt (AB)_infected_rep2

description:
8 rag +/+ I
3 wt zebrafish infected biological replicate 2

source_name: wt (AB)_infected


title: wt (AB)_infected_rep1

description:
4 rag +/+ I
3 wt zebrafish infected biological replicate 1


title: IGR39 (Expression Human Genome U133 Plus 2.0)

description: Primary (achromic) cutaneous tumor

source_name: Primary tumor cell line (MELANOMA)

value: primary (achromic) cutaneous tumor


title: rag1_control_rep1

description:
1 rag -/- NOI
3 rag1 zebrafish control biological replicate 1