title: MSK-PCa6

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: DNA Copy number

hyb_protocol: Per manufacturer's instructions

scan_protocol: Per manufacturer's instructions

data_processing: Images quantified with Agilent Feature Extraction ver9.1. Probe sequences were re-mapped to the hg18 build of the human genome and merged. Probe-level data was subsequently normalized for local GC content with a two-stage LOESS fit. Probe-level data is the log2 ratio of organoid-to-normal.

source_name: Organoid DNA

label_protocol: Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5

growth_protocol: Organoids were propagated in vitro in 3D culture. See Gao et. Al. for details.

extract_protocol: DNA was isolated using Qiagen DNAeasy blood and cell culture kit

value: Prostate cancer

tag: organoid

value: locally recurrent bladder invasion

source_name: Promega reference DNA

tag: phenotype

value: normal DNA


title: mESC differentiation at 96h, biological rep3

status: Public on Sep 09 2014

type: RNA

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

country: USA

institute: US FDA

description: Gene expression data during spontaneous differentiation

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: The values of individual probes belonging to one probe set in .CEL files were summarized using the robust multi-array average (RMA) algorithm embedded in the Expression Console software v.1.3 (Affymetrix), which comprises of convolution background correction, quantile normalization, and median polish summarization.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mESC 96h after EB formation

label_protocol: The total RNA samples (50 ng each) were labeled using the GeneChip WT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Pluripotent C57BL/6 mouse ESCs were seeded on 0.1% gelatin-coated flasks, and maintained at 37 °C in a 5% CO2 humidified incubator at standard densities (i.e., between 5×104/cm2 and 5×105/cm2) in ESGRO Complete Plus Clonal Grade Medium (EMD Millipore). The medium contains leukemia inhibitory factor (LIF), bone morphogenic protein 4 (BMP-4), and a glycogen synthase kinase-3b inhibitor (GSK3b-I) to help maintain pluripotency and self-renewal of the ESCs. Cells were passaged every 2-3 days (when reaching 60% confluence) with ESGRO Complete Accutase (EMD Millipore) at about 1:6 ratio.

extract_protocol: EBs were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: ESC differentiation cultures were exposed from the EB stage on day 3 for 24 h to 0.25 mM thalidomide (THD), 2.0 mM monobutyl phthalate (MBP), 1.0 mM valproic acid (VPA), or vehicle (0.25% DMSO).

tag: strain

tag: cell type

value: embryonic stem cell


title: mESC differentiation at 96h, biological rep2


title: Differentiated NPC culture from Caudal Spinal cord (Sp.c) of EAE rat, rep 1

city: Stockholm

first: Ruxandra

last: Covacu

country: Sweden

institute: Karolinska Institutet

description:
NPC culture harvested after second passage and 5 days of differentiation
Rats with EAE

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data processing involved background signal correction using the GC composition-based background correction algorithm (PM-GCBG), array normalization with global median and signal summarization using the probe logarithmic intensity error estimation (plier), all steps performed in the GeneChip Expression console from Affymetrix.
To calculate the statistical significance between naïve and EAE groups two-sided unpaired student’s t-test was used. The false discovery rate (FDR) was calculated using the q-value plugin for R and an FDR level of 5% was set.  The functional analysis and canonical pathway analysis of the entire data set was generated with Ingenuity Pathway Analysis
probe group file: RaGene-1_0-st-v1.r4.pgf
meta-probeset file: RaGene-1_0-st-v1.r4.mps

organism: Rattus norvegicus

source_name: Sp.c Caudal EAE

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

growth_protocol: NPC cultures propagated from different segments of the central nervous system: subventricular zone (SVZ) and the cervical, thoracic and caudal parts of the spinal cord. The segments were isolated from either healthy (naive) rats or rats with EAE.

extract_protocol: Total RNA extraction and on-column DNase treatment was performed using the RNeasy mini kit from Qiagen.

value: Dark Agouti

value: NPC culture

tag: npc culture propagated from

value: Caudal Spinal cord

tag: differentiation stage

value: Differentiated

tag: disease state

value: EAE


title: 2-act K562+IL-2

city: montpellier

first: martin

last: villalba

address: CHU Montpellier Hôpital Saint-Eloi 80, av. Augustin Fliche.

department: INSERM U1040

country: France

institute: Institut for Research in Biotherapy of Montpellier

description: SAMPLE 10

hyb_protocol: For the preparation of mixtures of hybridization, washing, and detection of the arrays, GeneTitan Hybridization, Wash and Stain kit for WT Array Plates were used. Hybridization, developing, washing and scanning of 1.1STHuman Gene arrays was performed on an automated GeneTitan System, as recommended by Affymetrix.

scan_protocol: GeneChips were scanned using the Gene Titan System.

data_processing:
Software used for the processing of the chips and the results were the Affymetrix GeneChip Command Console Software v3.0 (AGCC 3.0, Affymetrix®) and the Expression Console Software v1.1 (Affymetrix®).
We used the software dChip (www.dchip.org) to determine the existence of cross-hybridization and image contamination. We applied the program Expression Console ofAffymetrix (Gene arrays) and Partek Genomics Suite (miRNA arrays) to obtain the RLE (Relative Log Expression), in which the expression of each probe is normalized with an array of reference built with the average of all arrays for each probe set. The intensity values for each probe were processed and normalized by Robust Multichip Average (RMA). We eliminated sequences with intensities close to the background and, after normalization, those ones that did not change during the experiment in order to reduce the number of genes and the false positives. For the Gene Array we finally obtained a work list of 8711 sequences and for the miRNA we obtained 4581 (selection of all human miRNA present in the microarray).
The softwares consider as present all p-values under 0.06.

organism: Homo sapiens

source_name: NK cells_act K562+IL-2

label_protocol: cDNA was synthesized from total RNA and, after fragmentation, hybridized with the chips, following the protocol proposed by Affymetrix. Specifically, 16 total RNA samples were used to generate cDNA with the Ambion® WT Expression kit. The main steps of the protocol were: synthesis of cDNA with random oligonucleotides including the T7 promoter, transcription in vitro; new synthesis of cDNA from the resulting cRNA from above, including dUTP. The obtained cDNA was fragmented using UDG (uracil DNA glycosylase) and APE1 (apurinic/apyrimidinic endonuclease1) and labeled with terminal transferase using the terminal WT Labeling kit.

growth_protocol: 5 days RPMI 5%CO2, 37 C, 1 million/ml

extract_protocol: microRNA were isolated from enriched ex vivo or activated NK cells (more than 90% purity) by using the mirVana miRNA (Invitrogen) Isolation Kit

treatment_protocol: PBLs from 4 different donors were activated by 100 U/ml IL-2; K562+IL-2 or R69 cells. After 5 days we obtained RNA and miRNA from naïve NK cells or from NK cells activated with the above mentioned stimuli. The 16 RNA samples were used to generate cDNA libraries that were hybridized on Human Gene 1.1ST arrays (Affymetrix) and analyzed with the Affymetrix Gene Chip Command Console Software v3.0 (AGCC 3.0, Affymetrix®) and the Expression Console Software v1.1 (Affymetrix®).

tag: donor id

value: donor 2

value: peripheral blood lymphocytes

tag: activated by

value: MHC-I-deficient target cell (K562)+IL-2

tag: cell subtype

value: purified NK cells


title: Differentiated NPC culture from Thoracic Spinal cord (Sp.c) of Naive rat, rep 3

description:
NPC culture harvested after second passage and 5 days of differentiation
Healthy rats

source_name: Sp.c Thoracic Naive

value: Thoracic Spinal cord

value: Healthy


title: MSK-PCa5

type: genomic

description: DNA Copy number

molecule: genomic DNA

value: circulating tumor cell


title: 70380_Time-4

city: Baltimore

first: Ashwin

last: Balagopal

address: 855 North Wolf Street, Rangos Building Room 520

department: Medicine

institute: Johns Hopkins Univ. School of Medicine

description: Test

data_processing:
Crt values from the Expression Suite® (Life Technologies)  below 35 were quantile normalized using R (v.3.0.2)/Bioconductor (v.2.12).
Quantile normalized Crts are presented in the normalized matrix and 2^deltaCrt  values (using the pre-infection level as a reference) are shown in the fold-change matrix.
Please note that the normalized data set does not include controls and only includes genes that were detected in at least one sample of the non-normalized data set.

label: FAM

extract_protocol: 100 uL of plasma was extracted using the miRvana PARIS miRNA isolation kit (Life Technologies) according to the manufacturer's protocol for total RNA isolation. 5pmol of synthetic ath-miR-159a was added to each sample's lysis buffer prior to extraction.

tag: subject id

tag: acute hcv outcome

value: Persist

tag: time point

value: plasma


title: 3-act IL-2

description: SAMPLE 7

source_name: NK cells_act IL-2

value: donor 3


title: 70380_Time-3

description: Test


title: mESC differentiation at 96h, biological rep1


title: 70380_Initial-Viremia

description: Test

source_name: Initial-Viremia

value: Initial-Viremia


title: MSK-PCa4

description: DNA Copy number

value: Prostate cancer

value: pleural effusion

value: normal DNA


title: Differentiated NPC culture from Thoracic Spinal cord (Sp.c) of Naive rat, rep 2

value: Dark Agouti

value: NPC culture


title: 1-act IL-2

description: SAMPLE 5

value: donor 1


title: 2-act IL-2

description: SAMPLE 6

value: donor 2


title: MSK-PCa7

description: DNA Copy number

value: pelvic lymph node


title: 70380_Pre-Infection

description: Control

source_name: Pre-Infection

value: Pre-Infection


title: MSK-PCa2

description: DNA Copy number

value: bone metastasis


title: MSK-PCa1

description: DNA Copy number


title: 50027_Time-4

description: Test

value: Clear


title: Differentiated NPC culture from Thoracic Spinal cord (Sp.c) of Naive rat, rep 1

value: Thoracic Spinal cord

value: Differentiated

value: Healthy


title: Differentiated NPC culture from Thoracic Spinal cord (Sp.c) of EAE rat, rep 3

source_name: Sp.c Thoracic EAE

value: EAE


title: 50027_Time-3

description: Test

value: plasma


title: MSK-PCa3

description: DNA Copy number

value: pelvic metastasis


title: 4-naive

description: SAMPLE 4

source_name: NK cells_naive

value: donor 4

value: peripheral blood lymphocytes

value: none(naïve control)

value: purified NK cells


title: Differentiated NPC culture from Thoracic Spinal cord (Sp.c) of EAE rat, rep 2

value: Dark Agouti

value: NPC culture


title: mESC differentiation at 72h, biological rep2

source_name: mESC 72h after EB formation

value: embryonic stem cell


title: 50027_Initial-Viremia

description: Test

value: Initial-Viremia


title: 3-naive

description: SAMPLE 3

value: donor 3


title: 50027_Pre-Infection

description: Control

value: Pre-Infection


title: 2-naive

description: SAMPLE 2

value: donor 2


title: mESC differentiation at 72h, biological rep1


title: 1-naive

description: SAMPLE 1

value: donor 1


title: mESC differentiation at 48h, biological rep3

source_name: mESC 48h after EB formation


title: 70517_Time-4

description: Test

value: Persist


title: Differentiated NPC culture from Cervical Spinal cord (Sp.c) of Naive rat, rep 3

source_name: Sp.c Cervical Naive

value: Cervical Spinal cord

value: Differentiated

value: Healthy


title: mESC differentiation at 48h, biological rep1


title: Differentiated NPC culture from Cervical Spinal cord (Sp.c) of Naive rat, rep 2


title: 70517_Time-3

description: Test

value: plasma


title: Differentiated NPC culture from Cervical Spinal cord (Sp.c) of Naive rat, rep 1


title: Differentiated NPC culture from Thoracic Spinal cord (Sp.c) of EAE rat, rep 1

value: Thoracic Spinal cord

value: EAE


title: 70517_Pre-Infection

description: Control


title: mESC differentiation at 72h, biological rep3


title: 70517_Initial-Viremia

description: Test


title: Differentiated NPC culture from Cervical Spinal cord (Sp.c) of EAE rat, rep 3

source_name: Sp.c Cervical EAE


title: Differentiated NPC culture from Cervical Spinal cord (Sp.c) of EAE rat, rep 1


title: Differentiated NPC culture from SVZ of Naive rat, rep 2

source_name: SVZ Naive

value: SVZ


title: 50104_Time-4

description: Test

value: Clear


title: mESC differentiation at 0h, biological rep3

source_name: mESC 0h after EB formation


title: cells obtained from MSKCC, 002

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: no additional information

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: cells obtained from pleural effusion

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: age

tag: sex

value: F

tag: ethnic group

value: asian

tag: smoking status

value: non-smoker


title: mESC differentiation at 24h, biological rep2

source_name: mESC 24h after EB formation

value: embryonic stem cell


title: 50104_Time-3

description: Test


title: cells obtained from MSKCC, 001

description: no additional information

source_name: cells obtained from LN

value: white

value: unknown


title: Differentiated NPC culture from Cervical Spinal cord (Sp.c) of EAE rat, rep 2

value: Dark Agouti

value: NPC culture


title: mESC differentiation at 24h, biological rep3


title: 50104_Initial-Viremia

description: Test

value: Initial-Viremia


title: Differentiated NPC culture from SVZ of Naive rat, rep 3


title: mESC differentiation at 0h, biological rep1


title: cells obtained from MSKCC, 003

description: no additional information

source_name: cells obtained from lung tumor

value: M


title: cells obtained from MSKCC, 004

description: no additional information

source_name: cells obtained from pericardial effusion


title: large airways, basal cell culture smoker 353

description: no additional information

source_name: basal cell culture from large airway epithelial cells obtained by bronchoscopy and brushing

value: black

value: smoker, 35 pack-years


title: 50104_Pre-Infection

description: Control

value: Pre-Infection

value: plasma


title: mESC differentiation at 48h, biological rep2


title: large airways, basal cell culture smoker 328

description: no additional information

value: smoker, 20 pack-years


title: mESC differentiation at 24h, biological rep1


title: mESC differentiation at 0h, biological rep2


title: Differentiated NPC culture from SVZ of EAE rat, rep 3

source_name: SVZ EAE

value: SVZ

value: Differentiated

value: EAE


title: Differentiated NPC culture from SVZ of EAE rat, rep 2


title: 50068_Time-4

description: Test

value: Persist


title: 50068_Time-3

description: Test


title: large airways, basal cell culture smoker 359

description: no additional information

value: smoker, 9 pack-years


title: large airways, basal cell culture smoker 350

description: no additional information

value: smoker, 19 pack-years


title: Differentiated NPC culture from SVZ of EAE rat, rep 1


title: 50068_Initial-Viremia

description: Test

source_name: Initial-Viremia


title: hMSC AD D13 Rep3

city: Riyadh

first: Nehad

middle: M

last: Alajez

address: 1st floor College of Medicne

department: Anatomy

country: Saudi Arabia

institute: King Saud University College of Medicine

description:
microRNA expression on MSCs differentiated into adipocytes (day 13)
AD D13 Rep3

hyb_protocol: Labeled RNA was hybridized on the miRCURY LNA™ microRNA Array (6'th GEN). Array product number 208400  Array version 6'th GEN, Array batch number 34014, miRBase version 17, GPL16968.

scan_protocol: The miRCURY LNA™ microRNA  Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent  Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9  (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: hMSC_adipocytic differentiation_day13

label_protocol: The samples were labeled using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™

growth_protocol: Cells were grown in DMEM 4.5g/l glucose supplemented with 10% fetal bovine serum, 1% NEAA, 1% L-glutamine, 100 mg/l penicillin, and 100 mg/l streptomycin

extract_protocol: RNA was extracted using TRIZOL method

treatment_protocol: hMSC-TERT cells were cultured in basal medium in 24-well tissue culture plates. When cells reached 80-90% confluence, medium was replaced with Adipogenic induction medium (AIM) (DMEM medium supplemented with 10 % FBS, 10 % Horse Serum, 1 % Penicillin-Streptomycin, 100 nM dexamethasone, 0.45 mM isobutyl methyl xanthine (IBMX), 3 μg/mL insulin, and 1 μM Rosiglitazone. Control cells were cultured in parallel in normal DMEM medium. Cells pellets and RNA was extracted on days 0, 7, and 13.

value: human bone marrow MSCs (hMSC-TERT)

value: adipocytic differentiation for 13 days

source_name: common reference RNA pool

tag: sample type

value: equal amounts of all of the analyzed RNA samples


title: hMSC AD D13 Rep2

description:
microRNA expression on MSCs differentiated into adipocytes (day 13)
AD D13 Rep2


title: 50068_Pre-Infection

description: Control

source_name: Pre-Infection


title: Differentiated NPC culture from SVZ of Naive rat, rep 1

value: Dark Agouti

value: NPC culture

value: Healthy


title: 10113_Time-4

description: Test

value: Clear


title: hMSC AD D13 Rep1

description:
microRNA expression on MSCs differentiated into adipocytes (day 13)
AD D13 Rep1


title: 10113_Time-3

description: Test


title: hMSC AD D7 Rep3

description:
microRNA expression on MSCs differentiated into adipocytes (day 7)
AD D7 Rep3

source_name: hMSC_adipocytic differentiation_day7

value: adipocytic differentiation for 7 days


title: hMSC AD D7 Rep2

description:
microRNA expression on MSCs differentiated into adipocytes (day 7)
AD D7 Rep2


title: 10113_Initial-Viremia

description: Test

value: Initial-Viremia


title: Undifferentiated NPC culture from Caudal Spinal cord (Sp.c) of Naive rat, rep 2

description:
NPC culture harvested after second passage
Healthy rats

source_name: Sp.c Caudal Naive

value: Caudal Spinal cord

value: Undifferentiated


title: GV-MII-Replicate 4

city: Quebec

first: Eric

last: Fournier

state: Quebec

address: 2325 Rue de l'Universite

department: Departement des sciences animales

country: Canada

institute: Universite Laval

description: MII-D-GV-B

hyb_protocol: Slides were hybridized for 17 hours at 65°C then washed for 1 minute in gene expression wash buffer 1, 3 minute in gene expression buffer 2 then 10 seconds in 100% acetonitrile and 30 seconds in stabilization and drying solution (Agilent).

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.)

data_processing:
Features were extracted using ArrayPro version 6.3. Data was then processed using R v3.0.1 and the limma Bioconductor package, version 3.16.8. Loess curves were fitted to drosophila control probes for all channels of all arrays. Probe intensities were then normalized against this control curve. Further inter-array scale normalization was performed on the resulting intensities.
The normalized log2 ratio (GV/MII) data is provided in the 'normalized_data.txt' file. Please note that data were scanned/extracted using a different Agilent reference file, and thus the feature extraction number for a given probe (in both normalized and raw data files) is different from that in the official Agilent-041017 platform (GPL18537). The reference file used for this study is provided as a Series supplementary file (041017_D_DNAFront_BCBottom_20120517.txt).

organism: Bos taurus

source_name: Metaphase-II oocytes

label_protocol: Polyribosomal mRNA samples were amplified by in vitro transcription using RiboAmp HS plus RNA amplification kit (Life Science) to obtain antisense RNA. 825 ng of antisense RNA was labelled using ULS Fluorescent Labeling Kit (Kreatech) and hybridized on a microarray slide.

growth_protocol: Cumulus oocytes complexes (COC) having a minimum of five layers of cumulus were washed in HEPES-buffered Tyrode’s medium supplemented with bovine serum albumine, pyruvic acid and gentamycin. Oocytes at germinal vesicle (GV) stage were collected, pipetted up and down to remove cumulus cells then washed in PBS containing 100 μg/ml of cycloheximide (CHX) to stop translation and to prevent ribosomal run-off. To obtain metaphase II oocytes (MII), groups of 50 COC were placed in four-well petri dishes in maturation medium under mineral oil and incubated during 24 hours at 38.5°C with 5% CO2. MII oocytes were denuded the same way as GV oocytes.

extract_protocol: Oocytes used for polyribosomal fractionation were strongly vortexed with 1,0 mm zirconia-silica beads in 50 μl of polyribosome lysis buffer to break the bovine zona pellucida. After lysis, 50 μl of drosophila carrier sample was mixed to the dissolved oocytes and was then transferred in a new tube to discard the beads. Cell debris were removed by centrifuging at 12,000 x g for 20 minutes at 4°C. Each sample was loaded on a 4 ml linear 15%-45% sucrose gradient generated using a SG-15 gradient maker (Hoefer, Holliston, MA, USA). Sucrose solutions were prepared in isotonic buffer made of 150 mM KCl, 1,25 mM MgCl2 and 50 mM Tris adjusted to a pH of 8,7. The linear gradients were kept at 4°C until use. Once the bovine-drosophila mixed RNA was drop off on the top of the sucrose gradient, it was ultracentrifugated for 3 hours at 34,000 rpm using a SW 60 Ti rotor (Beckman Coulter, Brea, CA, USA). The gradients were processed using a BR-188 Density Gradient Fractionation System (Brandel, Gaithersburg, MD, USA). Fractions of 350 μl were collected with continuous monitoring of absorbance at 254 nm using an Isco UA-6 detector (Teledyne Isco, Lincoln, NE, USA). Each fraction was collected directly in 12 tubes containing 428 μl of 5.25 M  guanidinium thiocyanate (pH 5.5) and 2 μl (5 μg/μl) of linear polyacrylamide (Ambion, Austin, Texas, USA) that acts as an RNA co-precipitant. Fractions corresponding to polyribosomal RNA were defined according to the UV-distribution profile and pooled in 30 ml Corex tubes. To allow additional normalization, 1 μl of 1/10,000 ERCC spikes was added to the polyribosomal sample. NaOAC 3M ph 5,5 and 100% ethanol were added to allow RNA precipitation.  Samples were left overnight at -20°C. RNA precipitates were then re-suspended in the extraction buffer provided in the PicoPure RNA extraction kit (Life Science) and extracted with this kit.

tag: tissue

value: Metaphase-II oocytes

tag: pool size

tag: molecute subtype

value: Poly-ribosomal RNA

source_name: Germinal vesicle oocytes

value: Germinal vesicle oocytes


title: Undifferentiated NPC culture from Caudal Spinal cord (Sp.c) of Naive rat, rep 1

tag: strain

tag: cell type

tag: npc culture propagated from


title: hMSC AD D7 Rep1

description:
microRNA expression on MSCs differentiated into adipocytes (day 7)
AD D7 Rep1


title: GV-MII-Replicate 3

description: GV-B-MII-D


title: Undifferentiated NPC culture from Caudal Spinal cord (Sp.c) of Naive rat, rep 3

tag: differentiation stage

tag: disease state


title: Undifferentiated NPC culture from Caudal Spinal cord (Sp.c) of EAE rat, rep 3

description:
NPC culture harvested after second passage
Rats with EAE

source_name: Sp.c Caudal EAE

value: EAE


title: 10113_Pre-Infection

description: Control

value: Pre-Infection

value: plasma


title: hMSC AD D0 Rep2

description:
microRNA expression on MSCs D0
AD D0 Rep2

source_name: hMSC_adipocytic differentiation_day0

value: human bone marrow MSCs (hMSC-TERT)

value: adipocytic differentiation for 0 day (control)


title: hMSC AD D0 Rep3

description:
microRNA expression on MSCs D0
AD D0 Rep3

value: equal amounts of all of the analyzed RNA samples


title: GV-MII-Replicate 2

description: MII-C-GV-C


title: Undifferentiated NPC culture from Caudal Spinal cord (Sp.c) of EAE rat, rep 1

value: Dark Agouti


title: Undifferentiated NPC culture from Caudal Spinal cord (Sp.c) of EAE rat, rep 2

value: NPC culture


title: large airways, basal cell culture non-smoker 118

description: no additional information

value: F

value: white

value: non-smoker


title: hMSC AD D0 Rep1

description:
microRNA expression on MSCs D0
AD D0 Rep1


title: Undifferentiated NPC culture from Thoracic Spinal cord (Sp.c) of Naive rat, rep 2

source_name: Sp.c Thoracic Naive

value: Thoracic Spinal cord

value: Healthy


title: large airways, basal cell culture non-smoker 169

description: no additional information


title: Undifferentiated NPC culture from Thoracic Spinal cord (Sp.c) of Naive rat, rep 1

value: Undifferentiated


title: GV-MII-Replicate 1

description: GV-A-MII-A

value: Metaphase-II oocytes


title: Undifferentiated NPC culture from Thoracic Spinal cord (Sp.c) of Naive rat, rep 3


title: Undifferentiated NPC culture from Thoracic Spinal cord (Sp.c) of EAE rat, rep 2

source_name: Sp.c Thoracic EAE


title: Undifferentiated NPC culture from Thoracic Spinal cord (Sp.c) of EAE rat, rep 1


title: large airways, basal cell culture non-smoker 194

description: no additional information

value: M

value: black


title: Normal OPC 1

city: Eugene

first: Rui

middle: Pedro

last: Galvao

state: Oregon

address: 1229 University of Oregon

institute: University of Oregon

description: Normal OPC (1)

hyb_protocol: Agilent microarray protocol

scan_protocol: After scanning the images by using a GenePix 4000B scanner, the intensity values were extracted by using the Agilent Feature Extraction Software.

data_processing: Probe sequences were downloaded from the Agilent website and aligned to a transcript sequence database consisting of 49,040 Mus musculus genes from Ensembl57. After removing probes that did not align, or aligned with more than 5 mismatches (n = 19,194), or probes that aligned to multiple genes (n = 2,283), 23,006 probes representing 17,585 genes remained. Expression profiles were quantile normalized and log transformed

source_name: Normal OPC (immunopanned from P8 brains)

label_protocol: Test samples were labeled with Cy5 fluorophore. Reference samples were labeled with Cy3 fluorophore.

extract_protocol: Mice were decapitated and brains dissected. Tumor was identified by fluorescence under dissecting scope and acutely dissected. Tissue was placed in Trizol and total RNA was purified.

value: OPC

tag: treatment

tag: mutation induction age

source_name: common reference (RNA pool of four WT P17 mouse brain neocortex)

tag: reference

value: WT P17 mouse brain neocortex


title: Normal OPC 2

description: Normal OPC M2962 (2)

value: Normal OPC (immunopanned from P8 brains)


title: TempranilloBerrySkin_26ºBrix_FUV-_rep3

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the third of three replicates of 26 ºBrix berries for the FUV- (UV-blocking filter) treatment, each from separate blocks.

hyb_protocol: If the quality control was correct, then 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent technologies).

data_processing: After evaluation of hybridization quality by Experimental metrics report implemented in NimbleScan Software version 2.6 (NimbleGen-Roche), probeset signal values from all the microarray hybridizations were background corrected and normalized together using Robust Microarray Average (RMA) (Irizarry et al., 2003) in NimbleScan Software, which produces a calls file for each sample with normalized expression data for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera cv Tempranillo berry skin, skin from 26 ºBrix berries, FUV- filter treatment

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

growth_protocol: The field experiment was conducted in the 2012 season in a commercial vineyard located in Mendavia (Navarra, northern Spain, 42º 27’ N, 2º 14’ W, 371 m asl). Vitis vinifera L. cv. Tempranillo, grafted onto 110R rootstocks and planted in 2007 on clay-loam soil with NE-SW row orientation. The vines were spur-pruned (12 buds per vine) in a bilateral cordon and trained to a VSP trellis system. At pre-bloom (7 June 2012 , seven days before flowering), all vines were partially defoliated by removing the first six main basal leaves to increase and homogenize the exposure of fruits to solar radiation. Shoots were trimmed once at the end of July, before veraison. Vines were not irrigated during the growing season.

extract_protocol: About 15 frozen berries on each sample were peeled and frozen berry skins were used for RNA extraction. Total RNA was extracted as described by Reid et al. (Reid et al., 2006). DNase digestion of contaminating DNA in the RNA samples was carried out with the RNase-Free DNase Set (QIAGEN). Final RNA purification was carried out using the SpektrumTM Plant Total RNA kit (Sigma-Aldrich) according to standard protocols.

treatment_protocol: A completely randomized block design was set-up. Three blocks of nine vines were divided into three experimental conditions (three vines per replicate): no filter (Ambient), UV-transmitting filter (FUV+), and UV-blocking filter (FUV-). These two filtered treatments were established using colorless and transparent polymetacrylate filters (PMMA XT Vitroflex 295 and XT Vitroflex 395 Solarium Incoloro, Polimertecnic, Girona, Spain), which allowed and blocked, respectively, the transmission of UV radiation. Filters (1.30 x 0.75 m) were placed at 45º from the vertical axis of the plant, on both sides of the canopy, covering the fruiting zone and the first 0.7 m of the canopy of each grapevine. Filters were installed right after defoliation and   maintained until harvest (7 September 2012).

value: FUV-

tag: cultivar

value: Tempranillo

value: Berry skin

tag: berry total soluble solids

value: 26 ºBrix


title: Glioma grafted 1

description: 13724 (11)

source_name: Glioma grafted (acute dissection, no cell purification)

value: Glioma

value: Glioma grafted

value: Graft


title: TempranilloBerrySkin_26ºBrix_FUV-_rep2

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the second of three replicates of 26 ºBrix berries for the FUV- (UV-blocking filter) treatment, each from separate blocks.


title: Glioma grafted 2

description: 14205 (12)


title: Undifferentiated NPC culture from Cervical Spinal cord (Sp.c) of Naive rat, rep 3

source_name: Sp.c Cervical Naive

value: Dark Agouti

value: NPC culture

value: Cervical Spinal cord


title: TempranilloBerrySkin_26ºBrix_FUV+_rep3

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the third of three replicates of 26 ºBrix berries for the FUV+ (UV-transmitting filter) treatment, each from separate blocks.

source_name: Vitis vinifera cv Tempranillo berry skin, skin from 26 ºBrix berries, FUV+ filter treatment

value: FUV+


title: Fungal cells / Free bacteria aspergillusvsbacillus8

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University of Jena

description: identification of cross hybridization of Aspergillus niger RNA on B. subtilis platform (fungal RNA vs bacterial RNA)

hyb_protocol: Hybridization in a dye-swap design was performed using the Agilent Gene Expression Hybridization Kit (Agilent technologies CA, USA) at 65°C for 17 h to genome-wide multi-strain E. coli (8x15K) microarrays of 60-mer oligonucleotides (Agilent Technologies, CA, USA). Two microarrays in the slides were used per evolved colony type (two biological replicas). Each replica was labeled with a different dye (cy3 or cy5)  and hybridazed to the ancestors labeled with the oposite dye.

scan_protocol: Scanning was performed using GenePix autoloader 4200AL confocal laser scanner (Molecular devices Ltd.) according to the provider's protocol. http://www.moleculardevices.com

data_processing: Statistical analysis was performed using R Limma package (Linear Models for Microarrays Data)  (Smyth 2004), where the two microarrays per sample were normalized using lowess normalization method. Multiple-gene probes results were merged and normalized using the MA table conversion tool available on the MOLGEN Bioinformatics Server (http://server.molgenrug.nl/ - Molecular genetics, university of Groningen, the Netherlands).

organism: Bacillus subtilis

source_name: Bacterial cells

label_protocol: High quality RNA samples were reverse-transcribed into cDNA with the Superscript III reverse transcriptase kit (Invitrogen, Carlsbad, USA) and labeled with Dylight Amine-Reactive Dyes Cy3 and Cy5 (Thermo Scientific, Rockford, USA).

growth_protocol: B subtilis NCIB3610 cells were grown in the presence of Aspergillus niger CB 119.1 hyphae for 3 hours. The mycelium and the attached bacteria were separated from the non-attached B. subtilis cells via filtration through Miracloth. The mycelia and attached bacteria were briefly rinsed with TY medium, dried, and the sample was frozen in liquid nitrogen. Bacterial cells in the flow-through medium fraction were harvested by centrifugation at 10.397 g for 1 min.

extract_protocol: To extract RNA mainly from the bacterial cells, lysozyme solution and RiboLock (Thermo  Scientific) was added followed by incubation at 37 C for 30 minutes. Further RNA extraction was performed with the Macaloid/Roche method as described before (van Hijum et al., 2005, Kovács and Kuipers, 2011) but omitting the bead beater treatment and using RiboLock.

treatment_protocol: no treatment

value: free B. subtilis cells

organism: Aspergillus niger

source_name: Aspergillus niger

value: control - Aspergillus niger


title: Undifferentiated NPC culture from Thoracic Spinal cord (Sp.c) of EAE rat, rep 3

value: Thoracic Spinal cord

value: Undifferentiated

value: EAE


title: Undifferentiated NPC culture from Cervical Spinal cord (Sp.c) of EAE rat, rep 3

source_name: Sp.c Cervical EAE


title: Undifferentiated NPC culture from Cervical Spinal cord (Sp.c) of EAE rat, rep 2


title: TempranilloBerrySkin_26ºBrix_FUV+_rep2

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the second of three replicates of 26 ºBrix berries for the FUV+ (UV-transmitting filter) treatment, each from separate blocks.


title: Attached / Free bacteria aspergillusvsbacillus7

description: comparison of attached vs free B. subtilis cells

value: attached B. subtilis cells


title: Glioma P180 induction 4

description: 12065c (10)

source_name: Glioma P180 induction (acute dissection, no cell purification)

value: OPC

value: Glioma induction

value: WT P17 mouse brain neocortex


title: TempranilloBerrySkin_26ºBrix_FUV+_rep1

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the first of three replicates of 26 ºBrix berries for the FUV+ (UV-transmitting filter) treatment, each from separate blocks.

value: Tempranillo

value: Berry skin

value: 26 ºBrix


title: Undifferentiated NPC culture from Cervical Spinal cord (Sp.c) of Naive rat, rep 1

value: Healthy


title: TempranilloBerrySkin_26ºBrix_FUV-_rep1

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the first of three replicates of 26 ºBrix berries for the FUV- (UV-blocking filter) treatment, each from separate blocks.

value: FUV-


title: Glioma P180 induction 3

description: 12059 (9)


title: Undifferentiated NPC culture from Cervical Spinal cord (Sp.c) of Naive rat, rep 2

value: Dark Agouti

value: NPC culture


title: Glioma P180 induction 1

description: 13597 (7)


title: TempranilloBerrySkin_23ºBrix_FUV-_rep3

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the third of three replicates of 23 ºBrix berries for the FUV- (UV-blocking filter) treatment, each from separate blocks.

source_name: Vitis vinifera cv Tempranillo berry skin, skin from 23 ºBrix berries, FUV- filter treatment

value: 23 ºBrix


title: Undifferentiated NPC culture from Cervical Spinal cord (Sp.c) of EAE rat, rep 1

value: Cervical Spinal cord


title: Undifferentiated NPC culture from SVZ of Naive rat, rep 3

source_name: SVZ Naive

value: SVZ


title: Glioma P180 induction 2

description: 12065a (8)


title: Undifferentiated NPC culture from SVZ of Naive rat, rep 2


title: Glioma P45 induction 6

description: 12964 (6)

source_name: Glioma P45 induction (acute dissection, no cell purification)


title: Glioma P45 induction 5

description: 12948 (5)


title: Attached / Free bacteria aspergillusvsbacillus5

value: free B. subtilis cells


title: Undifferentiated NPC culture from SVZ of Naive rat, rep 1

value: Undifferentiated


title: Attached / Free bacteria aspergillusvsbacillus3


title: Attached / Free bacteria aspergillusvsbacillus4


title: Attached / Free bacteria aspergillusvsbacillus2


title: TempranilloBerrySkin_23ºBrix_FUV-_rep1

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the first of three replicates of 23 ºBrix berries for the FUV- (UV-blocking filter) treatment, each from separate blocks.


title: Undifferentiated NPC culture from SVZ of EAE rat, rep 2

source_name: SVZ EAE

value: EAE


title: TempranilloBerrySkin_23ºBrix_FUV+_rep3

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the third of three replicates of 23 ºBrix berries for the FUV+ (UV-transmitting filter) treatment, each from separate blocks.

source_name: Vitis vinifera cv Tempranillo berry skin, skin from 23 ºBrix berries, FUV+ filter treatment

value: FUV+


title: Glioma P45 induction 4

description: 12968 (4)

value: OPC


title: TempranilloBerrySkin_23ºBrix_FUV-_rep2

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the second of three replicates of 23 ºBrix berries for the FUV- (UV-blocking filter) treatment, each from separate blocks.


title: Undifferentiated NPC culture from SVZ of EAE rat, rep 3


title: Glioma P45 induction 3

description: 12963 (3)

value: Glioma induction


title: Undifferentiated NPC culture from SVZ of EAE rat, rep 1


title: Glioma P45 induction 2

description: 12960 (2)

value: WT P17 mouse brain neocortex


title: Glioma P45 induction 1

description: 12814 (1)


title: TempranilloBerrySkin_23ºBrix_FUV+_rep2

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the second of three replicates of 23 ºBrix berries for the FUV+ (UV-transmitting filter) treatment, each from separate blocks.

value: Tempranillo


title: Lgr5med_Ki67hi_rep4

status: Public on Sep 08 2014

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Mouse Gene ST 1.1 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: FACS sorted epithelial intestinal cells, Lgr5-EGFP-med, Ki67-RFP-high

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 200 ng of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: We used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter, and Ki67-TagRFP mice where the RFP is fused to the C-terminus of the endogenous Ki67 gene. RNA was isolated from several FACS sorted cell populations of combinations expressing different levels of GFP and RFP: GFP high RFP high (Lgr5hi Ki67hi), GFP high RFP low (Lgr5hi Ki67low), GFP medium RFP high (Lgr5med Ki67high) and GFP medium RFP low (Lgr5med Ki67low).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

tag: lgr5 expression level

value: medium

tag: ki67 expression level

value: high


title: Attached / Free bacteria aspergillusvsbacillus1

value: attached B. subtilis cells


title: Lgr5med_Ki67hi_rep3

value: FACS sorted epithelial intestinal cells, Lgr5-EGFP-med, Ki67-RFP-high


title: Lgr5med_Ki67low_rep1

source_name: FACS sorted epithelial intestinal cells, Lgr5-EGFP-med, Ki67-RFP-low

value: low


title: Lgr5med_Ki67low_rep2

value: FACS sorted epithelial intestinal cells, Lgr5-EGFP-med, Ki67-RFP-low


title: Lgr5med_Ki67hi_rep1


title: Lgr5med_Ki67hi_rep2


title: Lgr5hi_Ki67low_rep1

source_name: FACS sorted epithelial intestinal cells, Lgr5-EGFP-high, Ki67-RFP-low


title: Lgr5hi_Ki67low_rep2

value: FACS sorted epithelial intestinal cells, Lgr5-EGFP-high, Ki67-RFP-low


title: TempranilloBerrySkin_23ºBrix_FUV+_rep1

description: This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2012/09/07 noon time. It is the first of three replicates of 23 ºBrix berries for the FUV+ (UV-transmitting filter) treatment, each from separate blocks.

value: Berry skin

value: 23 ºBrix


title: Lgr5hi_Ki67hi_rep2

source_name: FACS sorted epithelial intestinal cells, Lgr5-EGFP-high, Ki67-RFP-high


title: large airways, basal cell culture non-smoker 165

description: no additional information

source_name: basal cell culture from large airway epithelial cells obtained by bronchoscopy and brushing

tag: age

tag: sex

value: M

tag: ethnic group

value: white

tag: smoking status

value: non-smoker


title: Lgr5hi_Ki67hi_rep1

value: FACS sorted epithelial intestinal cells, Lgr5-EGFP-high, Ki67-RFP-high


title: TCR WT2 CD62Lhi

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

description: TCRbeta-positive CD44loCD62Lhi Foxp3-positive CD4+ T cells from tamoxifen-treated Foxp3-CreERT2 CalphaFL/WT mice

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Expression arrays were normalized in Bioconductor, using RMA and median polish settings in the expresso package.

source_name: Spl and LN sorted cells

label_protocol: Affymetrix protocol

growth_protocol: Cells were harvested from 6-8wk old mice.  T cells were purified using positive selection and sorted on CD4, GFP, TCRbeta, CD44, CD62L.

extract_protocol: RNA was extracted using Trizol according to manufacturer's instructions.

value: Treg

tag: genotype/variation

value: TCRbeta-positive CD44loCD62Lhi


title: TCR KO3 CD62Lhi

description: TCRbeta-negative CD44loCD62Lhi Foxp3-positive CD4+ T cells from tamoxifen-treated Foxp3-CreERT2 CalphaFL/WT mice

tag: strain

value: TCRbeta-negative CD44loCD62Lhi


title: TCR WT2 CD44hi

description: TCRbeta-positive CD44hiCD62Llo Foxp3-positive CD4+ T cells from tamoxifen-treated Foxp3-CreERT2 CalphaFL/WT mice

tag: cell type

value: TCRbeta-positive CD44hiCD62Llo


title: TCR WT3 CD62Lhi


title: TCR KO2 CD62Lhi


title: TCR KO1 CD62Lhi


title: TCR WT1 CD44hi


title: TCR KO2 CD44hi

description: TCRbeta-negative CD44hiCD62Llo Foxp3-positive CD4+ T cells from tamoxifen-treated Foxp3-CreERT2 CalphaFL/WT mice

value: TCRbeta-negative CD44hiCD62Llo


title: TCR KO1 CD44hi


title: 4_110711

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

description:
total RNA (>200 nt)
Gene expression data from S. aureus HG001

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip S_aureus Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit..

scan_protocol: Arrays were scanned in an Affymetrix GeneChip scanner 3000 with G7 update

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

label: Biotin

organism: Staphylococcus aureus

source_name: S. aurueus HG001

label_protocol: Biotinylated cRNA were prepared according to the ExpressArt Bacterial mRNA amplification Micro kit  protocol starting from 2 µg total RNA.

growth_protocol: Strain HG001 was grown to exponential phase (OD600 0.6) in TSB media and treated with and without novobiocin (0.5 mg/L) for one hour.

extract_protocol: Cell pellets were lysed using mechanical disruption in a high-speed homogenizer (Savant Instruments, Farmingdale, NY, USA) with 0.5 ml zirconia beads (0.1 mm in diameter) for 10 sec at a speed of 6,500 rpm.  in the presence of Trizol (Invitrogen, Darmstadt, Ger-many). The lysates were processed as described in the instructions of the RNA isolation kit ExpressArt RNAready (#9007-A100, AmpTec, Hamburg, Germany), including an on-column DNase treatment to remove genomic DNA.

value: novobiocin


title: TCR WT1 CD62Lhi


title: Probe7

treatment_protocol: Strain HG001 was grown to exponential phase (OD600 0.6) in TSB media and treated with and without novobiocin (0.5 mg/L) for one hour.


title: 3_110711


title: Probe3

value: untreated


title: 2_110711


title: Fungal cells / Free bacteria aspergillusvsbacillus6

source_name: Fungal cells

value: control - Aspergillus niger

value: free B. subtilis cells


title: 1_110711


title: Genomic DNA from adenoma patient 39

city: Seattle

first: Yanxin

last: Luo

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
adenoma
1902

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Bio-conductor. Use SWAN for data normalization and Combat for batch-effect corrections.

label: Cy5 and Cy3

source_name: colorectal mucosa

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from fresh-frozen samples using Qiagen DNeasy Kit according to standard instructions.

tag: tissue

value: colorectal mucosa

tag: colon region

value: right

tag: disease status

value: adenoma

tag: gender

value: Male


title: A549-ctrl-AS30-long-time-A

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
C-2+22h-A-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum and AS30 NPs. After recovery time (22  hours in complete medium with 10% of serum) total RNA was extracted.

hyb_protocol: 1.65 μg of labeled aRNA was used in each reaction and hybridization was carried out at 65°C for 17 hours in a hybridization oven rotator (Agilent, Santa Clara, CA, USA). The arrays were washed using Agilent Gene expression washing buffers and Stabilization and Drying Solution, as suggested by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis. Gene expression data were performed on three biological replicates for each condition.

data_processing: Inter-array normalization of expression levels (gProcessedSignal) was performed with quantile method to correct possible experimental distortions. Normalization function was applied to the expression data of all the experiments and the values for within-arrays replicate spots were then averaged (according the same ProbeName ID). Feature Extraction Software, which provided spot quality measures, was used to evaluate the quality and reliability of the hybridization. In particular, the flag “positive and significative” (set to 1 if the spot had an intensity value significantly different from the local background and to 0 when otherwise) was used to filter out unreliable probes: the flag equal to 0 was to be noted as “not available (NA)” the spot intensity and therfore not used in the average calculation. Probes with a high proportion of NA values were removed from the dataset in order to carry out a more solid and unbiased statistical analyses. Thirty-three percent of NA was used as the threshold in the filtering process, and a total of 32.096 transcripts of 41.093 were used in the subsequent analysis. Differentially expressed genes identification (One-way ANOVA), hierarchical clustering analysis (Sperman Rank Correlation or Euclidean distance) using average linkage method were performed using the TMev suite. Gene Ontology analysis of differentially expressed genes was performed on web tool GeneCodis3. Cytoscape tool in association with the Agilent Literature Search plug-in (http://apps.cytoscape.org/apps/agilentliteraturesearch (accessed on 19 December)) was used to produce network of differentially expressed genes. Network was analyzed using Network Analyzer and CentiScaPe plug-in. Supervised pathway analysis was performed by GSEA  implemented in the Graphite web tool.

source_name: Control for A549 cells treated AS30 long recovery

label_protocol: 1 μg of total RNA was labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer's protocol. The synthesized cDNA was transcribed into aRNA and labeled with Cy3-dCTP. Labeled aRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA, USA). The quality of each aRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE, USA).

growth_protocol: The human cell lines A549 (lung adenocarcinoma), were obtained from American Type Culture Collection (ATCC, Rockville, USA) and cultured in monolayer. A549 cells were maintained in F12-K medium supplemented with 10 % heat-inactivated Fetal Calf Serum (FCS), 38 units/ml streptomycin, and 100 units/ml penicillin G in standard culture conditions and during the post-treatment recovery (complete medium). Cells were kept at 37 °C in a humidified atmosphere containing 5 % CO2.

extract_protocol: RNA extraction was performed using TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. All samples were quantitated using a NanoDrop ND-1000 spectrophotometer; RNA quality was then analyzed using the Agilent Bioanalyser 2100 (Agilent, Santa Clara, CA, USA) (Agilent RNA 6000 nano kit; RIN at least 7 accepted).

treatment_protocol: To evaluate the cytotoxicity induced by Ludox® NPs, the cells were plated and allowed to attach for 24 h. Then, NPs were diluted to appropriate concentrations and immediately applied to the cells. We used a short incubation for 2 h in serum-free medium, followed by a post-treatment recovery of 3 or 22 hours in complete medium (10 % FCS). NPs concentrations (0.005–0.6 mg/mL) were chosen to evaluate the dose/survival according to the treatment conditions. Control cells underwent the same steps of treated cells except for NP exposure.

tag: cell line

value: human lung adenocarcinoma epithelial cell

tag: silica nanoparticle type

value: AS30; 18 nm of diameter

tag: post-treatment recovery time

value: 22 hrs


title: Genomic DNA from adenoma patient 40

description:
adenoma
1186A

value: Female


title: Genomic DNA from adenoma patient 37

description:
adenoma
TY1374A


title: A549-ctrl-AS30-long-time-C

description:
C-2+22h-C-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum and AS30 NPs. After recovery time (22  hours in complete medium with 10% of serum) total RNA was extracted.


title: A549-ctrl-AS30-long-time-B

description:
C-2+22h-B-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum and AS30 NPs. After recovery time (22  hours in complete medium with 10% of serum) total RNA was extracted.


title: Genomic DNA from adenoma patient 42

description:
adenoma
2026


title: A549-AS30-long-time-A

description:
T-2+22h-A-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing AS30 NPs. After recovery time (22  hours in complete medium with 10% of serum) total RNA was extracted.

source_name: A549 cells treated AS30 long recovery


title: Genomic DNA from adenoma patient 32

description:
adenoma
16742

value: left

value: female


title: Genomic DNA from adenoma patient 41

description:
adenoma
7497


title: Genomic DNA from adenoma patient 28

description:
adenoma
16734


title: Genomic DNA from adenoma patient 35

description:
adenoma
TY1226B


title: Genomic DNA from adenoma patient 36

description:
adenoma
TY0652B


title: Genomic DNA from adenoma patient 27

description:
adenoma
16747

value: male


title: Genomic DNA from adenoma patient 34

description:
adenoma
16750


title: Genomic DNA from adenoma patient 33

description:
adenoma
16745


title: Genomic DNA from adenoma patient 29

description:
adenoma
16732


title: A549-AS30-long-time-B

description:
T-2+22h-B-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing AS30 NPs. After recovery time (22  hours in complete medium with 10% of serum) total RNA was extracted.


title: Genomic DNA from adenoma patient 30

description:
adenoma
16723


title: Genomic DNA from adenoma patient 38

description:
adenoma
TY0905A


title: Genomic DNA from adenoma patient 26

description:
adenoma
16736


title: Genomic DNA from adenoma patient 31

description:
adenoma
16739


title: A549-AS30-long-time-C

description:
T-2+22h-C-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing AS30 NPs. After recovery time (22  hours in complete medium with 10% of serum) total RNA was extracted.


title: A549-ctrl-AS30-short-time-B

description:
C-2+3h-B-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum and AS30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.

source_name: Control for A549 cells treated AS30 short recovery

value: 3 hrs


title: A549-ctrl-AS30-short-time-C

description:
C-2+3h-C-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum and AS30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.


title: Genomic DNA from adenoma patient 25

description:
adenoma
16733


title: Genomic DNA from adenoma patient 24

description:
adenoma
16749


title: A549-AS30-short-time-A

description:
T-2+3h_A-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing AS30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.

source_name: A549 cells treated AS30 short recovery


title: Genomic DNA from adenoma patient 23

description:
adenoma
16730


title: Genomic DNA from adenoma patient 21

description:
adenoma
16743


title: A549-AS30-short-time-B

description:
T-2+3h-B-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing AS30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.


title: Genomic DNA from adenoma patient 20

description:
adenoma
16740


title: A549-AS30-short-time-C

description:
T-2+3h-C-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing AS30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.


title: Genomic DNA from adenoma patient 22

description:
adenoma
16725


title: A549-SM30-A

description:
T-2+3h-A-SM30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing SM30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.

source_name: A549 cells treated SM30 short recovery

value: SM30; 9 nm of diameter


title: A549-ctrl-AS30-short-time-A

description:
C-2+3h-A-AS30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum and AS30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.


title: A549-ctrl-for-SM30-B

description:
C-2+3h-B-SM30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum,and SM30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.

source_name: Control for A549 cells treated SM30 short recovery


title: A549-ctrl-for-SM30-C

description:
C-2+3h-C-SM30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum,and SM30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.


title: A549-ctrl-for-SM30-A

description:
C-2+3h-A-SM30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum,and SM30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.


title: A549-SM30-C

description:
T-2+3h-C-SM30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing SM30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.


title: Genomic DNA from adenoma patient 19

description:
adenoma
16748


title: Genomic DNA from CRC patients 62

description: cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fresh-frozen samples using Qiagen DNeasy Kit according to standard instructions

value: Proximal

value: cancer

tag: Stage

value: IV


title: Genomic DNA from CRC patients 60

description: cancer

value: III


title: Hippocampus_rat Extreme Behavioral Response_rat 11R

city: Belmont

first: Nikolaos

last: Daskalakis

state: MA

address: Oaks Building 328, Mailstop 212, 115 Mill Street

department: Department of Psychiatry

institute: McLean Hospital/ Harvard Medical School

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: We retained probes for which the majority (>50%) of samples from each group displayed a detection P value lower than <0.05.

source_name: Rat Hippocampus

label_protocol: Biotinylated cRNA was prepared with Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: RNeasy Mini Kits (Qiagen) were used to isolate total RNA with the addition of on-column DNase digestion. Quality control was performed with ND-1000 spectrophotometer (NanoDrop Technologies) and 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Hippocampus was dissected on dry ice using established anatomical landmarks. Tissues were immediately submerged in RNA-stabilization solution (RNAlater, Ambion), and stored at −80 °C.

value: Sprague Dawley

value: Adult

value: Hippocampus

tag: group

value: Extreme Behavioral Response

tag: rat i.d.


title: A549-SM30-B

description:
T-2+3h-B-SM30
After 24 h, the culture medium was removed, and the cells were incubated for 2 hours with 150 μL of medium, without serum, containing SM30 NPs. After recovery time (3  hours in complete medium with 10% of serum) total RNA was extracted.

value: human lung adenocarcinoma epithelial cell


title: Hippocampus_rat Extreme Behavioral Response_rat 30R

description: replicate 3

tag: age


title: Hippocampus_rat Extreme Behavioral Response_rat 20R

description: replicate 4


title: Genomic DNA from CRC patients 64

description: cancer

value: colorectal mucosa


title: 8b_RMGX_Acetate_Stat_F4

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

hyb_protocol: Hybridizations were conducted using an 12-bay hybridization station (BioMicro Systems, Inc., UT), arrays dried using a Maui wash system (BioMicro Systems, Inc.).

scan_protocol: Arrays were scanned with a Surescan high-resolution DNA microarray scanner (Agilent Technologies, CA)

data_processing: The images were quantified using NimbleScan software (Roche NimbleGen, IN). Statistical analyses were done with JMP Genomics 4.1 software (SAS Institute, NC), essentially as described previously [27]. The data were normalized using the LOWESS normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the False Discovery Rate (FDR) testing method (p < 0.05).

organism: Zymomonas mobilis

label_protocol: ds-cDNA was labeled, hybridized, arrays washed, and scanned following the NimbleGen protocols.

growth_protocol: Z. mobilis 8b was revived from frozen glycerol stocks for ~6-8 hrs in 10 mL RM (10 g/L yeast extract, 2 g/L KH2PO4) + 2% glucose at 33oC prior to inoculating overnight seed cultures in RM + 5% glucose (5% glucose) using shake flasks filled to 80% capacity at 33oC at 120 rpm.  When the glucose concentration reached approximately 20-40 g/L, cells were spun down at 3,840 x g for 10 min at room temperature (RT) and resuspended in either RMG (8% glucose), RMX (8% xylose), or RMGX(4% glucose, 4% xylose) at a 10-fold concentration and used as inocula for fermentation studies. Fermentations were performed in BioStat-Q Plus fermentors (Sartorius Stedim Biotech, France) at 300-mL working volumes using Z. mobilis 8b. RMG, RMX or RMGX media were used for fermentation. The fermentors were inoculated at an OD600nm unit of 0.1 approximately. The fermentation was conducted at 30°C, 150 rpm, pH 6.0 with 2 N KOH for pH control.

extract_protocol: RNA was isolated essentially described previously [26]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: Cell biomass was frozen immediately after centrifugation.

value: Cell biomass


title: Genomic DNA from CRC patients 63

description: cancer

value: Distal

value: Female


title: 8b_RMGX_Acetate_Stat_F5


title: Genomic DNA from CRC patients 55

description: cancer

value: Male


title: Genomic DNA from CRC patients 61

description: cancer


title: Genomic DNA from CRC patients 59

description: cancer

value: II


title: Hippocampus_rat Extreme Behavioral Response_rat 43R

description: replicate 1

value: male


title: Hippocampus_rat Extreme Behavioral Response_rat 32R

description: replicate 2


title: Hippocampus_rat Minimal Behavioral Response_rat 12R

description: replicate 5

value: Minimal Behavioral Response


title: Genomic DNA from CRC patients 53

description: cancer


title: 8b_RMGX_Acetate_Transition_F6


title: 8b_RMGX_Acetate_Stat_F6


title: 8b_RMGX_Acetate_Transition_F4


title: Genomic DNA from CRC patients 58

description: cancer

value: Proximal


title: Genomic DNA from CRC patients 54

description: cancer

value: cancer


title: 8b_RMGX_Acetate_Transition_F5


title: 8b_RMGX_Acetate_log_F5


title: Genomic DNA from CRC patients 52

description: cancer


title: 8b_RMGX_Acetate_log_F4


title: Genomic DNA from CRC patients 50

description: cancer

value: Rectum

value: IV


title: Hippocampus_rat Minimal Behavioral Response_rat 10R

description: replicate 4

value: Sprague Dawley


title: Genomic DNA from CRC patients 57

description: cancer

value: III


title: Genomic DNA from CRC patients 51

description: cancer


title: Genomic DNA from CRC patients 48

description: cancer


title: Hippocampus_rat Minimal Behavioral Response_rat 9R

description: replicate 3

value: Adult

value: Hippocampus


title: Genomic DNA from CRC patients 56

description: cancer


title: 8b_RMGX_Stat_F2


title: 8b_RMGX_Stat_F1


title: 8b_RMGX_Acetate_log_F6


title: Genomic DNA from CRC patients 46

description: cancer


title: 8b_RMGX_Transition_F3


title: Genomic DNA from CRC patients 49

description: cancer

value: I


title: Genomic DNA from CRC patients 47

description: cancer

value: colorectal mucosa


title: 8b_RMGX_Transition_F2

value: Cell biomass


title: Genomic DNA from CRC patients 45

description: cancer


title: Genomic DNA from CRC patients 44

description: cancer

value: Distal


title: 8b_RMGX_log_F3


title: 8b_RMGX_Transition_F1


title: 8b_RMGX_log_F1


title: 8b_Xylose_F9


title: Hippocampus_rat Control_rat C5R

description: replicate 3

value: Control


title: 8b_RMGX_log_F2


title: 8b_Xylose_F8


title: Hippocampus_rat Minimal Behavioral Response_rat 8R

description: replicate 2


title: Hippocampus_rat Control_rat C6R

description: replicate 4


title: 8b_Glucose_Acetate_F6


title: Hippocampus_rat Control_rat C7R

description: replicate 5


title: Genomic DNA from CRC patients 41

description: cancer

value: Female


title: 8b_Glucose_Acetate_F5


title: 8b_Glucose_F3


title: Hippocampus_rat Control_rat C4R

description: replicate 2


title: Genomic DNA from CRC patients 42

description: cancer


title: Genomic DNA from CRC patients 40

description: cancer


title: 8b_Xylose_Acetate_F12


title: 8b_Xylose_F7


title: Genomic DNA from CRC patients 43

description: cancer

value: II


title: Hippocampus_rat Control_rat C2R

description: replicate 1

value: male


title: 8b_Glucose_F2


title: 8b_Glucose_Acetate_F4


title: 8b_Xylose_Acetate_F11


title: 8b_RMGX_Stat_F3


title: 8b_Glucose_F1


title: Hippocampus_rat Extreme Behavioral Response_rat F39

description: replicate 4

value: female

value: Extreme Behavioral Response


title: Hippocampus_rat Extreme Behavioral Response_rat F40

description: replicate 5


title: Genomic DNA from CRC patients 39

description: cancer

value: Transverse

value: cancer


title: 8b_Xylose_Acetate_F10


title: Hippocampus_rat Extreme Behavioral Response_rat F36

description: replicate 3


title: Genomic DNA from CRC patients 38

description: cancer

value: IV


title: Hippocampus_rat Extreme Behavioral Response_rat F44

description: replicate 2

value: Sprague Dawley


title: Ecoli_control_5h_rep4

city: METZ

first: Bénédicte

last: SOHM

address: 8 rue du Gal Delestraint

institute: CNRS

description: Expression profile of E.coli control culture, biological replicatee 4

hyb_protocol: For each samples, 825 ng of cRNA with a specific activity of at least 15 pmol of Cy3 per µg of cRNA (according to the manufacturer’s protocol) was hybridized in presence of GE Hybridization Buffer HI-RPM (Agilent) on the Agilent E. coli microarray (8x15K slide format, design ID: 020097) 17h at 65°C in a rotation oven (Agilent). Slides were washed successively 1 min in GE wash buffer 1 and 2 (Agilent) and dried by centrifugation.

scan_protocol: Microarray was scanned at 5 µm resolution with GenePix 4100 A (Molecular Devices, CA, USA).

data_processing: Image analysis was performed with GenePix Pro 7 software (Molecular Device), background was defined with the “Local features background median” method. Quantile normalization was applied on the total number of spots in R (version 2.11.1) with the LIMMA software package. Spots corresponding to the E. coli MG1655 K12 species were extracted.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E.coli, control culture, 5h in 10 mM NaCl, replicate 4

label_protocol: Total RNA was reverse transcribed, amplified, and labeled with cyanine 3 (Cy3) using the low Input Quick Amp WT labeling kit (Agilent, CA, USA). The labeled cRNA (antisense) was then purified with the RNeasy mini spin columns (Qiagen). Quantification and measure of incorporation level of Cy3 were done with a NanoDrop ND-1000 (Thermo Scientific, DE, USA).  The labeled cRNA was fragmented with Agilent fragmentation buffer 30 min at 60°C and RNA fragmentation was checked on BioAnalyseur.

growth_protocol: Cell exposure to NP-TiO2 was conducted in 50 ml of sterile Milli-Q water supplemented with 10 mM NaCl. Briefly, 500 µl of the E. coli bacterial suspension and 500 µl of the NP-TiO2 stock suspension (or mQ water for the control) were prepared as previously described and then added to the NaCl solution to obtain final concentrations of 10E7 cells/ml and 100 mg/l of TiO2 nanoparticles. The flasks were then incubated at 20°C on a dark rotary shaker (150 rpm) for 5 h.

extract_protocol: Total RNA was extracted from cells with the UltraClean Microbial RNA isolation kit (MO BIO, CA, USA). After extraction, contaminating DNA was digested with DNAse I (Sigma Aldrich) and total RNA was purified by phenol/chloroform extraction and ethanol precipitation. RNA purity and quantity was assess by optical density measurements (OD 260/280 and OD 260/230) and RNA integrity was checked with the Bioanalyseur 2100 (Agilent, CA, USA).

treatment_protocol: After 5 h of NP-TiO2 (or mQ water for the control) exposure, cells were incubated for 5 min with two volumes of RNAprotect Bacteria Reagent (Qiagen SAS, France) at room temperature. Cells were then pelleted by centrifugation (7,000 g, 10 min) and the pellet stored at -80°C.

tag: incubation medium

value: 10 mM NaCl

tag: incubation condition

value: In the dark, 5h, 20°C, 150 rpm


title: Ecoli_NP-TiO2_5h_rep2

description: Expression profile of E.coli exposed to TiO2 nanoparticles, biological replicatee 2

source_name: E.coli,  NP-TiO2 exposed culture, 5h in 10 mM NaCl 100mg/L NP-TiO2, replicate 2

value: 10 mM NaCl + 100mg/l TiO2 nanoparticles


title: Hippocampus_rat Extreme Behavioral Response_rat F45

description: replicate 1

value: Adult

value: Hippocampus


title: Ecoli_NP-TiO2_5h_rep1

description: Expression profile of E.coli exposed to TiO2 nanoparticles, biological replicatee 1

source_name: E.coli,  NP-TiO2 exposed culture, 5h in 10 mM NaCl 100mg/L NP-TiO2, replicate 1


title: Hippocampus_rat Minimal Behavioral Response_rat F21

description: replicate 5

value: Minimal Behavioral Response


title: Genomic DNA from CRC patients 36

description: cancer

value: colorectal mucosa

value: Distal

value: Male


title: Ecoli_NP-TiO2_5h_rep4

description: Expression profile of E.coli exposed to TiO2 nanoparticles, biological replicatee 4

source_name: E.coli,  NP-TiO2 exposed culture, 5h in 10 mM NaCl 100mg/L NP-TiO2, replicate 4


title: Ecoli_NP-TiO2_5h_rep3

description: Expression profile of E.coli exposed to TiO2 nanoparticles, biological replicatee 3

source_name: E.coli,  NP-TiO2 exposed culture, 5h in 10 mM NaCl 100mg/L NP-TiO2, replicate 3


title: Genomic DNA from CRC patients 35

description: cancer

value: Female


title: Genomic DNA from CRC patients 37

description: cancer


title: Hippocampus_rat Minimal Behavioral Response_rat F22

description: replicate 4


title: Ecoli_control_5h_rep2

description: Expression profile of E.coli control culture, biological replicatee 2

source_name: E.coli, control culture, 5h in 10 mM NaCl, replicate 2


title: Ecoli_control_5h_rep1

description: Expression profile of E.coli control culture, biological replicatee 1

source_name: E.coli, control culture, 5h in 10 mM NaCl, replicate 1


title: Hippocampus_rat Minimal Behavioral Response_rat F26

description: replicate 2


title: Hippocampus_rat Minimal Behavioral Response_rat F24

description: replicate 3


title: Hippocampus_rat Minimal Behavioral Response_rat 2R

description: replicate 1

value: male


title: Genomic DNA from CRC patients 34

description: cancer

value: Proximal


title: Genomic DNA from CRC patients 33

description: cancer


title: Hippocampus_rat Minimal Behavioral Response_rat F27

description: replicate 1

value: female


title: Ecoli_control_5h_rep3

description: Expression profile of E.coli control culture, biological replicatee 3

source_name: E.coli, control culture, 5h in 10 mM NaCl, replicate 3


title: Hippocampus_rat Control_rat F5

description: replicate 5

value: Control


title: Genomic DNA from CRC patients 30

description: cancer

value: cancer

value: II


title: Genomic DNA from CRC patients 32

description: cancer


title: Genomic DNA from CRC patients 31

description: cancer

value: Rectum

value: III


title: Oct4-GFP SNEL#1 rep2

city: Cambridge

first: Yossi

last: Buganim

address: 9 Cambridge Center

institute: Whitehead Institute

description: 252800514388_201207121006_S01_GE1-v5_10_Apr08_1_1.YB17

hyb_protocol: Agilent (mouse 8x60k) expression arrays were hybridized according to  manufacturer instructions and scanned using an Agilent DNA microarray scanner.

scan_protocol: Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.

data_processing: Arrays were quantile normalized using limma from Bioconductor in R.

source_name: High quality_SNEL iPSC line

label_protocol: Standard Agilent protocol

growth_protocol: Cells were grown in 2i medium withour feeder as described in the manuscript

extract_protocol: RNA was extracted using the Rneasy kit (Qiagen-74106), 300 ng were used for hybridization

treatment_protocol: No treartment, basal condition

tag: iPSc/esc line

value: Oct4-GFP SNEL#1

tag: iPSc group

value: High quality


title: Oct4-GFP ESCs rep2

description: 252800514388_201207121006_S01_GE1-v5_10_Apr08_1_4.YB20

source_name: control_ESC line

value: Oct4-GFP ESCs

tag: sample group

value: control


title: Nanog-GFP ESCs rep2

description: 252800514388_201207121006_S01_GE1-v5_10_Apr08_1_3.YB19

value: Nanog-GFP ESCs


title: KH2 ESCs rep2

description: 252800514388_201207121006_S01_GE1-v5_10_Apr08_1_2.YB18

value: KH2 ESCs


title: Hippocampus_rat Control_rat F3

description: replicate 3

tag: strain

value: Sprague Dawley

value: Adult

value: Hippocampus


title: Genomic DNA from CRC patients 28

description: cancer

source_name: colorectal mucosa

tag: tissue

value: colorectal mucosa

value: Distal

value: Male

value: IV


title: Nanog-GFP SNEL#3 rep2

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_2_3.YB15

source_name: Good quality_SNEL iPSC line

value: Nanog-GFP SNEL#3

value: Good quality


title: Nanog-GFP SNEL#2 rep2

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_2_4.YB16

value: Nanog-GFP SNEL#2


title: Oct4-GFP ESCs rep1

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_1_2.YB10


title: Genomic DNA from CRC patients 27

description: cancer

tag: colon region

value: Rectum

value: cancer

value: III


title: Hippocampus_rat Control_rat F1

description: replicate 1

value: female

value: Control


title: Genomic DNA from CRC patients 29

description: cancer

value: Proximal

tag: disease status

value: II


title: KH2_OSKM rep2

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_2_1.YB13

source_name: Poor quality_OSKM iPSC line

value: Poor quality


title: Genomic DNA from CRC patients 26

description: cancer

tag: gender


title: Oct4-GFP OSKM#2 rep2

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_1_4.YB12

value: Oct4-GFP OSKM#2


title: Amygdala_rat Extreme Behavioral Response_rat 20R

description: replicate 4

source_name: Rat Amygdala

treatment_protocol: Amygdala was dissected on dry ice using established anatomical landmarks. Tissues were immediately submerged in RNA-stabilization solution (RNAlater, Ambion), and stored at −80 °C.

value: Sprague Dawley

value: Adult

value: Amygdala

value: male

value: Extreme Behavioral Response


title: Amygdala_rat Extreme Behavioral Response_rat 11R

description: replicate 5


title: Nanog-GFP OSKM#2 rep2

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_1_3.YB11

value: Nanog-GFP OSKM#2


title: BC_2 OSKM rep2

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_2_2.YB14

source_name: Good quality_OSKM iPSC line

value: BC_2 OSKM

value: Good quality


title: Amygdala_rat Extreme Behavioral Response_rat 30R

description: replicate 3


title: Hippocampus_rat Control_rat F2

description: replicate 2

value: Hippocampus


title: Nanog-GFP ESCs rep1

description: 252800514387_201207121018_S01_GE1-v5_10_Apr08_1_1.YB9

value: Nanog-GFP ESCs

value: control


title: KH2 ESCs rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_2_4.YB8

value: KH2 ESCs


title: Genomic DNA from CRC patients 23

description: cancer

value: colorectal mucosa

value: Unknown

value: cancer

value: Female


title: Genomic DNA from CRC patients 25

description: cancer

value: Proximal

value: Male

value: II


title: Oct4-GFP SNEL#1 rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_2_3.YB7

value: Oct4-GFP SNEL#1

value: High quality


title: Nanog-GFP SNEL#3 rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_2_1.YB5

value: Nanog-GFP SNEL#3


title: Amygdala_rat Extreme Behavioral Response_rat 32R

description: replicate 2

value: Sprague Dawley

value: Adult

value: Amygdala

value: male

value: Extreme Behavioral Response


title: BC_2 OSKM rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_1_4.YB4

value: BC_2 OSKM

value: Good quality


title: Genomic DNA from CRC patients 24

description: cancer

value: colorectal mucosa

value: Distal

value: III


title: Genomic DNA from CRC patients 22

description: cancer

value: Unknown

value: cancer

value: IV


title: Nanog-GFP SNEL#2 rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_2_2.YB6

value: Nanog-GFP SNEL#2


title: Oct4-GFP OSKM#2 rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_1_2.YB2

value: Oct4-GFP OSKM#2

value: Poor quality


title: Amygdala_rat Minimal Behavioral Response_rat 12R

description: replicate 5

value: Minimal Behavioral Response


title: Nanog-GFP OSKM#2 rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_1_1.YB1

value: Nanog-GFP OSKM#2


title: Amygdala_rat Minimal Behavioral Response_rat 10R

description: replicate 4

value: Sprague Dawley

value: Adult


title: Amygdala_rat Minimal Behavioral Response_rat 9R

description: replicate 3

value: Amygdala

value: male


title: Genomic DNA from CRC patients 19

description: cancer

value: Male


title: mutant vs wild type in glucose 1

city: Paris

first: frederic

last: devaux

address: 15 rue de l'ecole de medecine

institute: Universite Pierre et Marie Curie

description: ch1 and ch2 strains were grown in glucose as sole carbon source (cf growth protocol)

hyb_protocol: We used the Agilent hyb protocol described in the Agilent booklet. 2µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in wash 1 buffer at room temperature and one minute in wash 2 buffer at 37°C. The array slides are then air dryed and ready for scanning

scan_protocol: The slides were scan using an Axon genepix 4000B microarray scanner.

data_processing: Normalization using Goulphar WebTool http://transcriptome.ens.fr/goulphar/ (http://transcriptome.ens.fr/goulphar/index.php). GenePix flags are removed from the analysis. Spots are considered as saturating spot above 60000 and removed. Background is not subtracted from the main signal. Global Lowess normalization method.

organism: Saccharomyces cerevisiae

source_name: dhh1 deleted strain

label_protocol: We used the aminoallyl indirect labelling technique. 2 µg RNA are retro transcribed using Superscript III retro transcriptase and incorporation of dUTP amino-allyl for indirect labeling. The cDNA are purified using QiaQuick column (Qiagen) and incubated 1 hour at room temperature in presence of 0.05M NaBicarbonate and NHS-ester Cy5. The coupling is stopped by addition of hydroxylamine to a final concentration of 0.6M. Labeled cDNA are purified using a QiaQuick column.

growth_protocol: Yeast cells were grown in YNB glucose 2.0 % (w/v) or in YNB formic acid (0.5 %, w/v, pH 5.0) , as indicated, and supplemented with adequate requirements for prototrophic growth. Growth was carried out in an automatic shaker at 30 ºC until an OD600nm of about 0.6.

extract_protocol: Total RNA was isolated using the standard hot acidic phenol protocol described at http://www.transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php.

tag: carbon source

value: glucose

value: W303-1A dhh1::kanMX4

source_name: wild type strain


title: Amygdala_rat Extreme Behavioral Response_rat 43R

description: replicate 1

value: Extreme Behavioral Response


title: Amygdala_rat Minimal Behavioral Response_rat 8R

description: replicate 2


title: mutant vs wild type in formate 1

description: ch1 and ch2 strains were grown in formate as sole carbon source (cf growth protocol)

value: formate


title: mutant vs wild type in glucose 2


title: mutant vs wild type in formate 2


title: Genomic DNA from CRC patients 17

description: cancer

value: colorectal mucosa

value: Proximal

value: Female

value: II


title: KH2_OSKM rep1

description: 252800514386_201207121030_S01_GE1-v5_10_Apr08_1_3.YB3


title: Genomic DNA from CRC patients 21

description: cancer

value: Distal

value: cancer

value: IV


title: Genomic DNA from CRC patients 20

description: cancer

value: III


title: Genomic DNA from CRC patients 18

description: cancer


title: leftventricle_I/R-surgery_5d_KO_rep3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
Cre_5d_18
I/R = myocardial ischemia/reperfusion surgery

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of mogene20st -type from Affymetrix. A Custom CDF Version 18 with Entrez-based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: left ventricular myocardium ischemic area, CaMKII delta/gamma DKO, I/R, 5d

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

growth_protocol: Mixed mouse background strain: 129/Sv and C57BL/6 with CaMKII delta/gamma double KO.

extract_protocol: Total RNA was isolated from ventricular tissue or from cultured cardiomyocytes using TRIzol (Invitrogen, Germany). Total RNA was digested with DNase, and cDNA synthesis from 500 ng of RNA was carried out using a SuperScript first-strand synthesis system for RT-PCR (Invitrogen).

treatment_protocol: Mice were anesthetized and subjected to myocardial ischemia/reperfusion injury. Briefly, after initiation of general anesthesia with Propofol 1% (0.002 ml/g bodyweight, retroorbital injection) and isoflurane anesthetic gas, the mice were intubated, ventilated with a rodent ventilator (MiniVent Type 845, Harvard Apparatus, Holliston, MA) and a left thoracotomy was performed. Anesthesia was maintained with isoflurane 2.0 %. The left anterior descending (LAD) coronary artery was ligated with an 8-0 suture, tied on top of a plastic tube, 0.9 mm in diameter, approximately 1 mm below the edge of the left atrial appendage. Successful ligation of the artery was confirmed by blanching of the left ventricular (LV) myocardium. After 60 minutes of ischemia, reperfusion was established by pulling out the occluding tube. 24 hours or 5 days post-surgery, mice were euthanized and hearts were harvested to obtain RNA.

tag: strain/background

value: mixed (129/Sv and C57BL/6)

tag: genotype/variation

value: CaMKII delta/gamma double-knockout (cre)

tag: treatment

value: myocardial ischemia/reperfusion surgery

tag: time point (post-surgery)


title: Genomic DNA from CRC patients 16

description: cancer

value: Rectum

tag: Stage


title: leftventricle_I/R-surgery_1d_KO_rep3

description:
Cre_1d_15
I/R = myocardial ischemia/reperfusion surgery

source_name: left ventricular myocardium ischemic area, CaMKII delta/gamma DKO, I/R, 1d


title: Amygdala_rat Control_rat C2R

description: replicate 1

value: Sprague Dawley

tag: age

value: Adult

value: Amygdala

value: male

tag: group

value: Control

tag: rat i.d.


title: Genomic DNA from CRC patients 15

description: cancer

value: colorectal mucosa

value: I


title: Amygdala_rat Minimal Behavioral Response_rat 2R

description: replicate 1

value: Minimal Behavioral Response


title: Amygdala_rat Extreme Behavioral Response_rat F40

description: replicate 5

value: female

value: Extreme Behavioral Response


title: leftventricle_I/R-surgery_5d_KO_rep2

description:
Cre_5d_17
I/R = myocardial ischemia/reperfusion surgery

value: left ventricular myocardium ischemic area


title: Amygdala_rat Control_rat C6R

description: replicate 4


title: leftventricle_I/R-surgery_5d_KO_rep1

description:
Cre_5d_16
I/R = myocardial ischemia/reperfusion surgery


title: leftventricle_sham-surgery_KO_rep3

description:
Cre_Sham_12
sham = sham surgery

source_name: left ventricular myocardium, CaMKII delta/gamma DKO, sham

value: sham surgery

value: left ventricular myocardium


title: Amygdala_rat Control_rat C4R

description: replicate 2


title: Genomic DNA from adenoma patient 18

description: adenoma

value: Left

value: adenoma

value: Female


title: Genomic DNA from adenoma patient 15

description: adenoma

value: Right


title: Hippocampus_rat Control_rat F4

description: replicate 4

source_name: Rat Hippocampus

value: Sprague Dawley

value: Hippocampus


title: Amygdala_rat Control_rat C7R

description: replicate 5

value: Adult

value: Amygdala


title: Amygdala_rat Extreme Behavioral Response_rat F39

description: replicate 4


title: Amygdala_rat Control_rat C5R

description: replicate 3

value: male

value: Control


title: leftventricle_I/R-surgery_1d_KO_rep1

description:
Cre_1d_13
I/R = myocardial ischemia/reperfusion surgery

value: mixed (129/Sv and C57BL/6)

value: CaMKII delta/gamma double-knockout (cre)

value: myocardial ischemia/reperfusion surgery


title: Genomic DNA from adenoma patient 16

description: adenoma

value: colorectal mucosa


title: leftventricle_sham-surgery_KO_rep2

description:
Cre_Sham_11
sham = sham surgery


title: leftventricle_I/R-surgery_1d_KO_rep2

description:
Cre_1d_14
I/R = myocardial ischemia/reperfusion surgery

value: left ventricular myocardium ischemic area


title: Genomic DNA from adenoma patient 17

description: adenoma

value: Male


title: leftventricle_I/R-surgery_5d_WT_rep3

description:
noCre_5d_9
I/R = myocardial ischemia/reperfusion surgery

source_name: left ventricular myocardium ischemic area, WT, I/R, 5d

value: wild-type (noCre)


title: leftventricle_sham-surgery_KO_rep1

description:
Cre_Sham_10
sham = sham surgery

value: sham surgery

value: left ventricular myocardium


title: leftventricle_I/R-surgery_5d_WT_rep2

description:
noCre_5d_8
I/R = myocardial ischemia/reperfusion surgery


title: Amygdala_rat Extreme Behavioral Response_rat F44

description: replicate 2

value: female

value: Extreme Behavioral Response


title: Amygdala_rat Extreme Behavioral Response_rat F36

description: replicate 3

value: Sprague Dawley


title: leftventricle_I/R-surgery_5d_WT_rep1

description:
noCre_5d_7
I/R = myocardial ischemia/reperfusion surgery


title: leftventricle_I/R-surgery_1d_WT_rep2

description:
noCre_1d_5
I/R = myocardial ischemia/reperfusion surgery

source_name: left ventricular myocardium ischemic area, WT, I/R, 1d


title: Amygdala_rat Minimal Behavioral Response_rat F22

description: replicate 4

value: Minimal Behavioral Response


title: Amygdala_rat Minimal Behavioral Response_rat F21

description: replicate 5

value: Adult


title: leftventricle_I/R-surgery_1d_WT_rep3

description:
noCre_1d_6
I/R = myocardial ischemia/reperfusion surgery


title: Amygdala_rat Extreme Behavioral Response_rat F45

description: replicate 1

value: Amygdala


title: Genomic DNA from adenoma patient 14

description: adenoma

value: Right

value: adenoma


title: Genomic DNA from adenoma patient 9

description: adenoma

value: Left

value: Female


title: leftventricle_I/R-surgery_1d_WT_rep1

description:
noCre_1d_4
I/R = myocardial ischemia/reperfusion surgery

value: mixed (129/Sv and C57BL/6)

value: myocardial ischemia/reperfusion surgery


title: Amygdala_rat Minimal Behavioral Response_rat F24

description: replicate 3


title: Genomic DNA from adenoma patient 11

description: adenoma

value: colorectal mucosa


title: Genomic DNA from adenoma patient 12

description: adenoma


title: Genomic DNA from adenoma patient 13

description: adenoma


title: Amygdala_rat Minimal Behavioral Response_rat F27

description: replicate 1


title: Genomic DNA of normal colon sample from CRC patient 24

description: normal-C

value: colon

value: normal-C


title: leftventricle_sham-surgery_WT_rep1

description:
noCre_Sham_1
sham = sham surgery

source_name: left ventricular myocardium, WT, sham

value: wild-type (noCre)

value: sham surgery


title: leftventricle_sham-surgery_WT_rep3

description:
noCre_Sham_3
sham = sham surgery

value: left ventricular myocardium


title: Amygdala_rat Minimal Behavioral Response_rat F26

description: replicate 2

value: female


title: leftventricle_sham-surgery_WT_rep2

description:
noCre_Sham_2
sham = sham surgery


title: Amygdala_rat Control_rat F5

description: replicate 5

value: Sprague Dawley

value: Control


title: Subject 2 NK cells

city: Lexington

first: Steven

middle: Ray

last: Presnell

state: KY

address: 800 Rose St.

department: Pathology, Medicine

institute: University of Kentucky

hyb_protocol: Hybridization to the miRNA microarrays were performed following the procedure described by the manufacturer.

scan_protocol: Hybridization signals were detected using the Genepix 4000B Scanner (Molecular Devices, Sunnyvale, CA).

data_processing:
Scanned images were analyzed using the Array-Pro Analyzer ver.4.5 software (Media Cybernetics, Rockville, MD). Because two different probe designs (lot numbers 31015 and 31078) were used, the common probes between them were extracted. The obtained miRNA microarray datasets were then normalized by the quantile normalization method using R statistical software version 2.12.1.
Further, all capture probes with Hy3 signals lower than 1.2x of the median signal intensity of the given slide are flagged as null.

source_name: purified NK cells, from PBMC

label_protocol: Total RNA was labeled with Hy3 fluorescent label using the miRCURY LNA microRNA Power Labeling kit (Exiqon)

growth_protocol: Human T and NK Cells were purified by negative selection (Rosette Sep for T or NK cells, Stem Cell Technologies) from PBMC's withdrawn by venipuncture ex vivo. The cells were not further purified.

extract_protocol: Cells were extracted with Triazol to purify total RNA, then a global miRNA expression analysis was performed using 2 µg of total RNA and the miRCURY LNA microRNA Array series (Exiqon, Vedbaek, Denmark).

treatment_protocol: No treatment

tag: individual

value: Subject 2

tag: cell type

value: purified NK cells


title: Subject 3 NK cells

value: Subject 3


title: Genomic DNA of normal colon sample from CRC patient 23

description: normal-C


title: Amygdala_rat Control_rat F4

description: replicate 4

value: Adult

value: Amygdala


title: Subject 1 NK cells

value: Subject 1


title: Genomic DNA of normal colon sample from CRC patient 22

description: normal-C

value: Female


title: Genomic DNA of normal colon sample from CRC patient 21

description: normal-C


title: Amygdala_rat Control_rat F2

description: replicate 2


title: Genomic DNA from adenoma patient 10

description: adenoma

value: Right

value: adenoma


title: Genomic DNA of normal colon sample from CRC patient 20

description: normal-C

value: colorectal mucosa

value: colon


title: Subject 1 T cells

source_name: purified T cells, from PBMC

value: purified T cells


title: Subject 2 T cells


title: Subject 3 T cells


title: Genomic DNA of normal colon sample from CRC patient 18

description: normal-C

value: normal-C


title: Genomic DNA of normal colon sample from CRC patient 19

description: normal-C

value: Male


title: Genomic DNA of normal colon sample from CRC patient 17

description: normal-C


title: Genomic DNA of normal colon sample from CRC patient 16

description: normal-C


title: Amygdala_rat Control_rat F1

description: replicate 1

value: female


title: Genomic DNA of normal colon sample from CRC patient 15

description: normal-C


title: Blood_rat Extreme Behavioral Response_rat 4R

description:
replicate 6
SAMPLE 45

data_processing: One array failed. We retained probes for which the majority (>50%) of samples from each group displayed a detection P value lower than <0.05.

extract_protocol: RNA was extracted from whole blood using the PAXgene Blood RNA Kit (Qiagen) with the addition of on-column DNase digestion. Globin mRNA interference in the total RNA was diminished by GLOBINclear method (Ambion). Quality control was performed with ND-1000 spectrophotometer (NanoDrop Technologies) and 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 2.5 mL whole peripheral blood from each rat was collected into PAXgene Blood RNA Tubes (Qiagen), incubated at room temperature for 4 h for RNA stabilization (PAXgene RNA stabilization system) and then stored at −80 °C

value: Sprague Dawley

value: Blood

value: MALE

value: Extreme Behavioral Response