title: KT2440_1 mM indole treatment

city: Seoul

first: Jisun

last: Kim

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

description: Control vs. 1 mM indole treatment

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner and Images were quantified using Agilent Feature Extraction Software (version A.7.5).

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

organism: Pseudomonas putida KT2440

source_name: non-treated P. putida KT2440 cells

label_protocol: 10 μg of total RNA were primed with 2 μl of 100 μM T16N2 DNA primer at 70℃ for 10 min, then reversed transcribed at 42℃ for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 μM each dATP, dTTP, dGTP, with 25 μM dCTP, 25 μM label

growth_protocol: P. putida KT2440 were grown overnight in LB and diluted 100 fold. When the diluted cells reached the exponential phase (OD600 ~0.4), cells were collected and washed 2 times with PBS. Appropriate dilutions of cells were spread on the LB plate containing 1 mM indole, 50 μg/ml Amp, or both 1 mM indole and 50 μg/ml Amp. After 12 h incubation at 30 °C, cells were collected from the plate.

extract_protocol: Total RNA extracted using Qiagen RNA miniprep kit following manufacturer's instructions

treatment_protocol: Exponentilally growing cells were spread on the LB plate containing 1 mM indole, 50 μg/ml Amp, or both 1 mM indole and 50 μg/ml Amp. After 12 h incubation at 30 °C, cells were collected from each plates

tag: treatment

source_name: 1 mM indole treated P. putida KT2440 cells

value: 1 mM indole


title: progeroid - control - animal 326

status: Public on Sep 09 2016

type: RNA

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen [miRBase 19.0] (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. 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.
The processed data file (Normalized_signal.txt) contains Log2-ratio for each sample to common reference. Column headers are: Probe ID, MicroRNA annotation, Number of Present calls followed by sample ID found in 'description' field.

molecule: total RNA

organism: Mus musculus

source_name: liver

label_protocol: MicroRNA experiments were conducted at Exiqon Services, Denmark. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Ercc1Δ/- mice were obtained by crossing Ercc1Δ/+ (in a pure C57BL6J or FVB background) with Ercc1+/- mice (in a pure FVB or C57BL6J background respectively) to yield Ercc1Δ/- with an F1 C57BL6J/FVB hybrid background. Wild-type F1 littermates were used as controls.All animals used in the studies described in this paper were of the same F1 C57BL6J/FVB hybrid background. Typical unfavorable characteristics, like blindness in an FVB background or deafness in a C57BL6J background, do not occur in this hybrid background. Mice were weighed, visually inspected weekly, and scored for gross morphological and motor abnormalities. Experiments were performed in accordance with the Principles of Laboratory Animal Care and with the guidelines approved by the Dutch Ethical Committee in full accordance with European legislation.

extract_protocol: Total RNA was extracted from liver of 11 week old wild type and Ercc1Δ/- mice on AL and DR feeding regimen (n=5). Total RNA was extracted using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN, Hilden, Germany), following Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Fisher Scientific) and quality assessment of the RNA using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) following manufacturer’s instructions.

treatment_protocol: All animals were bred and maintained on AIN93G synthetic pellets (Research Diet Services B.V., Wijk bij Duurstede, The Netherlands). The amount of DR was determined in a prior pilot study but as control food intake of the AL-fed mice was continuously monitored. DR was initiated at 7 weeks of age with 10% (2.1 g/day), when animals almost reached the maximum bodyweight preventing disruption of development of young mice. DR was gradually increased weekly with 10%, until 30% DR (1.6 g/day) was reached at 9 weeks of age. Wild type mice ate on average 3.0 g food per day, resulting in 2.1 g/day for 30% DR. Food was given to the animals just before the start of the dark (active) period to avoid alterations in the biological clock.

tag: genotype

value: progeroid  Ercc1 delta/-

tag: diet

value: control

tag: tissue

value: liver

tag: background strain

value: F1 C57BL6J/FVB

tag: sample type

value: common reference


title: Serum from mice exposed to 0Gy

status: Public on Sep 10 2016

city: Lanzhou

first: Wenjun

last: Wei

address: 509 Nanchang Road

country: China

institute: Institute of Modern Physics, Chinese Academy of Sciences

description:
Control
This sample represents three biological replicates (SAMPLE 1, SAMPLE 2, SAMPLE 3). Non-normalized data are provided individually for each replicate in the file Non-normalized_data.txt.

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using the GenEx qPCR analysis software (www.exiqon.com/mirna-pcranalysis).
Data normalization was performed using 4 Reference genes (miR-423-5p, miR-191-5p, miR-93-5p, RNU5G) according to the manufacturers instructions. If the non-normalized value is given as 'undetermined', the analysis software will use a default value of Ct = 35.
Matrix normalized worksheet reports 2^(-Avg.(Delta(Ct)), the average normalized signal (against housekeeping genes).
Fold Change worksheet reports the average fold-change for each miRNA from test 1 group and test 2 group to control goup as 2-ΔΔCt. P value calculating from Student’s t-tests were used to determine group difference.  All data analysis can also be found in the file Raw data analysis.xls.

label: SYBR Green

source_name: Serum

label_protocol: PCR assays were performed using miRCURY LNA™ Universal RT microRNA PCR, Ready-to-Use Mouse&Rat Panel I V3 (Exiqon, Denmark) following the Manufacturer’s instructions. Reverse transcription was performed from template RNA samples at a concentration of 20-25 ng in 14 μl using the  Universal cDNA Synthesis Kit II (Exiqon). Quantitative real-time PCR were performed by a Chromo4 system (Bio-Rad, USA) under the following conditions: initiation for 10 min at 95°C, followed by 45 thermal cycles each at 95°C for 10 s and at 60°C for 20 s and at 70°C for 10 s.

growth_protocol: Kunming male mice (6 weeks old) were kept to the age of 8 weeks (six per standard cage) at common condition before exposure.

extract_protocol: Serum RNA was extracted using miRNeasy Serum/Plasma Kit (Qiagen, Germany) following the manufacturer’s protocol.

treatment_protocol: 24 hours after exposure to radiation, Peripheral blood was collected in RNase free centrifuge tubes. Whole blood in tubes stayed during 2 hours at room temperature. To harvest the cell-free serum, blood samples were first centrifuged at 3000 rpm for 10 min at room temperature, then the supernatant was separated and centrifuged again at 12000 rpm for 10 min at 4℃ to remove residual blood cells.

tag: strain

value: Kunming

value: serum

tag: gender

value: male

tag: age

value: 8 weeks

tag: time after exposure

value: 24 hours


title: progeroid - control - animal 321


title: Serum from mice exposed to 2Gy

description:
Exposed to 2Gy
This sample represents three biological replicates (SAMPLE 7, SAMPLE 8, SAMPLE 9). Non-normalized data are provided individually for each replicate in the file Non-normalized_data.txt.


title: WP3-cold shock 30 min-rep2

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description:
raw data file: Cold0min-cy3+Cold30min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy3 and WP3 cDNA-cold shock 30 min was labeled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
For every microarray slide, there are 16416 spots, which were divided into 48 blocks. For every block, there are 18 columns and 19 rows. 16416=48*18*19.  There are 3 spots for a single gene on a single microarray slide, thus we get 3 ratios of the expression level of this gene in 2 samples (rep1, rep2 and rep3).  As dye-swaps were performed (label cDNA with different fluorecent dye), we can get another 3 ratios of the expression level of this gene in 2 samples (rep4, rep5 and rep6).
The replicate spots on the array were printed in the same row in adjacent columns.  Replicate number was assigned to the spots in ascending column order. For example, WP00027 is printed  in block 1, row 2, columns 13, 14 and 15. Replicate 1/4 is column 13, 2/5 is column 14 and replicate 3/6 is column 15.
S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model.  Microarray spots with P values <0.01 in the T-test and log2 ratio>1 or <-1 were regarded as differentially expressed genes.

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 0°C for 30 min.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: culture protocol

value: WP3 cells were cultured at 20°C in 2216E medium

source_name: WP3 cells at mid-exponential phase and were incubated at 0°C for 30 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 0℃ for 30 min


title: MILD831.1 [IgG]

type: protein

city: Irvine

first: Carolina

last: Lessa Aquino

address: 302 MedSurge II

country: USA

institute: University of California Irvine

hyb_protocol: Slides were washed 3 times with TTBS after each incubation

scan_protocol: Slides were scanned in a Perkin Elmer ScanArray confocal laser and intensities were quantified using QuantArray package

data_processing: Array signal intensity was quantified using QuantArray software. Spots intensity raw data were obtained as the mean pixel signal intensity with automatic correction forspot-specific background. Data was normalized by dividing the raw signal for each IVTT protein spot by the median of the sample-specific IVTT control spots (fold-overcontrol [FOC]) and then taking the base-2 logarithm of the ratio (log2 FOC).

molecule: protein

organism: Homo sapiens

source_name: acute serum sample

label_protocol: Biotinylated anti-human IgG, diluted 1/2000 in Blocking Buffer or anti-human IgM, diluted 1/400 in Blocking Buffer, was added to the arrays for one-hour incubation at room temperature. Bound antibodies were detected by one-hour incubation with streptavidin-conjugated SureLight P3.

extract_protocol: Human sera samples were diluted 1/100 in Protein Array Blocking Buffer containing E. coli lysate 10 mg/mL (McLab) at a final concentration of 10% v/v and incubated for 30 min at room temperature under constant mixing to remove background reactivity to E. coli proteins in the IVTT reactions. E. coli protein-antibody complexes were removed from the sample dilution mix via centrifugation prior to addition to the microarray

tag: platelet count

tag: hematocrit

tag: acute mat titer

tag: convalescent mat titer

tag: elisa

value: positive

tag: pcr

value: negative

tag: lab confirmation

tag: mat result

tag: number of days of symptoms

tag: respiratory failure

tag: icu admission

tag: oliguric renal failure


title: WP3-cold shock 30 min-rep1


title: MILD297.1 [IgG]

value: female


title: WP3-cold shock 30 min-rep3


title: Serum from mice exposed to 0.5Gy

description:
Exposed to 0.5Gy
This sample represents three biological replicates (SAMPLE 4, SAMPLE 5, SAMPLE 6). Non-normalized data are provided individually for each replicate in the file Non-normalized_data.txt.

tag: strain

tag: tissue


title: MILD123.1 [IgG]

tag: age

tag: gender


title: KT2440_1 mM indole and 50 μg/ml ampicillin treatment

description: Control vs. 1 mM indole and 50 μg/ml ampicillin treatment

tag: treatment

source_name: 1 mM indole and 50 μg/ml ampicillin treated P. putida KT2440 cells

value: 1 mM indole and 50 μg/ml ampicillin


title: KT2440_50 μg/ml ampicillin treatment

description: Control vs. 50 μg/ml ampicillin treatment

source_name: 50 μg/ml ampicillin treated P. putida KT2440 cells

value: 50 μg/ml ampicillin


title: progeroid - control - animal 323

tag: genotype

value: progeroid  Ercc1 delta/-

tag: diet

tag: background strain

tag: sample type


title: progeroid - restricted - animal 369

value: restricted


title: WP3-cold shock 30 min-rep5

description:
raw data file: Cold30min-cy3+Cold0min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy5 and WP3 cDNA-cold shock 30 min was labeled with Cy3

tag: culture protocol


title: progeroid - control - animal 325

value: control

value: liver


title: wild type - restricted - animal 424

value: wild type

value: F1 C57BL6J/FVB

value: common reference


title: wild type - restricted - animal 423


title: wild type - control - animal 405


title: wild type - restricted - animal 421


title: wild type - restricted - animal 422


title: wild type - control - animal 404


title: wild type - control - animal 403


title: wild type - control - animal 402


title: wild type - control - animal 401


title: wild type - restricted - animal 425


title: NORMAL_ID00996_Cerebellum_AMBION

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description: analysis of normal brain cerebellum

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values.

label: biotin

source_name: normal brain (cerebellum)

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

growth_protocol: Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )

extract_protocol: RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: normal brain (cerebellum)


title: PA_ID00563_1

description: reanalysis of GSM1214956

source_name: brain tumor (pilocytic astrocytoma)

value: brain tumor (pilocytic astrocytoma)


title: NFYB (Dharmacon) siRNA at 4hr, biological rep3

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Affymetrix Expression Console

source_name: U2OS ER-HA-E2F1 cells

label_protocol: Affymetrix standard protocol

growth_protocol: Cells grown in DMEM with 10% FBS.

extract_protocol: Rneasy Mini Kit with lysis by QIAshredder

treatment_protocol: Cell were transfected with siRNA. 18 hours later, cells were serum starved for 24 hours. Media was replaced by serum free media with 80nM OHT.

tag: cell line

value: U2OS ER-HA-E2F1


title: NORMAL_ID00514_Frontal

description: reanalysis of GSM1214937

source_name: normal brain (frontal lobe)

value: normal brain (frontal lobe)


title: PA_ID00519_1

description: reanalysis of GSM1214955


title: PA_ID00257_1

description: reanalysis of GSM1214951


title: Stromal _keratocytes_culture_rep2

city: GRANADA

first: MIGUEL

last: ALAMINOS

address: AV. INVESTIGACION 11, FAC. MEDICINA PTS

department: HISTOLOGY

country: Spain

institute: UNIVERSITY OF GRANADA

description:
Gene expression data from keratocytes cultures
8.KH4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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: Primary cell culture of stromal cornea keratocytes

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

growth_protocol: Culture of stromal keratocytes in DMEM basal medium with 10% FCS and antibiotics and epithelial cells in media rich in hormones and growth factors (see references)

extract_protocol: TRIZOL extraction and QIAgen RNAeasy purification, following manufacturer's recommendations

treatment_protocol: Combination of cultured cells and fibrin-agarose biomaterials to generate a human anterior lamelar artificial cornea (see references)

value: Corneal stroma


title: PA_ID00378_1

description: reanalysis of GSM1214953


title: NFYB (Dharmacon) siRNA at 8hr, biological rep3


title: NORMAL_ID00514_Cerebellum

description: reanalysis of GSM1214936


title: Bioengineered_anterior_lamelar cornea_rep2

description:
Fibrin-agarose artificial cornea with stroma and epithelium
8MA

source_name: Artificial human anterior cornea

value: Artificial cornea


title: Stromal _keratocytes_culture_rep1

description:
Gene expression data from keratocytes cultures
6.KH10


title: PA_ID00249_1

description: reanalysis of GSM1214950


title: NFYB (Dharmacon) siRNA at 8hr, biological rep1


title: NORMAL_ID00605_Frontal_1

description: reanalysis of GSM1214945


title: NFYB (Dharmacon) siRNA at 4hr, biological rep2


title: NORMAL_ID00897_Cerebellum_X_AMBION

description: analysis of normal brain cerebellum


title: NORMAL_ID00514_Temporal_AMBION

description: reanalysis of GSM1214942

source_name: normal brain (temporal lobe)

value: normal brain (temporal lobe)


title: PA_ID00476_1

description: reanalysis of GSM1214954


title: NORMAL_E00003_Frontal_1

description: reanalysis of GSM1214948


title: Bioengineered_anterior_lamelar cornea_rep1

description:
Fibrin-agarose artificial cornea with stroma and epithelium
1MA


title: PA_ID00631_1

description: reanalysis of GSM1214957


title: PA_ID00653_1

description: reanalysis of GSM1214958


title: PA_ID00160_1

description: reanalysis of GSM1214949


title: NORMAL_ID00897_Occipital_X_AMBION

description: analysis of normal brain occipital lobe

source_name: normal brain (occipital lobe)

value: normal brain (occipital lobe)


title: Corneal_epithelial_cells_culture_rep1

description:
Gene expression data from corneal epithelium cultures
CH1L

source_name: Primary cell culture of corneal epithelial cells

value: Corneal epithelium


title: NORMAL_ID00605_Cerebellum_AMBION

description: reanalysis of GSM1214944


title: PA_ID00363_1

description: reanalysis of GSM1214952


title: Corneal_epithelial_cells_culture_rep2

description:
Gene expression data from corneal epithelium cultures
LH5


title: NFYB (Dharmacon) siRNA at 8hr, biological rep2


title: NORMAL_Ambion_Cerebellum_1

description: analysis of normal brain cerebellum


title: NFYB (Dharmacon) siRNA at 4hr, biological rep1


title: NFYB (Dharmacon) siRNA at 0hr, biological rep2


title: MEDSHH_ID00831_1_AMBION

description: analysis of medulloblastoma surgical sample

source_name: brain tumor (medulloblastoma)

value: brain tumor (medulloblastoma)


title: MEDSHH_ID00719_1_AMBION

description: reanalysis of GSM1214927


title: NFYB (Ambion) siRNA at 8hr, biological rep1


title: NFYB (Ambion) siRNA at 4hr, biological rep3


title: MEDSHH_ID00801_1_AMBION

description: reanalysis of GSM1214930


title: MEDGP4_ID00437_1

description: reanalysis of GSM1214922


title: NFYB (Ambion) siRNA at 4hr, biological rep1


title: NFYB (Dharmacon) siRNA at 0hr, biological rep3


title: NFYB (Ambion) siRNA at 8hr, biological rep2


title: MEDSHH_ID00258_1

description: reanalysis of GSM1214917


title: NFYB (Ambion) siRNA at 0hr, biological rep3


title: MEDGP4_ID00330_1

description: reanalysis of GSM1214921


title: MEDSHH_ID00288_1

description: reanalysis of GSM1214920


title: MEDGP4_ID00262_1

description: reanalysis of GSM1214918


title: NFYB (Ambion) siRNA at 0hr, biological rep1


title: NFYB (Ambion) siRNA at 0hr, biological rep2


title: MEDGP3_ID00676_1_AMBION


title: Sigma-Aldrich negative control siRNA at 8hr, biological rep2


title: NFYB (Dharmacon) siRNA at 0hr, biological rep1


title: NFYB (Ambion) siRNA at 8hr, biological rep3


title: MEDGP4_ID00254_1

description: reanalysis of GSM1214916


title: MEDGP4_ID00186_1

description: reanalysis of GSM1214915


title: NFYB (Ambion) siRNA at 4hr, biological rep2


title: MEDGP3_ID00241_1

description: reanalysis of GSM869684


title: Sigma-Aldrich negative control siRNA at 8hr, biological rep3


title: MEDGP3_ID00277_1

description: reanalysis of GSM1214919


title: MEDGP3_ID00401_1

description: reanalysis of GSM869685


title: Sigma-Aldrich negative control siRNA at 8hr, biological rep1


title: MEDGP3_ID00231_1

description: reanalysis of GSM869683


title: Sigma-Aldrich negative control siRNA at 4hr, biological rep3


title: MED_ONS76uninf_AMBION

description: analysis of medulloblastoma cell line


title: HA_PSG4_1

description: analysis of normal human astrocyte cell culture

source_name: cell line monolayer (normal human astrocytes)


title: Sigma-Aldrich negative control siRNA at 4hr, biological rep2


title: Sigma-Aldrich negative control siRNA at 0hr, biological rep2


title: GBM_SF188_1_AMBION

description: analysis of glioblastoma cell line

source_name: brain tumor cell line monolayer (glioblastoma)


title: Sigma-Aldrich negative control siRNA at 4hr, biological rep1


title: Sigma-Aldrich negative control siRNA at 0hr, biological rep3


title: MED_DAOY_D1_Untreated

description: analysis of medulloblastoma cell line

source_name: brain tumor cell line monolayer (medulloblastoma)


title: Dharmacon negative control siRNA at 8hr, biological rep3


title: GBM_U251_1_AMBION

description: analysis of glioblastoma cell line

value: brain tumor cell line monolayer (glioblastoma)


title: Dharmacon negative control siRNA at 4hr, biological rep1


title: Dharmacon negative control siRNA at 8hr, biological rep1


title: GBM_ID00637_1

description: reanalysis of GSM1214894

source_name: brain tumor (glioblastoma)

value: brain tumor (glioblastoma)


title: Dharmacon negative control siRNA at 8hr, biological rep2


title: GBM_ID00309_1

description: reanalysis of GSM1214888


title: Dharmacon negative control siRNA at 4hr, biological rep2


title: Dharmacon negative control siRNA at 4hr, biological rep3


title: GBM_ID00391_1

description: reanalysis of GSM1214889


title: Dharmacon negative control siRNA at 0hr, biological rep2


title: Sigma-Aldrich negative control siRNA at 0hr, biological rep1


title: GBM_ID00281_1

description: reanalysis of GSM1214887


title: GBM_ID00098_1

description: reanalysis of GSM1214884


title: GBM_ID00434_1

description: reanalysis of GSM1214890


title: GBM_ID00089_1_AMBION

description: reanalysis of GSM1214883


title: GBM_ID00271_1

description: reanalysis of GSM1214885


title: GBM_ID00057_1

description: reanalysis of GSM1214882


title: VM CORIN+

city: Kyoto

first: Bumpei

last: Samata

address: 53 Kawahara-cho, Shogoin

country: Japan

institute: Kyoto university

description: Fetal brain.

hyb_protocol: Labeled cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with GeneSpring version 13.0 using default analysis settings and global scaling as normalization method (RMA16).

source_name: E11.5 fetal mouse ventral midbrain (CORIN+)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (Ambion WT Expression Kit, 2011, Affymetrix).

growth_protocol: The ESCs were cultured by SFEBq method before cell sorting.

extract_protocol: Total RNA was extracted by RNeasy micro Kit by Qiagen, according to manufacturer's protocol.

treatment_protocol: Sorted cells (at least 100000 cells) were subjected to RNA extraction.

tag: strain/background

value: fetal ventral mesencephalon

tag: developmental stage

tag: marker

value: CORIN+


title: Dharmacon negative control siRNA at 0hr, biological rep1


title: GBM_CULT00U87_SC_AMBION

description: analysis of glioblastoma cell line

source_name: brain tumor cell line stem cell culture (glioblastoma)


title: GBM_ID00000_1

description: reanalysis of GSM1214880


title: CORIN+LMX1A::GFP+

description:
Cultured cells.
LMX1A::GFP KI ESCs were generated by homologous recombination in 129SVEV ESC lines.

source_name: mES-derived cells (day9 CORIN+LMX1A::GFP+)

tag: cell type

value: differentiated mouse ESC-derived neural progenitors


title: Dharmacon negative control siRNA at 0hr, biological rep3


title: CORIN-LMX1A::GFP+

source_name: mES-derived cells (day9 CORIN-LMX1A::GFP+)


title: EPNST_ID00416_1

description: reanalysis of GSM1217883

source_name: brain tumor (ependymoma)

value: brain tumor (ependymoma)


title: APT121 rep 1

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

description: PIN lesion

hyb_protocol: Standard Affymetrix hybridization method

scan_protocol: Standard Affymetrix scanning method

data_processing: The Bioconductor package xps was used. Preprocess and normalize with RMA.  Filter data using detection above background (DABG, alpha1 = 0.05 and alpha2 = 0.07)).  Present/Absent calls done by assigning a p value for each probeset on a chip based on the rank order against the background probeset intensity (p ≤ 0.05: score = 1 or P; 0.05 < p ≤ 0.07: score = 0.6 or M; p > 0.07: score = 0 or A). For our final analysis differentially expressed transcripts were identified using the Significance analysis of microarray program (SAM v-3.09) only on transcripts determined to be present as a group (sum score of individual P/A scores >= 4.8 for control or 2.4 for APT121) . The log2-transformed data of each dataset were analyzed using the two class, unpaired analysis with t-statistics, 900 permutations, and a 5% false discovery rate (FDR).   Significant transcripts (FDR < 5%) with fold change between groups > 1.5 were subjected to functional analyses.  Functional analyses were performed using the GeneGo MetaCoreTM analysis and database suite (GeneGo, St. Joseph, MI).

source_name: anterior prostate lobe

label_protocol: Standard Affymetrix labeling methods

growth_protocol: ad libitum feed and water; AIN93G semi-purified diet; start diet at 3 weeks; terminate experiment at 12 weeks

extract_protocol: SV Total RNA isolation kit (Promega); prostates were crushed under liquid nitrogen and added to the kit lysis buffer to prevent RNA degradation.  Genomic DNA was removed by digestion with RNAase free DNAse and RNA was repurified with the RNAeasy mini kit.

value: B6D2F3, PIN lesion

value: male

value: mixed C57BL/6J and DBA/2 background (F3 generation)


title: EPNST_ID00333_1

description: reanalysis of GSM1217876


title: GBM_CULT00U87_M_AMBION

description: analysis of glioblastoma cell line


title: VM CORIN-

description: Fetal brain.

source_name: E11.5 fetal mouse ventral midbrain (CORIN-)

value: CORIN-


title: FIBRO_ID00001_AMBION

description: analysis of fibroblast cell line

source_name: cell line monolayer (fibroblast)

value: cell line monolayer (fibroblast)


title: GBM_CULT00U87_FC_AMBION

description: analysis of glioblastoma cell line

source_name: brain tumor cell line 3D culture (glioblastoma)


title: EPNST_ID00285_1

description: reanalysis of GSM1217869


title: APT121 rep 3

description: PIN lesion


title: APT121 rep 2

description: PIN lesion


title: EPNST_ID00388_1

description: reanalysis of GSM1217879


title: APT121 rep 4

description: PIN lesion


title: wild type rep 7

description: normal


title: EPNST_ID00135_1

description: reanalysis of GSM1217858


title: wild type rep 6

description: normal


title: wild type rep 8

description: normal


title: wild type rep 4

description: normal


title: wild type rep 5

description: normal


title: EPNPFB_ID00723_1

description: reanalysis of GSM1217898


title: EPNPFB_ID00811_4_AMBION

description: analysis of ependymoma surgical sample


title: EPNPFB_ID00811_1_AMBION

description: reanalysis of GSM1217904


title: EPNPFB_ID00811_5_AMBION

description: analysis of ependymoma surgical sample


title: wild type rep 3

description: normal


title: EPNPFB_ID00700_1

description: reanalysis of GSM1217897


title: wild type rep 2

description: normal


title: H1975_miR-196b

city: Albuquerque

first: Carmen

last: Tellez

state: NM

address: 2425 Ridgecrest Dr. SE

institute: Lovelace Respiratory Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Arrays were normalized using robust spline normalization and transformed using the variance stabilization method

source_name: cell line

label_protocol: Biotinylated cRNA were prepared with the Epicentre TargetAmp labeling kit kit for Illumina expression beadchip

extract_protocol: RNA was extracted with Trizol reagent, DNase I treatment  and clean up with QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.

tag: transfection

value: lung tumor dervied cell line


title: EPNPFB_ID00246_1

description: reanalysis of GSM1217867


title: EPNPFB_ID00364_1

description: reanalysis of GSM1217877


title: HBEC2MBT

value: human bronchial epithelial cells transformed with the carcinogens MNU and BPDE


title: HBEC2MBT_miR-196b


title: EPNPFB_ID00392_1

description: reanalysis of GSM1217880


title: H1975


title: EPNPFB_ID00110_1

description: reanalysis of GSM1217857


title: EPNPFB_ID00419_1

description: reanalysis of GSM1217884


title: EPNPFB_ID00483_1

description: reanalysis of GSM1217887


title: wild type rep 1

description: normal


title: EPNPFB_ID00080_1

description: reanalysis of GSM1217856


title: EPNPFA_ID00859_1_AMBION

description: reanalysis of GSM1217912


title: EPNPFA_ID00928_3_AMBION

description: analysis of ependymoma surgical sample


title: EPNPFA_ID00839_1_AMBION

description: analysis of ependymoma surgical sample


title: MaSC-enriched population isolated from ErbB2, stromal PTEN deletion mice-Experiment#1

city: Columbus

first: Gina

last: Sizemore

state: OH

address: 460 W. 12th Avenue

institute: Ohio State University

description: Gene expression data from Lin-CD24+CD29Hi MaSC-enriched epithelial subpopulations collected by pooling pre-neoplastic mammary tissue from 6-8 virgin ErbB2;Fsp-cre;Ptenfl/fl (8-9 weeks of age) mice

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC

data_processing: The resulting array data was assessed for statistical quality control and normalized in Expression Console (Affymetrix) using an SST RMA algorithm. Heat maps for each independent sample were then created using dChip software using fold change and p-value parameters of 1.5 and < 0.05, respectively. GSEA v2.0 was used to determine the enrichment of the C2 category within the Molecular Signatures Database (MSigDB) in our gene expression data. Statistical significance (q<0.05) was determined through generation of a normalized enrichment score (NES) and a false discovery rate (FDR).

source_name: MaSC-enriched population isolated by FACS (Lin-CD24+CD29hi) from experimental MMTV-ErbB2;Fsp-cre;Ptenfl/fl mice.

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

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and treated with DNAse I (DNA-free, Ambion). RNA quality was assessed using a NanoDrop TM2000 Spectrophotometer (Thermo Scientific). Sample quality was further ensured by characterizing size distribution via fluorescent capillary electrophoresis using the Bioanalyzer 2100 RNA 6000 Pico-Chip and Degradometer software (Agilent Technologies, Santa Clara, California, USA).

value: mammary

value: mammary stem cell population

tag: cell markers

value: 8-9 weeks


title: MaSC-enriched population isolated from ErbB2, stromal PTEN deletion mice-Experiment#3


title: MaSC-enriched population isolated from control ErbB2 mice-Experiment#1

description: Gene expression data from Lin-CD24+CD29Hi MaSC-enriched epithelial subpopulations collected by pooling pre-neoplastic mammary tissue from 6-8 virgin ErbB2;Ptenfl/fl (8-9 weeks of age) mice

source_name: MaSC-enriched population isolated by FACS (Lin-CD24+CD29hi) from control MMTV-ErbB2;Ptenfl/fl mice.


title: MaSC-enriched population isolated from control ErbB2 mice-Experiment#3


title: MaSC-enriched population isolated from control ErbB2 mice-Experiment#2


title: EPNPFA_ID00928_4 _AMBION

description: analysis of ependymoma surgical sample


title: MaSC-enriched population isolated from ErbB2, stromal PTEN deletion mice-Experiment#2


title: EPNPFA_ID00812_1a

description: reanalysis of GSM1217906


title: EPNPFA_ID00691_1a

description: reanalysis of GSM1217893


title: EPNPFA_ID00492_1

description: reanalysis of GSM1217889


title: EPNPFA_ID00928_1_AMBION

description: analysis of ependymoma surgical sample


title: EPN_CULT00928_3M_AMBION

description: analysis of ependymoma cell line

source_name: brain tumor cell line monolayer (ependymoma)


title: EPN_CULT00811_5FC_2_AMBION

description: analysis of ependymoma cell line

source_name: brain tumor cell line 3D culture (ependymoma)


title: EPNPFA_ID00195_1

description: reanalysis of GSM1217862


title: EPNPFA_ID00064_1

description: reanalysis of GSM1217854


title: EPN_CULT00928_4_M_AMBION

description: analysis of ependymoma cell line

value: brain tumor cell line monolayer (ependymoma)


title: EPN_CULT00928_3FC_AMBION

description: analysis of ependymoma cell line

value: brain tumor cell line 3D culture (ependymoma)


title: EPN_CULT00811_4B_AMBION

description: analysis of ependymoma cell line

source_name: brain tumor cell line monlayer (ependymoma)


title: ATRT_ID00517_1

description: reanalysis of GSM869627

source_name: brain tumor (atypical teratoid/rhabdoid tumor)


title: ATRT_ID00370_1

description: reanalysis of GSM869621

value: brain tumor (atypical teratoid/rhabdoid tumor)


title: Retina_Atrx wildtype_P17_rep2

city: Ottawa

first: Pamela

last: Lagali

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: The fragmented and labeled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Arrays (Affymetrix) and incubated at 45°C in the Genechip® Hybridization Oven 640 (Affymetrix) for 17 hours at 60 rpm. The arrays were then washed in a GeneChip® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain Kit according to the manufacturer’s instructions (Affymetrix).

scan_protocol: The microarrays were scanned on a GeneChip® Scanner 3000 (Affymetrix) according to the manufacturer's instructions.

data_processing: Raw data were independently processed and analyzed using the FlexArray version 1.6.3 Software Package (Génome Québec) and the Expression ConsoleTM and Transcriptome Analysis ConsoleTM Software (Affymetrix). Normalization of the data was performed using the Robust Multi-array Average (RMA) method. Gene level differential expression analysis was performed using a one-way between-subject ANOVA (unpaired) algorithm. Signal intensities were calculated using Tukey’s Bi-weight average of gene level intensity of all the samples in either the AtrxKO or wildtype condition (log2). Linear fold-change values were calculated as 2^[AtrxKO bi-weight average signal (log2) – wildtype bi-weight average signal (log2)].

source_name: total retina tissue (pooled from both eyes) for P17 wildtype mouse

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA using the Affymetrix GeneChip® WT PLUS Reagent Kit according to the manufacturer’s instructions (Affymetrix). The cDNA was fragmented and labeled with the Affymetrix GeneChip® WT Terminal Labeling Kit according to the manufacturer’s instructions (Affymetrix).

growth_protocol: Mice were maintained under a 12-hour light-dark cycle with food and water available ad libitum.

extract_protocol: Total RNA was extracted from manually homogenized retina samples using TRIzol reagent according to the manufacturer's protocol (Life Technologies, Inc.) and using 5 mg/ml glycogen as a carrier. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: Mice were sacrificed by cervical dislocation and retinal tissues were removed through a corneal incision following lensectomy. Retinas were flash-frozen in a sterile nuclease-free microfuge tube on dry ice and stored at -80°C until all samples were prepared.

value: retina

value: Chx10Cre-/-;Atrx flox/y


title: EPN_CULT00811_5C_AMBION

description: analysis of ependymoma cell line


title: Retina_Atrx wildtype_P17_rep3


title: EPNPFA_ID00507_1

description: reanalysis of GSM1217890


title: Retina_Atrx wildtype_P17_rep1


title: Retina_Atrx knockout_P17_rep2

source_name: total retina tissue (pooled from both eyes) for P17 Atrx conditional knockout mouse

value: Chx10Cre+/-;Atrx flox/y


title: Retina_Atrx knockout_P17_rep3


title: EPN_CULT00811_5FC_AMBION

description: analysis of ependymoma cell line


title: ATRT_ID00413_1

description: reanalysis of GSM869623


title: EPN_CULT00811_5_SC_AMBION

description: analysis of ependymoma cell line

source_name: brain tumor cell line stem cell culture (ependymoma)


title: ATRT_ID00504_1

description: reanalysis of GSM869624


title: EPN_CULT00811_4C_AMBION

description: analysis of ependymoma cell line

value: brain tumor cell line monlayer (ependymoma)


title: EPN_CULT00811_5_DMSO_AMBION

description: analysis of ependymoma cell line


title: ATRT_ID00514_1

description: reanalysis of GSM869625


title: ATRT_ID00737_1

description: reanalysis of GSM869631


title: ATRT_ID00404_1

description: reanalysis of GSM869622


title: ATRT_ID00343_1

description: reanalysis of GSM869620


title: Nrf2 null neutrophils SP rep1

city: Chapel Hill

first: Claire

middle: M.

last: Doerschuk

address: Marsico Hall 7205 CB#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

description: Gene expression data from mouse lung neutrophils

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays. Hybridization, washing, staining and scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

scan_protocol: Scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

data_processing:
Affymetrix Expression Console Software was used for basic data analysis and quality control. Microarray data were preprocessed by RMA (Robust Multiarray Average) background correction, GC content and sequence correction, quantile normalization, and median polish summarization, and expression levels compared using ANOVA on log2 intensities to identify transcripts that were differentially expressed between genotype and treatment groups.  Differentially expressed (DE) mRNAs were filtered at Benjamini-Hochberg FDR < 0.05, and fold change > 2, and expression patterns of DE transcripts were visualized using hierarchical clustering.  Expression analyses were performed using Partek Genomics Suite (Partek Inc., St. Louis. MO, USA).  Gene Set Enrichment Analysis (GSEA) was performed according to the method described (12, 13).  In addition to gene sets derived from Gene Ontology (GO) biological processes, GSEA for Nrf2 regulated genes was performed using lists of Nrf2 regulated genes from the literature (14, 15).
The .mps file used in this analysis is available on the Superseries record.

source_name: Lung neutrophils isolated from Nrf2 null (Nfe2l2 -/-) mice given S. pneumoniae

label_protocol: Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. The Affymetrix HT WT User Manual was followed to prepare the samples. Briefly, the WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.  The Beckman Coulter Biomek FXP Laboratory Automation Workstation with the Target Express set up was used to prepare the samples with these two kits.

extract_protocol: Total RNA was isolated using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Anesthetized mice received PBS or a suspension containing S. pneumoniae instilled intratracheally into the left lung at a dose of 2.3 µl/g mouse body weight. Neutrophils were isolated using MACS beads (Miltenyi, Auburn, CA) according to the manufacturer’s instructions. Briefly, single cell suspensions were prepared from dissected mouse lungs. The cells were washed with PBS containing 2 mM EDTA and 0.5% bovine serum albumin, and incubated with biotin-anti-Ly6G and magnetic beads coated with anti-biotin. The samples were passed through a column in a magnetic field, and cells bound to beads were collected for further analysis. Cells were kept at 4-8°C during staining and magnetic bead isolation.

value: Lung

value: neutrophils

value: Nrf2 null (Nfe2l2 -/-)

value: 6-12 weeks

tag: inoculation agent

value: Streptococcus pneumoniae


title: PB-Pten-NICD Met #1

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: After labeling, 2ug of each aRNA was mixed with 2 ug of reference RNA and purified with Qiagen MinElute PCR Purification kit according to manufacturer’s instructions. Eluted sample was mixed with 10× Blocking Solution and 2× HiRPM buffer (Agilent Technologies), incubated for 2 min at 95°C and hybridized on 8× 60K Whole Human Genome Oligo Microarray chip (Agilent Technologies) using SureHyb DNA Microarray Hybridization Chambers in DNA Microarray hybridization oven (Agilent Technologies) at 10 rpm, 65°C for 18 h.

scan_protocol: After hybridization, slides were washed in Gene Expression Wash Buffer 1 and 2 for 1 min. Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies) using Agilent-provided parameters (Red and Green photomultiplier tube (PMT) were each set at 100%, and scan resolution was set to 3 μm). The Feature Extraction Software v9.1.3.1 (Agilent Technologies) was used to extract and analyze the signals.

data_processing: Expression arrays were processed and loess-normalized using BioConductor.

label: Alexa Fluor 647

source_name: lung metastasis

label_protocol: The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.Briefly, 2ug of aRNA and Universal Human Reference RNA (Stratagene) were labeled in reverse transcription with Alexa647 and Alexa 555 aha-dUTPs respectively.

growth_protocol: An ROSA26-LSL-NICD transgenic line enables the expression of the active Notch1 intracellular domain at the endogenous ROSA26 locus upon excision of a floxed transcriptional stop signal. We bred ROSA26-LSL-NICD, ARR2PB-Cre, and Pten conditional mice and generated a cohort of ARR2PB-Cre;Ptenfl/fl;ROS26-LSL-NICDMut/Wt and ARR2PB-Cre:Ptenfl/fl mice (hereafter referred to as PB-Pten-NICD and PB-Pten mice, respectively).

extract_protocol: Total RNA samples were extracted with RNeasy Mini Kit (Qiagen) according to the manufacture’s recommendations. RNA quality was assessed with Nanodrop (Invitrogen). The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.

tag: tissue

value: lung metastasis

tag: strain

value: PB-Pten-NICD

label: Alexa Fluor 555

source_name: universal reference

value: reference RNA


title: Nrf2 null neutrophils PBS rep4

source_name: Lung neutrophils isolated from Nrf2 null (Nfe2l2 -/-) mice given PBS

tag: age

value: control (PBS)


title: ATRT_CULT00737_FC_AMBION

description: analysis of atypical teratoid rhabdoid cell line

source_name: brain tumor cell line 3D culture (atypical teratoid/rhabdoid tumor)


title: Nrf2 null neutrophils SP rep4


title: Retina_Atrx knockout_P17_rep1

tag: gender

value: male


title: ATRT_ID00119_1

description: reanalysis of GSM869619


title: ATRT_BT16_1_NT_20091215

source_name: brain tumor cell line monolayer (atypical teratoid/rhabdoid tumor)


title: ATRT_BT16_1_Correct

value: brain tumor cell line monolayer (atypical teratoid/rhabdoid tumor)


title: Nrf2 null neutrophils SP rep2

tag: genotype


title: PB-Pten-NICD Met #2


title: PB-Pten prostate 2

source_name: prostate tissue

value: prostate


title: ATRT_CULT00737_M_AMBION


title: ATRT_CULT00737_SC_AMBION

source_name: brain tumor cell line stem cell culture (atypical teratoid/rhabdoid tumor)


title: PB-Pten-NICD SV 2

source_name: seminal vesical

value: seminal vesical


title: PB-Pten-NICD SV 1


title: Nrf2 null neutrophils PBS rep3


title: Nrf2 null neutrophils SP rep3


title: WT neutrophils SP rep4

source_name: Lung neutrophils isolated from WT mice given S. pneumoniae

value: Wild type (WT)


title: PB-Pten prostate 1


title: WT neutrophils SP rep3


title: PB-Pten-NICD Prostate 1


title: PB-Pten-NICD Prostate 2


title: ATRT_ID00003_1

description: reanalysis of GSM869618

value: brain tumor (atypical teratoid/rhabdoid tumor)


title: ATRT_BT12_1_Correct


title: Nrf2 null neutrophils PBS rep1


title: Nrf2 null neutrophils PBS rep2


title: ATRT_BT12_1_NT_20091215


title: Naive CD8 T Restim replicate 1

city: LYON

first: Jacqueline

last: MARVEL

address: 21 AV TONY GARNIER

country: France

institute: INSERM

hyb_protocol: Following fragmentation,  cDNA were hybridized  on Affymetrix HT MG-430 PM arrays.

scan_protocol: Standard Affymetrix protocol

data_processing:
Affymetrix CEL files were analyzed in R 2.15 using the Bioconductor 2.10 suite of packages. Raw probe signals were background corrected using the maximum likelihood estimation of the normal-exponential mixture model (Silver et al., 2009 - limma 3.16.3) and normalized using the variance stabilization normalization (Huber et al., 2002 - vsn 3.28.0) followed by a quantile normalization (Bolstad et al., 2003). Summarization was performed using the median-polish (Irizarry et al., 2003 - affyPLM 1.36.0)
The CDF was further customized from the one provided by BrainArray:   htmg430pmmmentrezgaltrabio12124cdf_15.1.0.tar
Sample LM-Memory CD8 T cell Homeo replicate 4a (respectively sample LM-Memory CD8 T cell Restim replicate 2a) (respectively sample Naive CD8 T Homeo replicate 3a) is a technical replicate of sample LM-Memory CD8 T cell Homeo replicate 4 (respectively sample LM-Memory CD8 T cell Restim replicate 2) (respectively sample Naive CD8 T Homeo replicate 3)

source_name: Naive CD8 T Restim

label_protocol: Biotinylated cRNA were prepared according to the Ovation® Pico WTA System V2 and EncoreTM Biotin Module protocols

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

treatment_protocol: CD8 T cells were sorted by flow cytometry prior to restimulation (Restimulated) or not (Homeostatic)

tag: treatment

value: Naive

tag: condition

value: Restimulated

tag: dpi

tag: replicate


title: Naive CD8 T Restim replicate 3


title: WT neutrophils SP rep1

value: Lung

tag: background strain


title: WT neutrophils SP rep2

value: neutrophils


title: Met#4, technical replicate #2

tag: technical replicate

tag: sample type


title: WT neutrophils PBS rep4

source_name: Lung neutrophils isolated from WT mice given PBS


title: WT neutrophils PBS rep3


title: Naive CD8 T Restim replicate 4


title: PtNI-Met cell line, technical replicate #2

source_name: metastasis cell line

tag: cell line

value: PtNI-Met


title: Met#5, technical replicate #2


title: Met#7, technical replicate #2


title: Nrf2 null whole lung SP rep4

description: Gene expression data from mouse lung

source_name: Whole lung tissue from Nrf2 null (Nfe2l2 -/-) mice given S. pneumoniae

extract_protocol: Total RNA was isolated from mouse lungs using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: Anesthetized mice received PBS or a suspension containing S. pneumoniae instilled intratracheally into the left lung at a dose of 2.3 µl/g mouse body weight.

value: Whole lung

value: Nrf2 null (Nfe2l2 -/-)

value: 6-12 weeks


title: WT neutrophils PBS rep2

tag: cell type


title: PtNI-Pro cell line, technical replicate #2

source_name: prostate cell line

value: PtNI-Pro


title: Naive CD8 T Restim replicate 2


title: Met#6, technical replicate #2

value: lung metastasis

value: PB-Pten-NICD

value: reference RNA


title: Met#4, technical replicate #1


title: EPNPFA_ID00393_1

description: reanalysis of GSM1217881

source_name: brain tumor (ependymoma)

value: brain tumor (ependymoma)


title: PtNI-SV cell line, technical replicate #2

source_name: seminal vesical cell line

value: PtNI-SV


title: WT neutrophils PBS rep1

value: control (PBS)


title: PtNI-Met cell line, technical replicate #1


title: Met#3, technical replicate #2


title: Naive CD8 T Restim replicate 5


title: Nrf2 null whole lung SP rep1

description: Gene expression data from mouse lung

value: Streptococcus pneumoniae


title: PtNI-Pro cell line, technical replicate #1


title: Nrf2 null whole lung SP rep2

description: Gene expression data from mouse lung


title: Met#6, technical replicate #1


title: Naive CD8 T Homeo replicate 3a

source_name: Naive CD8 T Homeo

value: Homeostatic


title: Naive CD8 T Homeo replicate 1

value: Naive


title: Naive CD8 T Homeo replicate 3


title: Met#7, technical replicate #1

source_name: lung metastasis


title: LM-Memory CD8 T cell Restim replicate 2a

source_name: LM-Memory CD8 T cell Restim

value: List WT

value: Restimulated


title: Naive CD8 T Homeo replicate 5


title: LM-Memory CD8 T cell Restim replicate 5


title: Nrf2 null whole lung PBS rep4

description: Gene expression data from mouse lung

source_name: Whole lung tissue from Nrf2 null (Nfe2l2 -/-) mice given PBS


title: Nrf2 null whole lung PBS rep2

description: Gene expression data from mouse lung


title: Nrf2 null whole lung PBS rep3

description: Gene expression data from mouse lung


title: WT whole lung PBS rep3

description: Gene expression data from mouse lung

source_name: Whole lung tissue from WT mice given PBS

value: Wild type (WT)


title: E15.5 PGC_rep1

city: Sendai

first: Tamotsu

last: Sekinaka

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

description: Gene expression of PGCs from mouse E15.5 embryo genital ridges.

hyb_protocol: 1.65ug of Cy3-labelled cRNAs from each sample were fragmented and hybridized to microarrays according to the manufacturer's instructions using the Gene Expression Hybridization kit (Agilent 5188-5242) and Agilent hybridization oven. After hybridization, microarrays were washed using the Gene Expression Wash Pack (Agilent 5188-5327).

scan_protocol: The microarrays were scanned using the Agilent DNA microarray scanner (Agilent G2505C); the spot signals were quantified using Feature Extraction software.

data_processing: Data was normalized and analyzed by GeneSpring GX (Agilent).

label_protocol: Cy3-labeled cRNA samples were prepared using the Agilent Low Input Quick Amp Labeling Kit (one-color) (5190-2305) and RNA Spike-In Kit (one-color) (5188-5282) according to the manufacturer's instructions. Input was 100 ng of total RNA from each sample.

extract_protocol: Total RNA was purified using the RNeasy micro kit according to the manufacturer's instructions.

tag: strain/background

value: MCH x C57BL6/J (Oct4_delta_PE-GFP Tg)

value: female

value: primordial germ cell (PGC)

tag: developmental stage

value: genital ridge


title: WT whole lung PBS rep2

description: Gene expression data from mouse lung

value: Whole lung

value: 6-12 weeks

tag: inoculation agent


title: Met#5, technical replicate #1

tag: tissue

value: lung metastasis

value: PB-Pten-NICD

source_name: universal reference


title: Naive CD8 T Homeo replicate 2


title: WT whole lung SP rep4

description: Gene expression data from mouse lung

source_name: Whole lung tissue from WT mice given S. pneumoniae


title: LM-Memory CD8 T cell Restim replicate 3


title: E15.5 PGC_rep2


title: WT whole lung SP rep3

description: Gene expression data from mouse lung


title: LM-Memory CD8 T cell Restim replicate 2


title: LM-Memory CD8 T cell Restim replicate 1


title: OCKS+chem+VA5+Dnmt1 KD_rep2

description: Gene expression of MEFs 4 days after OCKS+chem+VA5+Dnmt1-KD treatment.

value: C57BL6/J (Vasa::RFP Tg) x C57BL6/J (Oct4_delta_PE-GFP Tg)

value: male

value: mouse embryonic fibroblast (MEF)


title: WT whole lung PBS rep4

description: Gene expression data from mouse lung

value: control (PBS)


title: PtNI-SV cell line, technical replicate #1

value: PtNI-SV

value: reference RNA


title: Met#3, technical replicate #1

tag: strain


title: WT whole lung SP rep2

description: Gene expression data from mouse lung

tag: age

value: Streptococcus pneumoniae


title: Nrf2 null whole lung PBS rep1

description: Gene expression data from mouse lung

value: Nrf2 null (Nfe2l2 -/-)


title: Nrf2 null whole lung SP rep3

description: Gene expression data from mouse lung


title: E15.5 PGC_rep3

tag: gender


title: WT whole lung PBS rep1

description: Gene expression data from mouse lung

tag: genotype

value: Wild type (WT)


title: OCKS+chem+VA5+Dnmt1 KD_rep1


title: OCKS+chem+VA5+Dnmt1 KD_rep3


title: LM-Memory CD8 T cell Homeo replicate 4a

source_name: LM-Memory CD8 T cell Homeo

tag: treatment

value: List WT

value: Homeostatic


title: OS+chem+VA5+Dnmt1 KD_rep3

description: Gene expression of MEFs 4 days after OS+chem+VA5+Dnmt1-KD treatment.


title: LM-Memory CD8 T cell Homeo replicate 2

tag: condition


title: LM-Memory CD8 T cell Homeo replicate 1

tag: dpi


title: LM-Memory CD8 T cell Homeo replicate 4

tag: replicate


title: LM-Memory CD8 T cell Homeo replicate 5


title: OS+chem+VA5+Dnmt1 KD_rep2


title: Naive CD8 T Homeo replicate 4

value: Naive


title: WT whole lung SP rep1

description: Gene expression data from mouse lung

tag: background strain


title: OS+chem+VA5+Dnmt1 KD_rep1


title: total RNA from neuroblastoma tumor 97

status: Public on Sep 08 2016

city: Heidelberg

first: Maral

last: Saadati

address: Im Neuenheimer Feld 280

department: Biostatistics

country: Germany

institute: German Cancer Research Center

description:
neuroblastoma
sample97

hyb_protocol: Hybridization was performed following the manufacturer's protocol. In brief, 1650 ng of Cy3-labeled cRNA was hybridized on 4x44K custom microarrays using Agilent's High-RPM Gene Expression Hyb Kit. Hybridization was performed for 17 hours at 65°C in a rotating hyb oven at 10 rpm according the company's recommendations.

scan_protocol: Scanning was according to Agilent's recommentdations.

data_processing:
TIFF-images were processed using Agilent's Feature Extraction software Version 9.5.1. R package limma was used for background correction (normexp method) and quantile normalization.
Normalized signal intensity. Data were normalized using the quantile algorithm from limma

source_name: neuroblastoma 97

label_protocol: Labeling was performed according to Agilent's recommentdations. In brief, 1µg total of tumor RNA was linearily amplified and labeled with Cy3 using Agilent's one-color Quick Amp Labeling Kit following the instructions of the protocol.

extract_protocol: Total RNA was isolated following the TRIzol protocol (Invitrogen) and RNA integrity was assessed using the 2100 Bioanalyzer (Agilent,Palo Alto, CA, USA). Only samples with an RNA Integrity Number >7.5 were taken for further analysis.

treatment_protocol: Samples were homogenized in a FastPrep FP120 disruptor (Qbiogene, Carlsbad, CA, USA)

value: neuroblastoma

tag: inss stage

tag: current risk category

value: low-risk

tag: age at diagnosis

value: <1.5 years

tag: mycn status

value: MYCN-nonamplified

tag: 1p status

tag: 11q status

value: 11q-whole loss

tag: 17q status

value: 17q-whole gain


title: LM-Memory CD8 T cell Homeo repl 3


title: MEF_rep3

description: Gene expression of control MEFs.

tag: strain/background

value: C57BL6/J (Vasa::RFP Tg) x C57BL6/J (Oct4_delta_PE-GFP Tg)

value: male

tag: cell type


title: total RNA from neuroblastoma tumor 91

description:
neuroblastoma
sample91

source_name: neuroblastoma 91

tag: tissue

value: high-risk

value: >=1.5 years

value: MYCN-amplified


title: total RNA from neuroblastoma tumor 101

description:
neuroblastoma
sample101

source_name: neuroblastoma 101


title: total RNA from neuroblastoma tumor 98

description:
neuroblastoma
sample98

source_name: neuroblastoma 98


title: total RNA from neuroblastoma tumor 94

description:
neuroblastoma
sample94

source_name: neuroblastoma 94


title: total RNA from neuroblastoma tumor 100

description:
neuroblastoma
sample100

source_name: neuroblastoma 100


title: total RNA from neuroblastoma tumor 99

description:
neuroblastoma
sample99

source_name: neuroblastoma 99


title: MEF_rep1

description: Gene expression of control MEFs.

tag: gender

value: mouse embryonic fibroblast (MEF)


title: total RNA from neuroblastoma tumor 92

description:
neuroblastoma
sample92

source_name: neuroblastoma 92


title: H1299_GCRA_1

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

institute: IDIBELL

description:
sample name: 040_MA__1200253949441026__Cy3_411_1_2
cancer cell line

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanner Agilent G2565CA Feature extraction 10.7

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Non Small Cell Lung Cancer (NSCLC)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells where growth on RPMI media with 10% FBS, 1% PS

extract_protocol: Total RNA were extracted using Trizol Reagent.

treatment_protocol: GCRA: Dexamethasone (1uM) + Retinoic Acid (1uM) 120hours; COMB: Dexamethasone (1uM) + Retinoic Acid (1uM) + Aza (0.2uM) + SAHA (0.2uM) 120 hours

tag: individual

value: Diseased donor

tag: cell line

tag: cell line type

value: BRG1 mutant

value: GCRA


title: total RNA from neuroblastoma tumor 96

description:
neuroblastoma
sample96

source_name: neuroblastoma 96


title: MEF_rep2

description: Gene expression of control MEFs.


title: total RNA from neuroblastoma tumor 105

description:
neuroblastoma
sample105

source_name: neuroblastoma 105


title: total RNA from neuroblastoma tumor 93

description:
neuroblastoma
sample93

source_name: neuroblastoma 93


title: total RNA from neuroblastoma tumor 103

description:
neuroblastoma
sample103

source_name: neuroblastoma 103


title: total RNA from neuroblastoma tumor 95

description:
neuroblastoma
sample95

source_name: neuroblastoma 95


title: total RNA from neuroblastoma tumor 104

description:
neuroblastoma
sample104

source_name: neuroblastoma 104


title: total RNA from neuroblastoma tumor 85

description:
neuroblastoma
sample85

source_name: neuroblastoma 85


title: total RNA from neuroblastoma tumor 78

description:
neuroblastoma
sample78

source_name: neuroblastoma 78


title: total RNA from neuroblastoma tumor 81

description:
neuroblastoma
sample81

source_name: neuroblastoma 81

value: intermediate-risk


title: total RNA from neuroblastoma tumor 82

description:
neuroblastoma
sample82

source_name: neuroblastoma 82


title: total RNA from neuroblastoma tumor 75

description:
neuroblastoma
sample75

source_name: neuroblastoma 75


title: total RNA from neuroblastoma tumor 83

description:
neuroblastoma
sample83

source_name: neuroblastoma 83


title: total RNA from neuroblastoma tumor 71

description:
neuroblastoma
sample71

source_name: neuroblastoma 71


title: total RNA from neuroblastoma tumor 76

description:
neuroblastoma
sample76

source_name: neuroblastoma 76


title: total RNA from neuroblastoma tumor 84

description:
neuroblastoma
sample84

source_name: neuroblastoma 84


title: total RNA from neuroblastoma tumor 77

description:
neuroblastoma
sample77

source_name: neuroblastoma 77


title: total RNA from neuroblastoma tumor 88

description:
neuroblastoma
sample88

source_name: neuroblastoma 88


title: total RNA from neuroblastoma tumor 70

description:
neuroblastoma
sample70

source_name: neuroblastoma 70

value: 1p-whole gain


title: total RNA from neuroblastoma tumor 68

description:
neuroblastoma
sample68

source_name: neuroblastoma 68

value: neuroblastoma


title: total RNA from neuroblastoma tumor 89

description:
neuroblastoma
sample89

source_name: neuroblastoma 89


title: total RNA from neuroblastoma tumor 69

description:
neuroblastoma
sample69

source_name: neuroblastoma 69


title: total RNA from neuroblastoma tumor 67

description:
neuroblastoma
sample67

source_name: neuroblastoma 67


title: total RNA from neuroblastoma tumor 73

description:
neuroblastoma
sample73

source_name: neuroblastoma 73


title: total RNA from neuroblastoma tumor 87

description:
neuroblastoma
sample87

source_name: neuroblastoma 87


title: total RNA from neuroblastoma tumor 102

description:
neuroblastoma
sample102

source_name: neuroblastoma 102

value: low-risk


title: total RNA from neuroblastoma tumor 80

description:
neuroblastoma
sample80

source_name: neuroblastoma 80

value: <1.5 years


title: total RNA from neuroblastoma tumor 66

description:
neuroblastoma
sample66

source_name: neuroblastoma 66


title: total RNA from neuroblastoma tumor 74

description:
neuroblastoma
sample74

source_name: neuroblastoma 74

value: MYCN-nonamplified


title: total RNA from neuroblastoma tumor 72

description:
neuroblastoma
sample72

source_name: neuroblastoma 72


title: total RNA from neuroblastoma tumor 65

description:
neuroblastoma
sample65

source_name: neuroblastoma 65


title: total RNA from neuroblastoma tumor 63

description:
neuroblastoma
sample63

source_name: neuroblastoma 63


title: total RNA from neuroblastoma tumor 79

description:
neuroblastoma
sample79

source_name: neuroblastoma 79

value: 11q-whole loss


title: total RNA from neuroblastoma tumor 86

description:
neuroblastoma
sample86

source_name: neuroblastoma 86


title: total RNA from neuroblastoma tumor 61

description:
neuroblastoma
sample61

source_name: neuroblastoma 61


title: total RNA from neuroblastoma tumor 58

description:
neuroblastoma
sample58

source_name: neuroblastoma 58

value: 17q-whole gain


title: total RNA from neuroblastoma tumor 60

description:
neuroblastoma
sample60

source_name: neuroblastoma 60


title: total RNA from neuroblastoma tumor 54

description:
neuroblastoma
sample54

source_name: neuroblastoma 54


title: total RNA from neuroblastoma tumor 62

description:
neuroblastoma
sample62

source_name: neuroblastoma 62


title: total RNA from neuroblastoma tumor 64

description:
neuroblastoma
sample64

source_name: neuroblastoma 64


title: total RNA from neuroblastoma tumor 56

description:
neuroblastoma
sample56

source_name: neuroblastoma 56


title: total RNA from neuroblastoma tumor 57

description:
neuroblastoma
sample57

source_name: neuroblastoma 57


title: total RNA from neuroblastoma tumor 48

description:
neuroblastoma
sample48

source_name: neuroblastoma 48


title: total RNA from neuroblastoma tumor 49

description:
neuroblastoma
sample49

source_name: neuroblastoma 49

value: 11q-whole gain


title: total RNA from neuroblastoma tumor 50

description:
neuroblastoma
sample50

source_name: neuroblastoma 50


title: total RNA from neuroblastoma tumor 47

description:
neuroblastoma
sample47

source_name: neuroblastoma 47


title: total RNA from neuroblastoma tumor 90

description:
neuroblastoma
sample90

source_name: neuroblastoma 90


title: total RNA from neuroblastoma tumor 52

description:
neuroblastoma
sample52

source_name: neuroblastoma 52


title: total RNA from neuroblastoma tumor 46

description:
neuroblastoma
sample46

source_name: neuroblastoma 46


title: total RNA from neuroblastoma tumor 59

description:
neuroblastoma
sample59

source_name: neuroblastoma 59


title: total RNA from neuroblastoma tumor 53

description:
neuroblastoma
sample53

source_name: neuroblastoma 53


title: total RNA from neuroblastoma tumor 55

description:
neuroblastoma
sample55

source_name: neuroblastoma 55


title: total RNA from neuroblastoma tumor 41

description:
neuroblastoma
sample41

source_name: neuroblastoma 41


title: total RNA from neuroblastoma tumor 45

description:
neuroblastoma
sample45

source_name: neuroblastoma 45


title: total RNA from neuroblastoma tumor 40

description:
neuroblastoma
sample40

source_name: neuroblastoma 40


title: total RNA from neuroblastoma tumor 43

description:
neuroblastoma
sample43

source_name: neuroblastoma 43


title: HT-29_Bevacizumab-resistant rep3

city: Chiba

first: Yukie

last: Yoshii

address: Anagawa 4-9-1, Inage

institute: National Institute of Radiological Sciences

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Bevacizumab-resistant rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were incubated in a humidified atmosphere of 5% CO2 in air at 37°C. DMEM medium (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum and antibiotics was used for growth medium. Exponentially growing cells were used for the experiments. Cells were trypsinized, and the number of viable cells was counted by the trypan blue dye-exclusion method.

extract_protocol: Total RNAs were extracted from samples with a PureLink RNA Mini Kit (Life Technologies).

treatment_protocol: HT-29 cells suspended in phosphate-buffered saline (PBS) (at 1 x 10^7) were subcutaneously injected into the flank of the BALB/c nude mouse. HT-29 tumor-bearing mice were treated with bevacizumab (5 mg/kg twice a week) for 3 weeks to obtain bevacizumab-resistant tumors. The bevacizumab-resistant HT29 tumors were compared to bevacizumab-untreated HT-29 tumors, which had almost similar size to the bevacizumab-resistant HT-29 tumors, as control. For mice with control tumors, an equivalent amount of saline was treated instead of bevacizumab.

tag: tissue type

value: Xenograft tumor

tag: treatment

value: Bevacizumab treatment (5 mg/kg twice a week for 5 weeks)


title: HT-29_Bevacizumab-resistant rep1

source_name: Bevacizumab-resistant rep1

value: Bevacizumab treatment (5 mg/kg twice a week for 3 weeks)


title: total RNA from neuroblastoma tumor 39

description:
neuroblastoma
sample39

source_name: neuroblastoma 39


title: total RNA from neuroblastoma tumor 42

description:
neuroblastoma
sample42

source_name: neuroblastoma 42

value: high-risk

value: MYCN-amplified


title: total RNA from neuroblastoma tumor 38

description:
neuroblastoma
sample38

source_name: neuroblastoma 38


title: total RNA from neuroblastoma tumor 36

description:
neuroblastoma
sample36

source_name: neuroblastoma 36


title: total RNA from neuroblastoma tumor 44

description:
neuroblastoma
sample44

source_name: neuroblastoma 44

value: >=1.5 years


title: HT-29_Bevacizumab-resistant rep2

source_name: Bevacizumab-resistant rep2

value: Bevacizumab treatment (5 mg/kg twice a week for 4 weeks)


title: total RNA from neuroblastoma tumor 37

description:
neuroblastoma
sample37

source_name: neuroblastoma 37


title: HT-29_Control_rep2

value: non-treated


title: HT-29_Control_rep3


title: H1BP ASO #2 replicate2

city: São Paulo

first: Sergio

last: Verjovski-Almeida

state: São Paulo

address: Av. Vital Brasil 1500

country: Brazil

institute: Instituto Butantan

description:
H1BP cells transfected with ASO #2 targeting HIPSTR lncRNA replicate 2
Raw data in CY5 channel of:
expt_2_1_2.txt

hyb_protocol: Hybridization samples were prepared with 825 ng labeled cRNA of each sample and Agilent Gene Expression Hybridization Kit. Hybridization samples were dispensed in Agilent hybridization gasket slide and enclosed in Agilent Hyb chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1) with Protocol GE2_107_Sep09.

source_name: H1BP transfected with ASO targeting HIPSTR lncRNA

label_protocol: 100 ng of total RNA were converted into Cy3- and Cy5-labeled cRNA using the Agilent Low Input Quick Amp Labeling Two Color Kit according to manufacturer's protocol.

growth_protocol: H1BP cells were maintained at 37 °C in 5 % CO2-humidified atmosphere in the hESC basal medium, which had been conditioned by a monolayer of γ-irradiated mouse embryonic fibroblast (MEF) feeder cells for 24 h, and then supplemented with 10 ng/ml FGF2. Medium was changed every day. For passaging, H1BP cells were detached with Gentle Cell Dissociation Reagent (STEMCELL Technologies) for 6-7 min at 37 °C, dispersed into clusters of 5-10 cells, and plated on 0.1 % gelatin-coated culture dishes of desired size.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with RNeasy Micro Kit (QIAGEN) according to manufacturer’s protocol, with on-column DNAse I treatment time extended to 1 h.

treatment_protocol: To silence HIPSTR expression in H1BP cells, 40000 cells were plated on 6-well plates 48 h before transfection; 0.013 µl of GenMute siRNA Transfection Reagent (SignaGen) per 1 pmol of ASO were used for transfection. Transfection mixes were prepared in 1x GenMute Transfection Buffer (SignaGen). A total of 300 pmol of ASO per well on 6-well plates was used for transfection. Cells were collected for subsequent RNA extraction 24 h after transfection with ASOs.


title: H1BP ASO CTL replicate1

description:
H1BP cells transfected with scrambled control oligo (ASO CTL) replicate 1
Raw data in CY3 channel of:
expt_2_1_1.txt

source_name: H1BP transfected with control scrambled ASO


title: H1BP ASO #2 replicate1

description:
H1BP cells transfected with ASO #2 targeting HIPSTR lncRNA replicate 1
Raw data in CY5 channel of:
expt_2_1_1.txt


title: H1BP ASO CTL replicate3

description:
H1BP cells transfected with scrambled control oligo (ASO CTL) replicate 3
Raw data in CY3 channel of:
expt_2_1_2.txt


title: total RNA from neuroblastoma tumor 35

description:
neuroblastoma
sample35

source_name: neuroblastoma 35


title: total RNA from neuroblastoma tumor 33

description:
neuroblastoma
sample33

source_name: neuroblastoma 33


title: HT-29_Control_rep1


title: total RNA from neuroblastoma tumor 34

description:
neuroblastoma
sample34

source_name: neuroblastoma 34


title: H1BP ASO CTL replicate2

description:
H1BP cells transfected with scrambled control oligo (ASO CTL) replicate 2
Raw data in CY5 channel of:
expt_2_2_1.txt


title: total RNA from neuroblastoma tumor 30

description:
neuroblastoma
sample30

source_name: neuroblastoma 30


title: total RNA from neuroblastoma tumor 29

description:
neuroblastoma
sample29

source_name: neuroblastoma 29


title: H1BP ASO #1 replicate2

description:
H1BP cells transfected with ASO #1 targeting HIPSTR lncRNA replicate 2
Raw data in CY5 channel of:
expt_2_1_4.txt


title: total RNA from neuroblastoma tumor 31

description:
neuroblastoma
sample31

source_name: neuroblastoma 31


title: H1BP ASO #0 replicate2

description:
H1BP cells transfected with ASO #0 targeting HIPSTR lncRNA replicate 2
Raw data in CY5 channel of:
expt_2_2_4.txt


title: total RNA from neuroblastoma tumor 27

description:
neuroblastoma
sample27

source_name: neuroblastoma 27

value: intermediate-risk


title: H1BP ASO #0 replicate1

description:
H1BP cells transfected with ASO #0 targeting HIPSTR lncRNA replicate 1
Raw data in CY3 channel of:
expt_2_2_2.txt


title: total RNA from neuroblastoma tumor 32

description:
neuroblastoma
sample32

source_name: neuroblastoma 32


title: total RNA from neuroblastoma tumor 25

description:
neuroblastoma
sample25

source_name: neuroblastoma 25


title: H1BP ASO #1 replicate1

description:
H1BP cells transfected with ASO #1 targeting HIPSTR lncRNA replicate 1
Raw data in CY3 channel of:
expt_2_2_3.txt


title: HEK293 ASO CTL replicate 3

description:
HEK293 cells transfected with scrambled control oligo (ASO CTL) replicate 3
Raw data in CY3 channel of:
expt_1_1_4.txt

source_name: HEK293 transfected with control scrambled ASO

label_protocol: 200 ng of total RNA were converted into Cy3- and Cy5-labeled cRNA using the Agilent Low Input Quick Amp Labeling Two Color Kit according to manufacturer's protocol.

growth_protocol: HEK293 cells were cultured at 37 °C in 5 % CO2-humidified atmosphere in DMEM medium (Vitrocell Embriolife) supplemented with 10 U/ml Penicillin, 0.01 mg/ml Streptomycin (1x Pen-Strep; Vitrocell Embriolife) and 10 % FBS (Vitrocell Embriolife)

treatment_protocol: 450000 HEK293 cells were plated on 6-well plates 24 h before transfection. The silencing was done using 0.025 µl of Lipofectamine RNAiMAX (Invitrogen) per 1 pmol of transfected ASO. Transfection mixes were prepared in OptiMEM I Reduced Serum Medium (Gibco). A total of 300 pmol of ASO per well on 6-well plates was used for transfection. Cells were collected for subsequent RNA extraction 24 h after transfection.


title: total RNA from neuroblastoma tumor 24

description:
neuroblastoma
sample24

source_name: neuroblastoma 24


title: HEK293 ASO CTL replicate 2

description:
HEK293 cells transfected with scrambled control oligo (ASO CTL) replicate 2
Raw data in CY5 channel of:
expt_1_2_3.txt


title: total RNA from neuroblastoma tumor 26

description:
neuroblastoma
sample26

source_name: neuroblastoma 26


title: HEK293 ASO CTL replicate 1

description:
HEK293 cells transfected with scrambled control oligo (ASO CTL) replicate 1
Raw data in CY3 channel of:
expt_1_1_3.txt


title: total RNA from neuroblastoma tumor 18

description:
neuroblastoma
sample18

source_name: neuroblastoma 18


title: total RNA from neuroblastoma tumor 17

description:
neuroblastoma
sample17

source_name: neuroblastoma 17


title: HEK293 ASO #1 replicate 2

description:
HEK293 cells transfected with ASO #1 targeting HIPSTR lncRNA replicate 2
Raw data in CY3 channel of:
expt_1_2_3.txt

source_name: HEK293 transfected with ASO targeting HIPSTR lncRNA


title: total RNA from neuroblastoma tumor 14

description:
neuroblastoma
sample14

source_name: neuroblastoma 14


title: total RNA from neuroblastoma tumor 15

description:
neuroblastoma
sample15

source_name: neuroblastoma 15


title: total RNA from neuroblastoma tumor 20

description:
neuroblastoma
sample20

source_name: neuroblastoma 20


title: HEK293 ASO #2 replicate 3

description:
HEK293 cells transfected with ASO #2 targeting HIPSTR lncRNA replicate 3
Raw data in CY5 channel of:
expt_1_1_2.txt


title: HEK293 ASO #2 replicate 1

description:
HEK293 cells transfected with ASO #2 targeting HIPSTR lncRNA replicate 1
Raw data in CY5 channel of:
expt_1_1_1.txt


title: total RNA from neuroblastoma tumor 22

description:
neuroblastoma
sample22

source_name: neuroblastoma 22


title: HEK293 ASO #1 replicate 3

description:
HEK293 cells transfected with ASO #1 targeting HIPSTR lncRNA replicate 3
Raw data in CY5 channel of:
expt_1_1_4.txt


title: HEK293 ASO #2 replicate 2

description:
HEK293 cells transfected with ASO #2 targeting HIPSTR lncRNA replicate 2
Raw data in CY3 channel of:
expt_1_2_1.txt


title: HEK293 ASO #1 replicate 1

description:
HEK293 cells transfected with ASO #1 targeting HIPSTR lncRNA replicate 1
Raw data in CY5 channel of:
expt_1_1_3.txt


title: total RNA from neuroblastoma tumor 28

description:
neuroblastoma
sample28

source_name: neuroblastoma 28


title: total RNA from neuroblastoma tumor 21

description:
neuroblastoma
sample21

source_name: neuroblastoma 21


title: total RNA from neuroblastoma tumor 19

description:
neuroblastoma
sample19

source_name: neuroblastoma 19


title: total RNA from neuroblastoma tumor 16

description:
neuroblastoma
sample16

source_name: neuroblastoma 16


title: total RNA from neuroblastoma tumor 23

description:
neuroblastoma
sample23

source_name: neuroblastoma 23


title: total RNA from neuroblastoma tumor 13

description:
neuroblastoma
sample13

source_name: neuroblastoma 13


title: total RNA from neuroblastoma tumor 10

description:
neuroblastoma
sample10

source_name: neuroblastoma 10


title: total RNA from neuroblastoma tumor 8

description:
neuroblastoma
sample8

source_name: neuroblastoma 8


title: total RNA from neuroblastoma tumor 7

description:
neuroblastoma
sample7

source_name: neuroblastoma 7


title: total RNA from neuroblastoma tumor 5

description:
neuroblastoma
sample5

source_name: neuroblastoma 5


title: total RNA from neuroblastoma tumor 9

description:
neuroblastoma
sample9

source_name: neuroblastoma 9


title: total RNA from neuroblastoma tumor 12

description:
neuroblastoma
sample12

source_name: neuroblastoma 12


title: total RNA from neuroblastoma tumor 6

description:
neuroblastoma
sample6

source_name: neuroblastoma 6


title: total RNA from neuroblastoma tumor 4

description:
neuroblastoma
sample4

source_name: neuroblastoma 4


title: total RNA from neuroblastoma tumor 11

description:
neuroblastoma
sample11

source_name: neuroblastoma 11


title: total RNA from neuroblastoma tumor 3

description:
neuroblastoma
sample3

source_name: neuroblastoma 3


title: Heart_Ctrl + aldosterone treatment_ sample 4 (mouse n° 257)

first: Smail

last: Messaoudi

address: 451 smyth road

department: BMI

institute: University of Ottawa

description:
Sample 9
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.

hyb_protocol: 825 ng of Cy5-labelled samples and 825 ng of Cy3-labelled references were incubated at 60° for 30 min in fragmentation buffer.  Hybridization buffer was then added, and sample/reference couples (1 couple per microarray) were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an G2505 Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version v 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.Data were processed using  genespring software v11.0.

source_name: Heart_Ctrl + aldosterone treatment

label_protocol: Labelling of the RNAs weas performed according to Agilent's instruction. Briefly, 100 ng of total RNA + spikes  were primed with 1.8µl of T7 promoter primer mix at 70°C for 10 min, then reversed transcribed at 40°C for 2 h in presence of a mix containing first strand buffer, 20 mM DTT, 2 mM DNTP mix and AffinityScript rnase block mix. Reaction was stopped by heating samples at 70° foc 15 min. New synthetized cDNA was then labelled and amplified at 40° for 2h in presence of a mix containing transcription buffer, NTP mix, 20mM DTT, T7 RNA polymerase and CY3-CTP or CY5-CTP.

extract_protocol: Total RNA was prepared from ventricle samples with the RNeasy Mini Kit (Qiagen S.A) according to the manufacturer's instructions and its quality was assessed with Bioanalyzer 2100 (Agilent technologies)

value: male

value: Aldosterone

tag: treatment duration

value: 7 days

value: Heart ventricle

source_name: Total RNA pooled  from several tissues (liver, brain, heart kidney, spleen), labeled with Cyanine-3, used as reference

tag: tissue composition of reference

value: liver, brain, heart kidney, spleen


title: Heart_Ctrl_no treatment_ sample 1 (mouse n° 210)

description:
Sample 1
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.

source_name: Heart_Ctrl_no treatment

value: no treatment


title: Heart_Ctrl + aldosterone treatment_ sample 1 (mouse n° 203)

description:
Sample 6
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.


title: Heart_Ctrl + aldosterone treatment_ sample 2 (mouse n° 232)

description:
Sample 7
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.


title: Heart_Ctrl_no treatment_ sample 3 (mouse n° 223)

description:
Sample 3
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.


title: total RNA from neuroblastoma tumor 2

description:
neuroblastoma
sample2

source_name: neuroblastoma 2

value: neuroblastoma

tag: inss stage

tag: current risk category

value: MYCN-nonamplified


title: total RNA from neuroblastoma tumor 1

description:
neuroblastoma
sample1

source_name: neuroblastoma 1

tag: age at diagnosis

value: <1.5 years

tag: mycn status


title: CEF_serum_starved_rep2

city: Hamilton

first: Bart

middle: Michal

last: Maslikowski

address: 1280 Main St. West

department: Biology

institute: McMaster University

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown under conditions of serum starvation.
Biological replicate 2.

hyb_protocol: cRNA was fragmented and hybridized onto Affymetrix Chicken GeneChip arrays for 16 hours at 45˚C. Washing, staining and scanning were done in accordance with the Affymetrix EukGE-WS2v4 protocol.

scan_protocol: Scanning was done using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were analysed using Affymetrix Expression Console software v1.1. Array data were normalized and probe intensities were estimated using the Affymetrix probe logarithmic intensity error (PLIER) algorithm.

organism: Gallus gallus

label_protocol: 15 µg of total RNA was used to prepare biotin-labeled complementary RNA (cRNA). cDNA was generated by one-cycle target labeling protocol using SuperScript II (Invitrogen). Biotinylated cRNA was generated from purified cDNA using the Enzo IVT kit.

growth_protocol: Early passage (n<10) CEF were cultured at 41.5°C in Richter-improved minimal medium containing insulin and zinc (I+ medium, Irvine Scientific, Santa Ana, CA) with 5% heat-inactivated cosmic calf serum, 5% tryptose phosphate broth and 1% L-Glutamine, penicillin and streptomycin solution (GIBCO BRL).

extract_protocol: Total cell RNA was isolated using Trizol reagent (Invitrogen) according to manufacturer's instructions. RNA quality was assessed by gel electrophoresis and examined by Bioanalyzer (Agilent). RNA samples with a RNA Integrity Index of less than 9.7 were discarded.

treatment_protocol: For the cycling condition, CEFs were grown in complete medium and collected during log phase of growth. For the contact-inhibited condition, cells were grown to 100% confluence and the medium was replenished in order to prevent cells from becoming starved. For the serum-starved condition, normal cycling CEFs were starved in medium without the serum after being washed twice with the serum-free medium. Cells grown in the contact-inhibited and starved condition were grown to 100% confluence whereupon the cells were washed twice with serum-free medium and replenished with medium without serum. All cells were washed twice with 1xPBS and collected in 1xPBS.

tag: breed

value: White Leghorn

value: chicken embryonic fibroblast cells (CEFs)

tag: developmental stage

value: day 10 embryo

tag: growth condition

value: serum starvation


title: Heart_Ctrl + aldosterone treatment_ sample 3 (mouse n° 253)

description:
Sample 8
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.


title: CEF_serum_starved_rep1

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown under conditions of serum starvation.
Biological replicate 1.

tag: cell type


title: Heart_Ctrl + aldosterone treatment_ sample 5 (mouse n° 226)

description:
Sample 10
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.

tag: tissue


title: CEF_serum_starved_rep3

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown under conditions of serum starvation.
Biological replicate 3.


title: Heart_Ctrl _no treatment_ sample 5 (mouse n° 215)

description:
Sample 5
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.

tag: gender


title: Heart_Ctrl_no treatment_ sample 4 (mouse n° 272)

description:
Sample 4
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.


title: Heart_Ctrl _no treatment_ sample 2 (mouse n° 217)

description:
Sample 2
Hearts were rinsed in cold PBS,  frozen in liquid nitrogen, and kept at –80°C.


title: 3F_Day12

city: Barcelona

first: Miki

last: Ebisuya

address: PRBB Building, C/ Dr. Aiguader, 88

department: EMBL Barcelona

institute: EMBL

description:
3F_Day12
Gene expression data from MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4), day 12.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol with Affymetrix Scanner 3000 7G

data_processing: The probeset signals were calculated using Agilent GeneSpring software.

source_name: MEFs infected with retroviruses encoding the four transcription factors (Oct4, Sox2 and Klf4)

label_protocol: Biotinylated cRNAs were prepared from 120 ng (rep1) or 300 ng (the others) total RNAs according to the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay manual.

growth_protocol: MEFs were maintained in Dulbecco's Modified Eagle's medium (DMEM) containing 10% foetal bovine serum (FBS).

extract_protocol: Total RNAs were extracted using the Qiagen RNeasy kit according to the manufacturer's protocol. On-column DNase digestion was performed.

treatment_protocol: MEFs were infected with retroviruses encoding the four transcription factors (Oct4, Sox2, Klf4 and c-Myc), three transcription factors (Oct4, Sox2 and Klf4) or GFP (control) at day 0.

value: mouse embryonic fibroblasts (MEFs)

tag: retrovirus

value: infected with retroviruses encoding 3 transcription factors (Oct4, Sox2 and Klf4)

tag: time

value: day 12


title: CEF_contact-inhibited_rep4

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown to contact-inhibition.
Biological replicate 4.

source_name: CEF grown to contact-inhibition

value: contact-inhibition


title: CEF_cycling_rep1

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown under normal cycling conditions.
Biological replicate 1.

value: normal cycling


title: CEF_cycling_rep3

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown under normal cycling conditions.
Biological replicate 3.


title: total RNA from neuroblastoma tumor 51

description:
neuroblastoma
sample51

source_name: neuroblastoma 51

value: high-risk

value: >=1.5 years

value: MYCN-amplified

tag: 1p status

tag: 11q status

tag: 17q status


title: CEF_contact-inhibited_rep2

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown to contact-inhibition.
Biological replicate 2.


title: 3F_Day8

description:
3F_Day8
Gene expression data from MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4), day 8.

value: day 8


title: CEF_contact-inhibited_and_serum_starved_rep2

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown to contact-inhibition and serum starved.
Biological replicate 2.

value: contact-inhibition and serum starvation


title: CEF_cycling_rep2

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown under normal cycling conditions.
Biological replicate 2.


title: CEF_contact-inhibited_rep3

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown to contact-inhibition.
Biological replicate 3.


title: 3F_Day3

description:
3F_Day3
Gene expression data from MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4), day 3.

value: day 3


title: CEF_contact-inhibited_and_serum_starved_rep3

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown to contact-inhibition and serum starved.
Biological replicate 3.


title: CEF_contact-inhibited_and_serum_starved_rep1

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown to contact-inhibition and serum starved.
Biological replicate 1.


title: CEF_contact-inhibited_rep1

description:
Chicken embryonic fibroblast cells (CEFs) derived from day 10 embryos (White Leghorn breed).
Gene expression data from CEF grown to contact-inhibition.
Biological replicate 1.


title: 3F_Day5

description:
3F_Day5
Gene expression data from MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4), day 5.

value: day 5


title: IMR5_75 DMSO replicate 1

type: genomic

first: Manuel

last: Wiesenfarth

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to llumina HumanMethylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Raw data files generated by the iScan array scanner were read and preprocessed using minfi Bioconductor package (Aryee et al., 2014). With the minfi package the same preprocessing steps as in Illumina's Genomestudio software were performed, except for one modification. Namely, in the R-function call normalize.illumina.control() the reference value was set fixed as 10000 rather than the sum of averages of green and red intensities of the first patient.   The following filtering criteria were applied: Removal of probes targeting the X and Y chromosomes (n = 11,551), removal of probes containing a single nucleotide polymorphism (dbSNP132 Common) within five base pairs of and including the targeted CpG-site (n = 24,536), and probes not mapping uniquely to the human reference genome (hg19) allowing for one mismatch (n = 9,993). In total, 438,370 probes were kept for analysis. No batch correction has been applied (since cell lines are analyzed independently).

molecule: genomic DNA

source_name: IMR5-75 neuroblastoma cell line

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were grown in RPMI medium (10%FCS) under standard conditions.

extract_protocol: Genomic DNA was extracted from neuroblastoma cell lines using standard procedures.

treatment_protocol: The neuroblastoma cell lines Be(2)-C and IMR5-75 were treated with a combination of DAC (1µM, 72h) and EPZ-6438 (1µM 96h). Controls were treated with solvent (DMSO).

tag: agent

value: DMSO

tag: cell line

value: IMR5-75 neuroblastoma cell line


title: GFP_Day12

description:
GFP_Day12
Gene expression data from MEFs infected with retroviruses encoding GFP, day 12.

value: GFP


title: Be2C DMSO replicate 1

source_name: Be(2)-C neuroblastoma cell line

value: Be(2)-C neuroblastoma cell line


title: Be2C DMSO replicate 2