title: R1 Myc-ER Myc+Dkk1/Sfrp1 mESC rep.3

description:
replicate 3
SAMPLE 12

value: 50 nM 4-hydroxytamoxifen (OHT)+Dkk1 100ng/ml+Sfrp1 100ng/ml


title: mouse EpiSC rep.3

status: Public on Mar 31 2016

type: RNA

city: Milan

first: Alessio

last: Zippo

address: Via Francesco Sforza, 35

country: Italy

institute: National Institute of Molecular Genetics

description:
replicate 3
SAMPLE 9

hyb_protocol: Standard Illumina hybridization protocol to MouseRef-8 v2  BeadChip Arrays (Illumina, 1128893), following the Direct Hybridization Assay guideline.

scan_protocol: BeadChip Arrays were scanned with a HiScan Array Scanner (Illumina) using the iScan Control Software (Illumina).

data_processing: The data were normalised using quantile normalization and background subtraction implemented by the GenomeStudio Gene Expression Module v1.0 Software (Illumina).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Epiblast Stem Cell

label_protocol: 500 ng of each sample RNA were processed to generate biotinylated cRNAs following the Illumina TotalPrep RNA amplification Kit (Ambion, AMIL1791) protocol for Illumina Arrays.

growth_protocol: R1 mESC cells were cultured without feeders on plastic coated with 0.1% gelatin in the DMEM supplemented with 15% FCS (Hyclone Millipore, cat. ES-009-B), 100 mM 2‐mercaptoethanol (Sigma, cat. M7522), 1 × MEM non‐essential amino acids (Invitrogen, cat. 1140‐036), 2 mM l‐glutamine, 1 mM sodium pyruvate (both from Invitrogen). GOF18 EpiSCs were cultured in N2B27 medium supplemented with BSA 0,033%, Glutamax, b-Mercaptoethanol 0,1mM, bFGF 12ng/ml (Invitrogen, cat. 13256029) and Activin-A 20 ng/ml (R&D, cat. 338-AC). EpiSC were grown on fibronectin-coated plates and splitted every three days 1:20 by dissociation into small clumps with Collagenase Type IV 0,5 mg/ml (Gibco, cat. 17104-019).

extract_protocol: Total RNAs were isolated from cell cultures after 3 days growth in indicated conditions, using TRIzol® Reagent (Ambion, cat.15596-026), followed by clean up in accordance with the manifacturer's protocol provide with the kit.

treatment_protocol: ESC were treated with the following reagents as indicated above: 100 units/ml LIF (Millipore, cat. ESG1107); 50 nM 4-hydroxytamoxifen (OHT) (Sigma, cat. H6278); Dkk1 100ng/ml (R&D, cat. 5897-DK); Sfrp1 100ng/ml (R&D, cat. 1384-SF).

tag: strain

tag: age

value: day 5.5

tag: tissue

value: Epiblast

tag: clone


title: NHP_I131B_TBInfected_Week1_ReplicateArray1

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

country: United Kingdom

institute: UK Health Security Agency

description: Genisphere amplified Total RNA

hyb_protocol: Total amplified primate PBL mRNAs from each time-point were labelled with Cy3-labelled dCTP as described previously [50,51] and hybridised to replicate Operon Human Genome AROS V4.0 slides (n = 3/ sample/time point (http://www.microarrays.com/dna-arrays.php). This is a human oligonucleotide microarray comprising some 35,035 oligonucleotide probes, which represent approximately 25,100 unique genes and 39,600 transcripts. A subset of the total probe set (31,387 probes) is contained within the span of a single exon to provide the microarray detection precision at both the transcript and gene levels.  Microarray slides were pre-hybridized for 30 minutes at 42 °C in a hybridization solution containing 5 x standard saline citrate (SSC), 0.1% sodium dodecyl sulfate (SDS) and 4 x Denhardts solution, followed by a 1 minute wash in molecular reagent grade double distilled water then a brief rinse in isopropanol. The slides were then dried by centrifugation at 1500 rpm for 5 minutes. Prior to hybridization, 20 μg of Cy3-labelled mRNA was combined with 20 μg of Cot1 Human DNA (10 μg/μl) and 20 μg of polyA RNA (10 μg/μl) (Invitrogen) to a final volume of 40 μl in RNAase-free water and denatured at 95 oC for 2 minutes to denature the mRNA target. The mixture was then mixed 1:1 with 2 x concentrate hybridization solution (10 x SSC, 0.2% SDS, 8 x Denhardts solution) pre-warmed to 65 oC. The microarray slide was placed in the chamber of a Slidebooster microarray hybridisation platform (Olympus Advalytix, Germany) pre-heated to 42 oC and a lifterslip covering the area of the array affixed in place (http://www.thermoscientific.com/content/tfs/en/ product/lifterslips-cover-slips-microarray-slides.html). The prepared sample was applied to the array and drawn under the lifterslip by capillary action. This was then hybridised at 42 °C for 6 hours in the presence of proprietary formamide-free AdvaHum humidifying buffer (Olympus Advalytix, Germany) at maximum mixing power (M27). After completion of hybridisation lifterslips were removed and the slides were washed in two separate wash solutions for two minutes each at 42 oC - Buffer A (1x SSC 1% SDS) Buffer B1 (0.1x SSC 1% SDS), then a further wash in Buffer B2 (1% SSC) for two minutes at room temperature.

scan_protocol: The slides were air-dried and scanned using an Affymetrix 480 microarray scanner, at a gain of 65.

data_processing: Feature extraction was conducted using the microarray quantification package BlueFuseTM (BlueGnome; now a subsidiary of www.illumina.com). Raw data were exported and hybridisation fluorescence intensities quantified using default background subtraction and normalisation methods, to remove data generated from poor-quality spots and hybridisation artefacts. All raw data were then processed further using the microarray analysis package Genespring 12.5. Data output files from BlueFuse were imported into GeneSpring 12.5 (GX12.5) for differential gene expression and statistical analysis. Raw data was normalized to the 50th percentile followed by median baseline transformed to each animals corresponding pre-bleed sample. This was conducted to normalise data across all time points and assess differential gene expression of each gene entity, relative to a baseline i.e. pre-bleed level of expression prior to M. tuberculosis challenge. Mean values across three replicate sample slides were used for further ongoing analysis. Data were assessed for quality, then filtered on gene expression where entities in all samples and all conditions had normalised expression values within the cut-off -10.699 to 7.037. Statistically significant features were identified using one-way ANOVA analysis across all entities and time points, using either the Benjamini-Hochberg False Discovery Rate (BH-FDR), or the more parsimonious Bonferroni Family-Wise Error Rate (B-FWER), with multiple testing corrections at a cut-off p ≤ 0.05. To identify temporally, differentially expressed entities between time-points post-infection, fold-change cut-off analyses were conducted using the default cut-off setting ≥ 2.0 all referenced against the pre-bleed condition,  where the minimum number of pairs was equal to one out of the four condition pairs i.e. weeks one, two, four or six. These were further analysed and depicted graphically using the heat map, hierarchical cluster analysis and other functions in Genespring 12.5, using default settings.

organism: Macaca fascicularis

source_name: Total peripheral blood leukocytes Tuberculosis infected

label_protocol: Due to the small volumes of blood used in the study and consequently low yield of total RNA recovered, an enrichment step was then performed using the Genisphere SenseAmp RNA amplification kit according to manufactures instructions (http://genisphere.com/). The resulting amplified mRNA was purified using RNeasy Min-Elute Cleanup kit (Qiagen), again according to the manufacturers’ protocol. The mRNA concentration and purity (A260/A280 ratio ≥ 1.8) was then assessed by spectrophotometry using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: The samples analysed in this investigation were collected from six Cynomologus macaques (Macaca fascicularis) aged between 2 – 4 yrs in a pilot study set up  to characterise and compare the outcome of high dose M. tuberculosis aerosol challenge, using previously described methods [49]. None of the animals had been used previously for experimental procedures. They were confirmed as naïve in terms of prior exposure to mycobacterial antigens (M. tuberculosis infection or environmental mycobacteria),  by  negative tuberculin test while in their original breeding colony and prior to the start of the study using  the gamma interferon (IFN-γ)-based Primagam test kit (Biocor; CSL).  The animals were of two distinct genotypes; Chinese (diverse) and Mauritian (restricted). Following aerosol exposure animals were monitored for 12 weeks for changes in behaviour and clinical parameters such as body weight, temperature, anaemia and inflammation. Disease progressed to meet endpoint criteria in all three Cynomolgus macaques of the Mauritian genotype six weeks after challenge. The macaques of Chinese genotype controlled disease for the remainder of the study period and were euthanased twelve weeks after challenge.    The Cynomolgus macaques of Mauritian genotype were obtained from an established UK breeding colony, whilst the Cynomolgus macaques of Chinese genotype were obtained from a UK Home Office approved breeding facility in China.   Absence of previous exposure to mycobacterial antigens was confirmed by a tuberculin skin test and screening using an ex-vivo IFNγ ELISPOT (MabTech, Nacka. Sweden) to measure responses to PPD (SSI, Copenhagen, Denmark), and pooled 15-mer peptides of ESAT6 and CFP10 (Peptide Protein Research LTD, Fareham, U.K.). The animals were housed in compatible social groups, in accordance with the Home Office (UK) Code of Practice for the Housing and Care of Animals Used in Scientific Procedures (1989), (now updated to Code of Practice for the housing and Care of Animals Bred, Supplied or Used for Scientific Purposes, December 2014, and the National Committee for Refinement, Reduction and Replacement (NC3Rs), Guidelines on Primate Accommodation, Care and Use, August 2006 (NC3Rs, 2006)).  Animals were sedated by intramuscular (IM) injection with ketamine hydrochloride (Ketaset, 100mg/ml, Fort Dodge Animal Health Ltd, Southampton, UK; 10mg/kg) for procedures requiring removal from their housing. None of the animals had been used previously for experimental procedures. All animal procedures were approved by the Public Health England Ethical Review Committee, Porton Down, UK, and authorized under an appropriate UK Home Office project license.    The challenge was performed on sedated animals placed within a “head-out” plethysmography chamber (Buxco, Wilmington, NC), to enable the aerosol to be delivered simultaneously with the measurement of the respiration rate. This process has been shown previously to deliver a known number of viable M. tuberculosis bacilli in a target volume of inspired aerosol. Clinical assessment post-challenge; animal behaviour was observed daily throughout the study for contra-indicators such as depression, withdrawal from the group, aggression, food and water intake, changes in respiration rate, or cough. Animals were sedated every weeks to measure weight, body temperature, blood haemoglobin levels, and erythrocyte sedimentation rate (ESR) and to collect blood samples for immunology and RNA extraction.

extract_protocol: One ml of TRIzol® was added to the PBL pellet, then total RNA was extracted from the lysed PBL pellet according to the manufacturer’s instructions (www.Invitrogen.com) using aqueous-phase separation with chloroform isoamyl alcohol and the precipitation using 2-isopropanol. Recovered, dried RNA pellets were re-suspended in 10 μl of diethylpyrocarbonate (DECP) water (Invitrogen), then concentration and purity (A260/A280 ratio ≥ 1.8) assessed by spectrophotometry using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). Genomic DNA was removed prior to its use in further procedures using the DNase I kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Whole heparinised blood was obtained at three independent time points prior to challenge and at one, two, four and six weeks post M. tuberculosis challenge. Within one hour of collection, 1 ml of blood from each animal was mixed with 5 ml of Erythrocyte Lysis (EL) Buffer (Qiagen) followed by incubation on ice for 10-15 minutes. Peripheral blood leukocytes (PBLs) were recovered from erythrocyte-lysed blood by centrifugation at 400 x g for 10 minutes at 4 °C and re-suspended in a further 2 ml of EL buffer. PBLs were again recovered by centrifugation as described above and processed for recovery of total RNA.

tag: gender

value: Female

tag: origin

value: Mauritian Genotype

value: blood


title: R1 Myc-ER Myc+Dkk1/Sfrp1 mESC rep.2

description:
replicate 2
SAMPLE 11

source_name: Embryonic Stem Cell

value: day 3.5

value: Inner cell mass

tag: treatment


title: NHP_I131B_Uninfected_Prebleed_ReplicateArray2

description: Genisphere amplified Total RNA

source_name: Total peripheral blood leukocytes non-Tuberculosis infected


title: R1 Myc-ER Myc+Dkk1/Sfrp1 mESC rep.1

description:
replicate 1
SAMPLE 10


title: NHP_I131B_Uninfected_Prebleed_ReplicateArray3

description: Genisphere amplified Total RNA


title: 4OHT treated organoid at day4

city: Koto-ku

first: Ryoji

last: Yao

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: The JFCR-Cancer Institute

description:
Gene expression data from Apc-deficientl intestinal organoid
Apcfl/fl-day4-4OHT

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on Mouse Geneome 430_2.0 array in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GenePattern (Broad Institute) using default analysis setting and global scailing as normaization method.

source_name: Apc organoids 4OHT treated (day4)

label_protocol: Biotinylated cRNA were prepared from 100ng of total RNA using 3' IVT PLUS Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Organoids were treated with 4OHT for 24 hours and cultured for 4 or 6 days.

extract_protocol: Total RNA was isolated using a Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Organoids were recovered from Matrigel using Cell Recovery Sollution (Corning), washed with PBS once and collected by centrifugation.

value: mouse intestinal organoid


title: mouse EpiSC rep.1

description:
replicate 1
SAMPLE 7


title: NHP_0201191_TBInfected_Week6_ReplicateArray2

description: Genisphere amplified Total RNA

value: Male

value: Chinese Genotype


title: R1 Myc-ER mESC LIF rep.3

description:
replicate 3
SAMPLE 3

value: 100 units/ml LIF


title: NHP_0201191_TBInfected_Week4_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0201191_TBInfected_Week6_ReplicateArray3

description: Genisphere amplified Total RNA


title: R1 Myc-ER Myc mESC rep.1

description:
replicate 1
SAMPLE 4

value: 50 nM 4-hydroxytamoxifen (OHT)


title: NHP_0201191_TBInfected_Week6_ReplicateArray1

description: Genisphere amplified Total RNA


title: R1 Myc-ER Myc mESC rep.3

description:
replicate 3
SAMPLE 6


title: R1 Myc-ER Myc mESC rep.2

description:
replicate 2
SAMPLE 5


title: R1 Myc-ER mESC LIF rep.1

description:
replicate 1
SAMPLE 1


title: NHP_0201191_TBInfected_Week4_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0201191_TBInfected_Week2_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0201191_TBInfected_Week4_ReplicateArray1

description: Genisphere amplified Total RNA


title: 1853

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

country: USA

institute: Penn State College of Medicine

description:
5125380030_C
Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization

source_name: Liver

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

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

treatment_protocol: Untreated 9 month old livers from male mice carrying different genotypes.  P10: Pten deleted in the liver; DM: Pten and Akt2 double deleted livers; WT: controls.

tag: group

value: DM


title: NHP_0201191_TBInfected_Week2_ReplicateArray1

description: Genisphere amplified Total RNA


title: R1 Myc-ER mESC LIF rep.2

description:
replicate 2
SAMPLE 2


title: NHP_0201191_TBInfected_Week2_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0201191_TBInfected_Week1_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_0201191_TBInfected_Week1_ReplicateArray3

description: Genisphere amplified Total RNA


title: 4893

description:
5125380029_F
Replicate 2


title: 1859

description:
5125380029_H
Replicate 3


title: 4892

description:
5125380029_C
Replicate 1


title: Experiment, biological replicate1

city: Hyderabad

first: Utpal

last: Bhadra

state: TG

address: Uppal Road

department: UB group

country: India

institute: CCMB

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

scan_protocol: The gene chips were scanned on an Affymetrix Scanner

data_processing: The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to GeneSpring 13.1.1 - GX - PA   (Agilent Technology) for further analysis. The RMA and PLIER16 algorithms were used for data normalization

label: Biotin

organism: Drosophila melanogaster

source_name: mle/mle homozygous

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mle/mle homozygous male larvae were segregated from heterozygous mle/ T(2-3)Tb and wild type cancon S genotypes.  The third instar larvae of each genotype were further processed

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

treatment_protocol: The larvae of each genotypes were collected based on the phenotype and washed throughly in the  wash buffer. The cleaned larvae of each gonotype were used for RNA extraction procedure.

tag: genotype

value: mle/mle homozygous

tag: developmental stage

value: third instar larvae


title: 1297

description:
5125380030_E
Replicate 5

value: WT


title: 1296

description:
5125380030_B
Replicate 4


title: 1257

description:
5125380030_G
Replicate 5


title: NHP_0201191_Uninfected_Prebleed_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week6_ReplicateArray3

description: Genisphere amplified Total RNA


title: mouse EpiSC rep.2

description:
replicate 2
SAMPLE 8


title: NHP_0201191_Uninfected_Prebleed_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week4_ReplicateArray3

description: Genisphere amplified Total RNA


title: 1295

description:
5125380029_E
Replicate 2


title: Kidney cortex_90 kBq 131I i.v. injected at 9 am, excised after 24h_rep1

city: Gothenburg

first: Britta

last: Langen

address: Gula stråket 2B

department: Department of Radiation Physics

country: Sweden

institute: Sahlgrenska Academy at University of Gothenburg

scan_protocol: Standard Illumina iScan N240 scanning protocol; scan setting file: Direct Hyb

data_processing: The data were normalized using quantile normalization with BASE

source_name: Mouse kidney cortex, 90 kBq 131I, 9 am

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Excised organs were flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: Balb/c

value: female

value: Kidney cortex

tag: injected activity

value: 90 kBq

tag: time of day

tag: time point

tag: nuclide


title: NHP_0201191_Uninfected_Prebleed_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0201191_TBInfected_Week1_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week6_ReplicateArray1

description: Genisphere amplified Total RNA


title: 1294

description:
5125380029_G
Replicate 3


title: NHP_0201011_TBInfected_Week4_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week4_ReplicateArray1

description: Genisphere amplified Total RNA


title: 1301

description:
5125380029_B
Replicate 1


title: Caki-2_LEF-48h_rep2

city: Hangzhou

first: yicheng

last: chen

address: 3 East Qingchun Road

department: Department of Urology

country: China

institute: Sir Run-Run Shaw Hospital, College of Medicine, Zhejiang University

description: “Caki-2_LEF-48h_rep2”stand for “cl-2”

hyb_protocol: see attached supplementary file (protocols.xls)

scan_protocol: Imaging is done by laser scanner GenePix4000B(Molecular Device). At first, remove the microarray from the clamp and place it horizontally. Then cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip cover it,taking care not to introduce air bubbles. At last, load the microarray into the scanner to scan.

data_processing: Raw signals were normalized with subtract background correction and quantile normalization method, Normalized intensities were transformed to gene expression log2 value. Ratio and log2 ratio of normalized spot intensites between test sample and control sample were calculated. The p-values are calculated with ANOVA Method(O'Mahony, Michael (1986). Sensory Evaluation of Food: Statistical Methods and Procedures. CRC Press. pp. 487. ISBN 0-8247-7337-3). It means the probability of control sample and test sample are no differential expression. So, if p-value (Differentially expressed) is greater than thethreshold it means no differential expression was observed.

organism: Homo sapiens

growth_protocol: Caki-2 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), penicillin (100 U/ml), and streptomycin (100 μg/ml) under a humidified atmosphere containing 5% CO2 maintained at 37 ˚C.

treatment_protocol: Caki-2 cells treated with 200 μM LEF or vehicle control for 48 h.

tag: cell line

tag: cell type

value: Renal Clear Cell Cancer


title: 1254

description:
5125380030_D
Replicate 4


title: 1253

description:
5125380030_A
Replicate 3


title: 1298

description:
5125380029_D
Replicate 2


title: NHP_0201011_TBInfected_Week6_ReplicateArray2

description: Genisphere amplified Total RNA

value: blood


title: Caki-2_DMSO-48h_rep2

description: “Caki-2_DMSO-48h_rep2”stand for “cD-4”

label_protocol: see attached supplementary file (protocols.xls)


title: NHP_0201011_Uninfected_Prebleed_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week1_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week2_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week2_ReplicateArray3

description: Genisphere amplified Total RNA


title: 1293

description:
5125380029_A
Replicate 1


title: NHP_0201011_TBInfected_Week1_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0201011_TBInfected_Week2_ReplicateArray2

description: Genisphere amplified Total RNA


title: Caki-2_DMSO-48h_rep1

description: “Caki-2_DMSO-48h_rep1”stand for “cD-2”

extract_protocol: see attached supplementary file (protocols.xls)


title: NHP_0201011_TBInfected_Week1_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week6_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0201011_Uninfected_Prebleed_ReplicateArray2

description: Genisphere amplified Total RNA


title: Caki-2_LEF-48h_rep1

description: “Caki-2_LEF-48h_rep1”stand for “cl-1”


title: NHP_0201011_Uninfected_Prebleed_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week6_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week2_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week1_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week6_ReplicateArray3

description: Genisphere amplified Total RNA


title: HeLa haboring AK4 shRNA #3

city: Ube

first: Koichi

last: Fujisawa

state: Yamaguchi

address: 1-1-1, minami-kogushi

department: Department of Gastroenterology and Hepatology

institute: Yamaguchi University Graduate School of Medicine

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray SurePrint G3 Human GE Microarray Kit 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of seven samples were normalized by the quantile algorithm with the Bioconductor.

source_name: HeLa, AK knockdown, rep3

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: DMEM with 10% FBS

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: AK4 was knockdown by shRNA

value: HeLa

tag: transfectant

value: AK4 shRNA


title: NHP_0111231_TBInfected_Week2_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0111231_Uninfected_Prebleed_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0111231_Uninfected_Prebleed_ReplicateArray2

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week4_ReplicateArray1

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week4_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_I131B_Uninfected_Prebleed_ReplicateArray1

description: Genisphere amplified Total RNA

value: Female

value: Mauritian Genotype


title: HeLa haboring AK4 shRNA #2

source_name: HeLa, AK knockdown, rep2


title: NHP_0111231_TBInfected_Week2_ReplicateArray1

description: Genisphere amplified Total RNA

value: Male

value: Chinese Genotype


title: NHP_0111231_TBInfected_Week1_ReplicateArray3

description: Genisphere amplified Total RNA


title: NHP_0111231_TBInfected_Week4_ReplicateArray2

description: Genisphere amplified Total RNA


title: CP79

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina DASL hybridization protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: breast cancer tumor

label_protocol: According to whole genome DASL assay (Illumina)

tag: tumor size

tag: lymph node status

value: pos

tag: grade

value: II

tag: response

value: PR

value: breast cancer tumor


title: NHP_0111231_TBInfected_Week1_ReplicateArray1

description: Genisphere amplified Total RNA

tag: gender

tag: tissue


title: CQ25

value: III

value: CR


title: CQ15

value: neg


title: HeLa haboring AK4 shRNA #1

source_name: HeLa, AK knockdown, rep1


title: HeLa haboring control shRNA #3

source_name: HeLa, control, rep3

value: control shRNA


title: 7 hour after light time in the second day

city: St. Louis

first: Himadri

last: Pakrasi

state: Missouri

address: One Brookings Dr.

department: Biology

institute: Washington University in St. Louis

hyb_protocol: The microarrays were hybridized at MoGene by using 750 ng of RNA and a specific activity of 50 pmol for each dye.

scan_protocol: Technology: Agilent.SingleColor.17371

data_processing: The data from each microarray were independently normalized to correct for variations in labeling intensities between channels. The background signal for each measurement was subtracted from the raw signal. A LOWESS curve was fit to the training set by using a window length of 25% the number of points fit. The signals were then normalized with the fit LOWESS curve by using linear interpolation to correct points that fell between two points in the training set.

organism: Synechocystis sp. PCC 6803

label_protocol: Total RNA (2.5 µg) was labeled directly with Cy3 and Cy5 dyes by using the Micromax ASAP RNA labeling kit (Perkin–Elmer Life and Analytical Sciences) according to the manufacturer’s instruction.

growth_protocol: Synechocystis sp. PCC 6803 cells cultured  in BG11 medium were diuluted 100-fold after a week growth under 12h/12h light/dark cycles condition, and this new culture was hold in 30°C with bubbling by air for another four days for sampling.

extract_protocol: RNA was isolated by using RNAwiz reagent (Ambion) according to the manufacturer’s instructions and quantified with the NanoDrop ND-1000 UVVIS Spectrophotometer.

treatment_protocol: 50 mL of cluture was collected every two hours in two diurnal cycles with steps of spinning down, frozen by liquid nitrogen, and holding in -80°C freezer.

tag: sample type

value: test

source_name: An equimolar mixture of RNA from all time points

value: reference


title: HeLa haboring control shRNA #4

source_name: HeLa, control, rep4


title: 9 hour after light time in the second day


title: CP82


title: TLDA-85

city: Shinjyuku

first: Tomohiro

last: Umezu

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

description:
test
SAMPLE 13

data_processing:
ath-miR-159 were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).
With the use of SDS2.2 software and Data Assist (Thermo Fisher Sciences), the expression of plasma miRNAs was calculated based on cycle threshold (Ct) values normalized by those of ath-miR-159, which was spiked in each plasma sample. Data analysis was done using GeneSiferⓇ software (Perkin Elmer, Waltham, MA, USA). The Benjamini-Hochberg algorithm was used for estimation of false discovery rates.
Fold Change worksheet reports test/control ratios.

label: TaqMan probe (FAM-MGB)

source_name: Plasma

label_protocol: The RT reaction and pre-amplification step were set up according to the recommendations. MiRNAs were reverse transcribed with Megaplex Prime Pools (Human Pools A v2:1; Thermo Fisher Sciences, Waltham, MA, USA). The miRNA expression profiles were determined with a TaqMan miRNA Array Human Card A (Thermo Fisher Sciences).

extract_protocol: Total RNA was isolated with the mirVana PARIS kit (Ambion, Austin, TX, USA) from seven unselected healthy volunteers and seven STOP-IM patients. Five hundred micro liters plasma was diluted with 500 μl of binding solution. After a 5-min incubation, 1 μl of 1 nM ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) was added to aliquot followed by vortexing for 30 s and incubation on ice for 10 min. Subsequent phenol extraction and filter cartridge was performed according to the manufacture’s instruction.

treatment_protocol: Plasma samples were harvested form 2ml of whole blood.

tag: condition

value: chronic myeloid leukemia


title: 11 hour after light time in the second day


title: NHP_0111231_Uninfected_Prebleed_ReplicateArray1

description: Genisphere amplified Total RNA

tag: origin

value: blood


title: TLDA-68

description:
test
SAMPLE 10


title: TLDA-69

description:
test
SAMPLE 11


title: CP95


title: 5 hour after light time in the second day


title: TLDA-86

description:
test
SAMPLE 14


title: TLDA-67

description:
test
SAMPLE 9


title: HeLa haboring control shRNA #2

source_name: HeLa, control, rep2

value: HeLa


title: CP89


title: 9 hour after dark time in the second day


title: CQ20


title: 11 hour after dark time in the second day


title: CP73


title: CQ28


title: 1 hour after light time in the second day


title: HeLa haboring control shRNA #1

source_name: HeLa, control, rep1


title: 7 hour after dark time in the second day


title: 3 hour after light time in the second day


title: CP64


title: CP70


title: TLDA-79

description:
test
SAMPLE 8


title: CP97


title: CP61


title: TLDA-84

description:
test
SAMPLE 7

value: helthy


title: TLDA-77

description:
test
SAMPLE 5


title: TLDA-82

description:
test
SAMPLE 6


title: TLDA-74

description:
test
SAMPLE 4


title: 5 hour after dark time in the second day


title: TLDA-71

description:
test
SAMPLE 1


title: TLDA-72

description:
control
SAMPLE 2


title: TLDA-73

description:
test
SAMPLE 3


title: 3 hour after dark time in the second day


title: 1 hour after dark time in the second day


title: 9 hour after light time in the first day


title: CQ12


title: TLDA-145

description:
test
SAMPLE 6

source_name: exosome

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA). RT reaction products from the exosome sample were further amplified using the Megaplex PreAmp Primers (Primers A v2.1).

extract_protocol: Total RNA was isolated with the mirVana PARIS kit (Ambion, Austin, TX, USA).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were harvested form 10ml of whole blood.


title: CQ23

value: I


title: 11 hour after light time in the first day


title: TLDA-144

description:
test
SAMPLE 5


title: 7 hour after light time in the first day


title: CQ09


title: 3 hour after light time in the first day


title: CQ03


title: CQ06


title: 5 hour after light time in the first day


title: CP67


title: 9 hour after dark time in the first day

source_name: 9 hour after dark time in the first day


title: TLDA-143

description:
test
SAMPLE 4


title: CP59


title: 1 hour after light time in the first day


title: TLDA-141

description:
test
SAMPLE 3

value: healty


title: CP76


title: CQ00


title: TLDA-140

description:
test
SAMPLE 2


title: 11 hour after dark time in the first day


title: TLDA-139

description:
test
SAMPLE 1


title: 7 hour after dark time in the first day

source_name: 7 hour after dark time in the first day


title: 3 hour after dark time in the first day

source_name: 3 hour after dark time in the first day


title: 5 hour after dark time in the first day

source_name: 5 hour after dark time in the first day


title: TLDA-70

description:
test
SAMPLE 12


title: 1 hour after dark time in the first day

source_name: 1 hour after dark time in the first day


title: human_ESCs_Glc+_1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: hESCs

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Human ESCs were maintained under mTeSR1 culture medium. Human ESC-derived cardiomyocytes were metabolically selected and mainteined under MEMα plus 5% FBS condition.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: Human ESCs and ESC-derived cardiomyocytes were cultivated under high glucose culture medium (DMEM) for 3 hours prior to extract materials.

value: Human ESCs

tag: treated with

value: high glucose culture medium (DMEM) for 3 hrs


title: CP87

value: pos


title: healthy donor control 10006823017_R05C01

status: Public on Mar 30 2016

type: genomic

city: Berlin

first: Eva

middle: Kristin

last: von der Heide

address: Hindenburgdamm 30

department: Hematology

country: Germany

institute: Charite Berlin

hyb_protocol: 500 ng bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol. Sample preparation and readout was done by High Throughput sequencing unit at German Cancer Research Center (Heidelberg, Germany).

scan_protocol: Arrays were imaged using iScan SQ instrument (Illumina)  using standard recommended Illumina scanner setting

data_processing: Partek Genomic Suite software (6.6)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: bone marrow

label_protocol: Standard Illumina Protocol

growth_protocol: Bone marrow aspirates were obtained from AML patients and healthy donors, mononuclear cells were isolated using density centrifugation and BM-MSC were generated using their plastic adherent probability and expanded up to passage four

extract_protocol: genomic DNA was extracted from BM-MSC derived from AML patients and healthy donors using AllPrep DNA/RNA Mini Kit (Qiagen)

tag: disease status

value: healthy donor control

value: BM-MSC

tag: expansion step

value: passage 4


title: healthy donor control 10006823005_R03C02


title: healthy donor control 10006823019_R05C01


title: healthy donor control 3999875022_R05C01


title: healthy donor control 10006823010_R01C02


title: healthy donor control 9379086150_R04C02


title: healthy donor control 9379086150_R02C02


title: First diagnosis 10006823020_R02C01

value: First diagnosis


title: CQ18

value: III

value: PR

value: breast cancer tumor


title: human_ESC-CMs_Glc+_1

value: Human ESC-derived cardiomyocytes


title: human_ESC-CMs_Glc+_2


title: healthy donor control 3999875028_R05C01


title: First diagnosis 10006823015_R01C01


title: First diagnosis 10006823010_R04C01


title: First diagnosis 10006823017_R04C01


title: healthy donor control 9379086150_R06C02


title: healthy donor control 3999875024_R05C01


title: healthy donor control 3999875003_R05C01


title: First diagnosis 10006823020_R04C01


title: First diagnosis 10006823017_R03C01


title: First diagnosis 9969477041_R03C01


title: healthy donor control 10006823012_R01C02


title: First diagnosis 10006823014_R03C01


title: First diagnosis 9969477037_R05C02


title: First diagnosis 9969477038_R03C02


title: First diagnosis 9969477037_R06C01


title: First diagnosis 9969477038_R01C01


title: First diagnosis 9969477037_R04C01


title: First diagnosis 9379086150_R04C01


title: First diagnosis 9969477038_R05C02


title: First diagnosis 9379086146_R02C02


title: First diagnosis 9969477034_R02C02


title: First diagnosis 9969477041_R01C01


title: First diagnosis 9969477034_R03C01


title: First diagnosis 9969477034_R04C01


title: First diagnosis 10006823005_R02C02


title: First diagnosis 9969477034_R06C01


title: First diagnosis 9379086120_R03C02


title: First diagnosis 9969477037_R02C01


title: First diagnosis 3999875028_R02C01


title: First diagnosis 3999875024_R04C01


title: First diagnosis 9379086120_R03C01


title: First diagnosis 3999875022_R01C01


title: First diagnosis 3999875003_R03C01


title: First diagnosis 3999875028_R01C01


title: First diagnosis 3999875003_R04C01


title: First diagnosis 3999875024_R03C01


title: ASO ISIS761932 1

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

hyb_protocol: Samples were hybridized using Phalanx OneArray Plus Protocol. 5ug Cy5-labeled aRNA was used

scan_protocol: Agilent 0.1 XDR Protocol

data_processing: GPR files were loaded into Rosetta Resolver System (Rosetta Biosoftware) to process data analysis. The error due to random factors and systematic biases were estimated by an error model. Data from repeated probes were averaged and median-scaling (normalization) was performed on dataset without flagged and control data

source_name: HeLa_ASO ISIS761932

label_protocol: Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization

growth_protocol: HeLa cells were cultured at 37 oC, 5% CO2,  in Dulbecco’s modified Eagle’s medium supplemented with 10% Fetal Bovine Serium (FBS), 0.1- g/ml streptomycin and 100 units/ml penicillin. Cells were seeded at ∼50% confluency and grown for 16 h before transfection.

extract_protocol: Cells were washed once with 1X PBS, and collected by trypsin, and pelleted. After washing with 1XPBS, total RNA was prepared from  cell pellet using Rneasy column (Qiagen), treated with Dnase, and eluted with water, based on the manufacturer's protocol.

treatment_protocol: Cells were wither mock transfected (UTC), or transfected with either 5 nM siRNA, or 30 nM oligonucleotides for 15 hr. Transfection was performed using 4 ug/ml Lipofectamine 2000, based on manufacturer's protocol.

tag: agent

value: ISIS761932 oligonucleotide

tag: agent concentration


title: ASO ISIS761932 3

tag: cell line


title: ASO ISIS761909 1

source_name: HeLa_ASO ISIS761909

value: ISIS761909 oligonucleotide


title: ASO ISIS761909 3

value: HeLa


title: ASO ISIS761909 2


title: UTC control 2

source_name: HeLa_UTC control

value: mock-transfected


title: ASO ISIS761932 2


title: UTC control 3


title: T-ALL Sample 116

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

institute: Umeå University

hyb_protocol: bisulphite converted DNA (EZ DNA methylation gold) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol.

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

data_processing:
GenomeStudio software v2010.3 with the Methylation module. Intergenic CpG-sites, CpG-sites at chromosome X and Y, CpG probes that align to multiple places in the genome or were located less than 3 bp from a SNP, Detection P-value > 0.05 and nbeads<=3 were filtered (set to NA). Probe type normalization was performed using the BMIQ Method.
Average Beta, unmethylated and methylated signal intensities in Series supplementary files

source_name: T-ALL

extract_protocol: Genomic DNA was extracted according to standard protocols and DNA purity and concentration determined by spechtrophotometry and Qubit.

tag: tumor/control

value: Tumor

tag: cimp subgroup

value: CIMP-

value: T-ALL bone marrow Sample


title: siRNA 3

value: luciferase siRNA


title: T-ALL Sample 105

value: CIMP+


title: T-ALL Sample 114

value: T-ALL peripheral blood Sample


title: UTC control 1


title: T-ALL Sample 103


title: T-ALL Sample 115


title: T-ALL Sample 99


title: T-ALL Sample 113


title: T-ALL Sample 117


title: T-ALL Sample 102


title: siRNA 1


title: siRNA 2


title: T-ALL Sample 97


title: T-ALL Sample 96


title: T-ALL Sample 104


title: T-ALL Sample 112


title: T-ALL Sample 110


title: T-ALL Sample 111


title: T-ALL Sample 106


title: T-ALL Sample 98


title: T-ALL Sample 100


title: T-ALL Sample 101


title: T-ALL Sample 94


title: T-ALL Sample 95


title: T-ALL Sample 93


title: Cg Wt 200 mM NaCl Vs 200 mM pipecolic replicate 2

city: Bielefeld

first: Fernando

last: Pérez

state: Deutschland

address: Laue Str.

institute: Herr

description: Technical replicate 2 of 4

hyb_protocol: DNA microarray hybridization was performed as described previously with modification (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ). Hybridization and washing was performed with HS4800 (Tecan).

scan_protocol: Image was attained with LS200 (Tecan).

data_processing: Normalization and evaluation of the microarray data was done with the software package EMMA 2 (Dondrup, M., Albaum, S. P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C. K., Küster, H., Linke, B., Mertens, D., et al. (2009). EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics 10, 50.). Genes which were up- or downregulated in WT with 200 mM pipecolic in both replicates were taken into account for further analysis (p-value < 0.05, mRNA value > 2).

organism: Corynebacterium glutamicum

source_name: Growth of C. glutamicum in minimal medium supplemented with 200mM of pipecolic

label_protocol: cDNA synthesis from total RNA and labeling were performed as described previously (Netzer, R., Krause, M., Rittmann, D., Peters-Wendisch, P. G., Eggeling, L., Wendisch, V. F., and Sahm, H. (2004). Roles of pyruvate kinase and malic enzyme in Corynebacterium glutamicum for growth on carbon sources requiring gluconeogenesis. Arch. Microbiol. 182, 354–363.; Polen, T., Schluesener, D., Poetsch, A., Bott, M., and Wendisch, V. F. (2007). Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol. Lett. 273, 109–119. ).

growth_protocol: LB seed culture was inoculated from an agar plate and grown overnight. The cells were harvested by centrifugation (4000 x g, 10 min) and washed once with CGXII medium lacking the carbon source. Finally, 50 mL of CGXII medium containing 4% of glucose, the necessary supplements, and either 200 mM NaCl or 200 mM pipecolic was inoculated to an OD600 of 1.0. Cells were grown until mid-exponential phase (OD between 15 and 26) and were spilled in two falcons (half filled with ice) and centrifuged (4000 x g, 10 minutes, 4ºC). Supernatant was discarded and cells were kept at -80ºC.

extract_protocol: RNA isolation was performed as described previously with some modification (Wendisch, V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. J. Biotechnol. 104, 273–285.). Total RNA was isolated using the RNeasy Mini   Kit(Qiagen). The purified RNA was analyzed by spectrophotometer (NanoDrop) for quantity and gel electrophoresis for quality. The RNA sample was stored at −80 °C until further use.

treatment_protocol: 200 mM NaCl or 200 mM pipecolic were added to CGXII medium  from the beginning of the growth

tag: strain

source_name: Growth of C. glutamicum in minimal medium supplemented with 200mM of NaCl


title: T-ALL Sample 107


title: T-ALL Sample 92


title: Cg Wt 200 mM NaCl Vs 200 mM pipecolic replicate 4

description: Technical replicate 4 of 4


title: Cg Wt 200 mM NaCl Vs 200 mM pipecolic replicate 3

description: Technical replicate 3 of 4


title: Cg Wt 200 mM NaCl Vs 200 mM pipecolic replicate 1

description: Technical replicate 1 of 4


title: CaSR 11

city: Esplugues

first: Carmen

last: de Torres

state: Barcelona

address: Santa Rosa 39

department: Oncology

country: Spain

institute: Hospital Sant Joan de Deu

description: Gene expression from neuroblastoma xenografts

hyb_protocol: 5 ug of fragmented and labeled ssDNA was hybridized per array using standard Affymetrix protocols (WT Plus Reagent kit)

scan_protocol: Arrays were scanned in the Genetitan Platformf for 17 hours at 45º

data_processing: Data were processed using the limma (v3.24) package in the R (v3.2) environment. Probeset level expression was derived using Robust Multi-array Average normalization. Non-specific filtering of 50% less intense and variable data was applied. Data were summarized and limited to core probe set only.

source_name: drug treated tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA using WT Plus Reagent kit

growth_protocol: Neuroblastoma cells were grown in immunocompromised mice

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

treatment_protocol: Oral gavage, daily

value: neuroblastoma tumor

tag: treatment

value: CaSR allosteric activator


title: T-ALL Sample 90


title: CaSR 7


title: CaSR 10


title: CaSR 9


title: T-ALL Sample 83


title: T-ALL Sample 89


title: Vehicle 12

source_name: vehicle treated tumor

value: vehicle


title: T-ALL Sample 72


title: CaSR 8


title: T-ALL Sample 87


title: T-ALL Sample 84


title: T-ALL Sample 85


title: T-ALL Sample 88


title: T-ALL Sample 82


title: T-ALL Sample 81


title: T-ALL Sample 74


title: T-ALL Sample 79


title: Vehicle 10


title: T-ALL Sample 75


title: T-ALL Sample 76


title: T-ALL Sample 80


title: T-ALL Sample 68


title: T-ALL Sample 86


title: CaSR 5


title: T-ALL Sample 78


title: T-ALL Sample 69


title: Vehicle 11


title: CaSR 4


title: T-ALL Sample 77


title: T-ALL Sample 71


title: Vehicle 6


title: Vehicle 5


title: trisomic_pre_mid_pach_SC_1

city: Prague

first: David

last: Homolka

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics AS CR

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Bioconductor and R statistics using the gcRMA method with default settings and custom chip description file (probes were annotated to Entrez identifiers - NCBI build 37) mm430mmentrezg, created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.

source_name: Ts43H_pre-mid-pachytene spermatocytes

label_protocol: Between 20 to 30 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: All the male mice used for isolation of spermatogenic populations were two months old.

extract_protocol: Total RNA was isolated using RNeasy Micro kit (Qiagen) according to manufacturer‘s protocol.

treatment_protocol: Mice were euthanized by cervical dislocation. For isolation of spermatogenic populations the single cell suspension from testicular tubules was prepared and the populations were isolated using fluorescence activated cell sorting of testicular single cell suspension according to ref. (Bastos et al. 2005).

tag: genotype

value: male

tag: age

value: adult (2 moths)

value: pre-mid-pachytene spermatocytes


title: Vehicle 9


title: Vehicle 8


title: trisomic_pre_mid_pach_SC_3

tag: gender


title: T-ALL Sample 70

tag: tissue


title: euploid_pre_mid_pach_SC_2


title: Vehicle 7


title: T-ALL Sample 66


title: euploid_pre_mid_pach_SC_3


title: trisomic_pre_mid_pach_SC_2


title: T-ALL Sample 65


title: trisomic_spermatids_3

value: spermatids


title: trisomic_spermatids_2


title: T-ALL Sample 67


title: euploid_mid_late_pach_SC_2

value: mid-late-pachytene spermatocytes


title: trisomic_spermatids_1


title: euploid_spermatids_2


title: euploid_spermatids_3


title: trisomic_mid_late_pach_SC_2

source_name: Ts43H_ mid-late-pachytene spermatocytes


title: euploid_mid_late_pach_SC_1


title: euploid_pre_mid_pach_SC_1


title: trisomic_mid_late_pach_SC_1


title: euploid_spermatids_1


title: trisomic_liver_3

value: liver


title: trisomic_liver_2


title: T-ALL Sample 59


title: euploid_liver_2


title: T-ALL Sample 62


title: T-ALL Sample 60


title: T-ALL Sample 58


title: trisomic_liver_1


title: euploid_liver_1


title: T-ALL Sample 64


title: CaSR 10

value: neuroblastoma xenograft


title: CaSR 5


title: T-ALL Sample 61


title: CaSR 6


title: CaSR 9


title: CaSR 11


title: CaSR 7


title: Dedifferentiated PDMSCs for 1 day, biological rep2

first: Chenxia

last: Hu

state: Zhejiang

address: School of Medicine; First Affiliated Hospital; Zhejiang University

institute: Zhejiang University

description: Gene expression data from dedifferentiated PDMSCs for 1 day

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: The data were analyzed with Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized byRMA algorithm, Affy packages in R.

source_name: Dedifferentiation of hepatogenic PDMSCs for 1 day

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3' IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

value: Placenta


title: T-ALL Sample 53

value: Tumor


title: CaSR 8


title: Dedifferentiated PDMSCs for 1 day, biological rep3

department: First Affiliated Hospital; Zhejiang University


title: T-ALL Sample 63


title: T-ALL Sample 57


title: T-ALL Sample 51


title: T-ALL Sample 55

value: CIMP-


title: Dedifferentiated PDMSCs for 1 day, biological rep1


title: Vehicle 12


title: Hepatogenic PDMSCs for 11 days, biological rep3

description: Gene expression data from Hepatogenic PDMSCs for 11 days

source_name: Hepatogenic PDMSCs for 11 days


title: T-ALL Sample 52

value: T-ALL bone marrow Sample


title: T-ALL Sample 56


title: T-ALL Sample 54


title: T-ALL Sample 50


title: Hepatogenic PDMSCs for 11 days, biological rep2


title: Vehicle 10


title: Hepatogenic PDMSCs for 11 days, biological rep1


title: Vehicle 11


title: Vehicle 9


title: Human PDMSCs, biological rep3

description: Gene expression data from human PDMSCs

source_name: Human PDMSCs isolated from one individual


title: T-ALL Sample 73


title: Vehicle 7


title: GFP3+

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Scanned on an Agilent G2505C scanner.

scan_protocol: 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.

source_name: eGFP-positive

label_protocol: manufacturer's instructions

growth_protocol: FVB/N transgenic (Tg) 11.5kb-GFP mice were housed and bred in accordance with institutional guidelines for humane animal treatment and all animal studies were conducted in accordance with Institutional Animal Care and Use Committee approved protocols.

extract_protocol: Total RNA extracted using manufacturer's instructions: RNeasy Plus Mico (Qiagen) kit was used for RNA extraction followed by amplification with Ovation® Pico WTA System Kit (NuGEN).

treatment_protocol: No treatment.

value: FVB/N

value: Prostate

tag: Sex


title: GFP3-

source_name: eGFP-negative


title: Vehicle 5


title: Vehicle 6


title: GFP2-


title: Human PDMSCs, biological rep2

description: Gene expression data from human PDMSCs


title: GFP2+


title: Vehicle 8


title: Y. pestis/Ciprofloxacin 4 µg / 120 min. replicate 1

city: Ness-Ziona

first: Ida

last: Steinberger-Levy

address: P.O. box 19

country: Israel

institute: IIBR

hyb_protocol: Each slide (containing 8 arrays) was hybridized with samples originating from 2 independent biological experiments representing the same time point, performed with Cy3-Cy5 dye swap. Each array represent hybridization of treated sample with its growth-control sample. Hybridization was done using the Agilent Gene Expression Hybridization Kit according to Agilent protocol for two-color Microarray-Based Gene Expression Analysis.

scan_protocol: Scanned on an Agilent DNA microarray G2505B scanner. Images were quantified using Agilent Feature Extraction (FE) Software (version 9.5.1.1), with linear and LOWESS normalization.

data_processing:
Agilent FE Software (9.5.1.1) was used for background subtraction and LOWESS normalization. Statistical analysis was performed using the Limma (Linear Models for Microarray Data) package from the Bioconductor project (http://www.bioconductor.org). The processed signal from the FE was read into Limma using the “read.maimages” function. Background subtraction and LOWESS normalization were performed for each array. Quantile normalization was applied between arrays. The Benjamini-Hochberg false discovery rate (FDR) was used to correct for multiple comparisons.
Values are the average of 2 independent biological experiments, normalized log2 ratio of ciprofloxacin exposed/non treated sample  (Cy5/Cy3 of one biological experiment and Cy3/Cy5 of the duplicate biological experiment) .

organism: Yersinia pestis

source_name: control

label_protocol: Complementary RNA (cRNA) was produced from the total RNA samples and fluorescently labeled using the MessageAmpTM II-Bacteria kit (Ambion) according to the manufacturer’s instructions. Each experiment comprised of samples representing 4 different ciprofloxacin concentrations labeled with either Cy3-CTP or Cy5-CTP, which were co-hybridized with the growth control sample labeled with the 2nd dye (Cy5-CTP or Cy3-CTP, accordingly).

growth_protocol: BHIA-plated Y. pestis Kimberley53 (5x10^5 CFU/ml) was suspended in MH broth (MHB) and incubated at 28oC, 150 rpm for 2 h for the adjustment of the culture to the MHB medium.

extract_protocol: Total RNA were extracted using RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. Residual DNA was removed by 15 min on-column digestion using the RNase-free DNase kit (QIAGEN).

treatment_protocol: Ciprofloxacin exposure: The adjusted culture was  divided into five samples of 400 ml each. Ciprofloxacin stock solutions (4 ml of 100X) were added to four culture samples to obtain final concentrations of 0.001, 0.016, 0.5 and 4 µg/ml, and the non-treated culture was used as growth control. Each of the five cultures was then further divided into 4×100 ml in 0.5 L flasks. The 0.5 L Erlenmeyer flasks were incubated at 28ºC, 150 rpm for 120 min. 40 ml of each culture were centrifuged at 3,200× g for 15 min at 4°C. Bacterial pellets were frozen by liquid nitrogen and stored at -70°C until RNA extraction.

value: none (untreated control)

source_name: Ciprofloxacin 4 µg for 120 min

value: Ciprofloxacin 4 µg for 120 min


title: GFP1+


title: GFP1-


title: Replication timing of A-T fibroblasts 2

status: Public on Mar 29 2016

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: submitted as of 2/24/16

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 1.1 kb across the human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing:
NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].
Log2 transformed early/late replication timing ratio (average of 2 biological replicates of two patient lines)

source_name: Early-replicating DNA of ATF1 fibroblast cells

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: diagnosis

value: Ataxia-Telangiectasia

tag: age (yrs)

value: M

tag: disease stage

tag: karyotype

source_name: Late-replicating DNA of ATF1 fibroblast cells


title: Y. pestis/Ciprofloxacin 4 µg / 120 min. replicate 2

tag: treated with


title: Replication timing of A-T fibroblasts 4

description: submitted as of 2/24/16

source_name: Early-replicating DNA of ATF2 fibroblast cells

source_name: Late-replicating DNA of ATF2 fibroblast cells


title: Replication timing of A-T fibroblasts 1

description: submitted as of 2/24/16


title: Replication timing of A-T fibroblasts 3

description: submitted as of 2/24/16


title: Y. pestis/Ciprofloxacin 0.5 µg / 120 min. replicate 2

source_name: Ciprofloxacin 0.5 µg for 120 min

value: Ciprofloxacin 0.5 µg for 120 min


title: CT26-FL3 murine colon cancer parental cell line_high liver metastasis_rep3

city: Columbia

first: Maria Marjorette

middle: Ociones

last: Pena

state: SC

address: 715 Sumter St. CLS 401

department: Biological Sciences

institute: University of South Carolina

description: Sample name: CT26-FL3 2

hyb_protocol: 17 hours, 60 degrees C according to Agilent protocol using an Agilent recommended hybridization oven.

scan_protocol: Agilent B scanner (Agilent Technologies Scanner G2505B US 22502617)

data_processing:
Data extracted with Agilent Feature Extraction software version A8.5.3, and normalized intensities were uploaded and analyzed using GeneSifter software (Geospiza, Inc.)
Note: The supplementary .txt file does not represent the original raw data file (which is not available). It represents an intermediate file type generated by Resolver. The Resolver-generated .txt file was subsequently normalized.  The normalized data are presented in the Data table.

source_name: CT26-FL3 cell, replicate 3

label_protocol: Agilent low input amplification kit, 500 ng input.

growth_protocol: Cells were cultivated in Dubecco's Modification of Eagle's Medium (DMEM) with 4.5 g/L glucose (Mediatech, Manassas, VA) supplemented with 10% fetal bovine serum (FBS, Atlanta Biologicals, Lawrenceville, GA) and 1% Penicillin/Streptomycin (Pen/Strep, Mediatech, Manassas, VA) at 37 °C and 5% CO2 in a humidified atmosphere.

extract_protocol: Total RNA was isolated using Rneasy RNA isolation kit (Qiagen, Valencia, CA) following manufacturer's protocol.  RNA quality was assessed using an Agilent  Bioanalyzer.  RNA integrity numbers (RIN) ranged from 8 to 10.

treatment_protocol: Highly metastatic CT26-FL3 colon cancer cell line was isolated by in vivo selection after three passages through the liver.  Metastatic lesions were excised from the liver, minced and digested with collagenase, Dnase and hyaluronidase to obtain a single cell suspension. Cells were briefly grown in culture to remove stromal cells prior to microarray analysis.

value: Balb/c

value: Male

value: CT26-FL3 colon cancer cell line


title: Human PDMSCs, biological rep1

description: Gene expression data from human PDMSCs


title: Replication timing of A-T iPSCs 3

description: submitted as of 2/24/16

source_name: Early-replicating DNA of A2-1 iPSCs

source_name: Late-replicating DNA of A2-1 iPSCs


title: Y. pestis/Ciprofloxacin 0.5 µg / 120 min. replicate 1


title: CT26-FL3 murine colon cancer parental cell line_high liver metastasis_rep5

description: Sample name: CT26-FL3 4

source_name: CT26-FL3 cell, replicate 5


title: Replication timing of A-T iPSCs 2

description: submitted as of 2/24/16

source_name: Early-replicating DNA of A1-3 iPSCs

source_name: Late-replicating DNA of A1-3 iPSCs


title: Y. pestis/Ciprofloxacin 0.001 µg / 120 min. replicate1

source_name: Ciprofloxacin 0.001 µg for 120 min

value: Ciprofloxacin 0.001 µg for 120 min


title: CT26-FL3 murine colon cancer parental cell line_high liver metastasis_rep2

description: Sample name: CT26-FL3 1

source_name: CT26-FL3 cell, replicate 2


title: CT26-FL3 murine colon cancer parental cell line_high liver metastasis_rep4

description: Sample name: CT26-FL3 3

source_name: CT26-FL3 cell, replicate 4


title: Replication timing of A-T iPSCs 1

description: submitted as of 2/24/16


title: CT26 murine colon cancer parental cell line_poor liver metastasis_rep4

description: Sample name: CT26 4

source_name: CT26 cell, replicate 4

value: CT26 colon cancer cell line


title: Y. pestis/Ciprofloxacin 0.016 µg / 120 min. replicate 1

source_name: control

source_name: Ciprofloxacin 0.016 µg for 120 min

value: Ciprofloxacin 0.016 µg for 120 min


title: Y. pestis/Ciprofloxacin 0.001 µg / 120 min. replicate2


title: CT26 murine colon cancer parental cell line_poor liver metastasis_rep2

description: Sample name: CT26 2

source_name: CT26 cell, replicate 2


title: Y. pestis/Ciprofloxacin 0.016 µg / 120 min. replicate 2


title: Pool control

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

institute: Universidad de Zaragoza

description: Gene expression data from liver male mice on a chow diet (Teklad Mouse/Rat Diet no. 2014, Harlan Teklad, Harlan Ibérica, Barcelona, Spain) and  1% (v/v) of glycerol solution as beverage for 10 weeks

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Murine Genome MOE430A 2.0

scan_protocol: GeneChips were scanned using the GeneArray Scanner (Agilent Technologies, Palo Alto, CA, USA)

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA

growth_protocol: Two-month old male mice with a C57BL/6J/ OLA129 genetic background were fed with chow diet whose glycerol beverage containing squalene to provide a dose of 1 g/kg/day for 10 weeks

extract_protocol: Tri reagent extraction of total RNA was performed according to the manufacturer's instructions. RNA was extracted using a Quiagen RNeasy kit.

treatment_protocol: Liver were removed, washed to remove blood, frozen in liquid nitrogen and stored at -70C

tag: background strain

tag: genotype/variation

value: apolipoprotein E-deficient

value: 2 month

value: male

tag: fed with

value: chow diet whose beverage contained 1% (v/v) of glycerol solution for 10 wks

value: liver


title: Pool squalene

description: Gene expression data from liver apolipoprotein E-deficient male mice ona chow die t(Teklad Mouse/Rat Diet no. 2014, Harlan Teklad, Harlan Ibérica, Barcelona, Spain) and  1% (v/v) of glycerol solution as beverage containing squalene to provide a dose of 1 g/kg/day for 10 weeks

value: chow diet and whose glycerol beverage containing squalene to provide a dose of 1 g/kg/day for 10 wks


title: CT26 murine colon cancer parental cell line_poor liver metastasis_rep3

description: Sample name: CT26 3

source_name: CT26 cell, replicate 3

tag: cell line


title: Replication timing of A-T iPSCs 4

description: submitted as of 2/24/16

source_name: Early-replicating DNA of A2-1 iPSC cells

source_name: Late-replicating DNA of A2-1 iPSC cells


title: CT26 murine colon cancer parental cell line_poor liver metastasis_rep1

description: Sample name: CT26 1

source_name: CT26 cell, replicate 1


title: Mm_S3_AdWT_B838_bssilva_IMM_JS

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

hyb_protocol: 3.5 µg of  fragmented and labeled cDNA was used in a 150-µl hybridization cocktail containing added hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix), of which 120 ul were hybridized on array strips for 20 h at 48°C. Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system, followed by scanning of the array strips.

scan_protocol: standard Affymetrix protocol

data_processing: All the microarray data analysis was done using R and several packages available from CRAN (Team 2011) and Bioconductor (Huber et al. 2015). The raw data (CEL files) were normalized and summarized with the Robust MultiArray Average method implemented in the ‘oligo’ package (Carvalho and Irizarry 2010).

label: Streptavidin Phycoerythrin (SAPE)

source_name: WT γδ thymocytes

label_protocol: 20 ug of this cRNA was used for a second cycle of single-strand cDNA synthesis (Genechip WT Pico Reagent Kit; Affymetrix). 5.5 ug of single stranded cDNA was fragmented and labeled (Genechip WT Pico Reagent Kit; Affymetrix). Size distribution of the fragmented and labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

extract_protocol: High Pure RNA isolation Kit (Roche)

treatment_protocol: Concentration and purity was determined by spectrophotometry and integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA).RNA was processed for use on Affymetrix (Santa Clara, CA, USA) MoGene 2.1 ST Array by using the Affymetrix Genechip WT Pico Reagent Kit, according to the manufacturer’s protocols. Starting material:  2 ng of total RNA

value: wild type

tag: developmental stage

value: Adult stage (6 weeks)

value: Thymus

tag: cell type

value: Lymphocyte


title: Cbt>69B embryos at 10-13 stage, rep3

city: BURJASSOT

first: YAIZA

last: BELACORTU

state: VALENCIA

address: DR. MOLINER

department: GENETICS

institute: UNIVERSITY OF VALENCIA

description: Expression profiling by array

hyb_protocol: Hybridization was performed following Affymetrix protocol, chips were washed and stained using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450

scan_protocol: Affymetrix scanner GeneChip 3000 7G was used to read the arrays

data_processing: Pre-processing of data was performed using the RMA (robust Multi-Array) function of the affy package and differential expression analysis using LIMMA (Lineal Models for Microarray Data) package, both from Bioconductor (

source_name: dechorionated embryo

label_protocol: RNA was label with Biotin according to standard Affymetrix protocol

extract_protocol: Total RNA was extracted from  aproximated 1000 dechorionated cbtEP(2)2237E1 and Cbt>69B embryos at 10-13 stage and purified with the mrVANATM miRNA insolation kit (Ambion·AM1260) following manufacturer´s instructions. RNA quality and quantification was performed in a Biorad Experion bioanalyzer. Three  cbtEP(2)2237E1,  three w1118 and three 69B>Cbt  RNA samples were prepared and used to  hybridize to Drosophila Genome  2.0 Affymetrix  Microarrays following manucaturer´s instructions.

value: dechorionated embryo

value: homozygote embryos overexpressed Cbt in epidermis (69BGal4>UAS-Cbt)

value: 10-13 stage, from germ band retraction to finish dorsal closure process


title: Mm_S2_EmDG_B837_bssilva_IMM_JS

source_name: CD3DH γδ thymocytes

value: CD3DH (reduced TCR expression)

value: Embryonic stage (E18)


title: CaSR 4

source_name: drug treated tumor

value: neuroblastoma xenograft

tag: treatment

value: CaSR allosteric activator


title: cbtEP(2)2237E1 embryos at 10-13 stage, rep2

description: Expression profiling by array

tag: genotype

value: homozygote embryos of line cbtEP(2)2237E1


title: euploid_liver_3

tag: age

value: adult (2 moths)


title: Cbt>69B embryos at 10-13 stage, rep2

description: Expression profiling by array


title: Cbt>69B embryos at 10-13 stage, rep1

description: Expression profiling by array


title: cbtEP(2)2237E1 embryos at 10-13 stage, rep1

description: Expression profiling by array


title: Mm_S4_AdDG_B839_bssilva_IMM_JS


title: white 1118 embryos at 10-13 stage, control,  rep3

description: Expression profiling by array

value: white 1118 embryos


title: A2-1-p5-2

description: Gene expression data obtained from iPS cells derived from A-T Disease patient2 fibroblast

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA

source_name: A-T Disease patient2 iPSC passage5 replicate2

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications


title: A1-3-p5-1

description: Gene expression data obtained from iPS cells derived from A-T Disease patient1 fibroblast

source_name: A-T Disease patient1 iPSC passage5 replicate1


title: white 1118 embryos at 10-13 stage, control,  rep1

description: Expression profiling by array


title: A1-3-p5-2

source_name: A-T Disease patient1 iPSC passage5 replicate2

value: iPS cells derived from A-T Disease patient1 fibroblast


title: peripheral airway epithelial cells, smoker 40

city: new york

first: Jun-Chieh

middle: James

last: Tsay

state: NY

address: 562 First Ave. NBV 7N27

department: Medicine

institute: NYU Langone Medical Center

description:
lower airway microbiome resembles background
rep 1

hyb_protocol: Ten µg of cRNA was hybridized to the array, and was processed with the Affymetrix system, including GeneChip Hybridization Oven 640

scan_protocol: GeneChips scanned with Fluidics Station 450 and Scanner 3000.

data_processing: Normalization of Affymetrix array data was by Robust Multichip Average (RMA) through the RMexpress software package (http://rmaexpress.bmbolstad.com/).

source_name: peripheral airway epithelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).  Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).  Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical

extract_protocol: extracted total RNA using Qiagen miRNeasy Mini Kit (Valencia, CA) according to the company protocol

treatment_protocol: The cytology brush was spun down and the cell pellet was collected and stored at - 80° C until RNA extraction

value: lung

value: epithelial

tag: gender

value: male

tag: case

value: PneumotypeBPT


title: Mm_S1_EmWT_B836_bssilva_IMM_JS

value: wild type

tag: tissue

value: Thymus


title: cbtEP(2)2237E1 embryos at 10-13 stage, rep3

description: Expression profiling by array

value: dechorionated embryo


title: AF2-1

description: Gene expression data obtained from A-T Disease patient2 fibroblast

source_name: A-T Disease patient2 fibroblast replicate1

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine. Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 uM nonessential amino acids, 100 uM 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

value: A-T Disease  patient2 fibroblast


title: peripheral airway epithelial cells, smoker 51


title: peripheral airway epithelial cells, smoker 8

value: female


title: peripheral airway epithelial cells, smoker 7


title: peripheral airway epithelial cells, smoker 28


title: peripheral airway epithelial cells, smoker 3


title: white 1118 embryos at 10-13 stage, control,  rep2

description: Expression profiling by array

value: 10-13 stage, from germ band retraction to finish dorsal closure process


title: A2-1-p5-1

source_name: A-T Disease patient2 iPSC passage5 replicate1

value: iPS cells derived from A-T Disease patient2 fibroblast


title: AF2-2

source_name: A-T Disease patient2 fibroblast replicate2

value: A-T Disease patient2 fibroblast


title: AF1-1

description: Gene expression data obtained from A-T Disease patient1 fibroblast

source_name: A-T Disease patient1 fibroblast replicate1

value: A-T Disease patient1 fibroblast


title: AF1-2

source_name: A-T Disease patient1 fibroblast replicate2

value: A-T Disease  patient1 fibroblast


title: peripheral airway epithelial cells, smoker 4


title: 4B

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

description: 4after x-ray

hyb_protocol: Hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip or Illumina HumanWG-6 v3.0 expression BeadChip using the standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol of iScan.

data_processing:
The data were transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.
The Sample data table includes values only for those probes that are in-common between Platforms GPL6884 and GPL10558.

source_name: breast tumour, LumA, after x-ray

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

extract_protocol: mRNA from paired excised tumour biopsies after resection and after X-ray were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: Sex

tag: disease

value: primary ER+ breast carcinoma

tag: subtype

value: LumA

value: breast tumour

tag: sampling time

value: after x-ray

tag: delay

value: 45 minutes


title: 4A

description: 4after excision

source_name: breast tumour, LumA, after excision

value: after excision


title: 1A

description: 1after excision

source_name: breast tumour, LumB, after excision

value: LumB

value: 40 minutes


title: 5A

description: 5after excision

value: 25 minutes


title: 18B

description: 18after x-ray


title: peripheral airway epithelial cells, smoker 49

description:
lower airway microbiome resembles suprglottic samples
rep 1

value: lung

value: epithelial

value: male

value: PneumotypeSPT


title: 1B

description: 1after x-ray

value: female


title: 3B

description: 3after x-ray

value: 20 minutes


title: Cell line [C-41 O2]

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description: C-41 O2.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: Uterine cervical cancer

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

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated out in plastic dishes (3x10^5 cells for 6 cm dishes, 9x10^5 for 10 cm dishes) 24 h prior to exposure to hypoxic (0.2% O2, 5% CO2) or normoxic (95% air, 5% Co2) conditions for 24 h at 37°C. The hypoxia treatment was performed in an Invivo2200 chamber (Ruskinn Technology Ltd, Bridgend, UK) with accurate O2 and CO2 controls.

tag: histology

value: Squamous cell carcinoma

tag: exposed to

value: normoxic (95% air, 5% Co2) conditions for 24 h at 37°C (untreated)


title: peripheral airway epithelial cells, smoker 30


title: 5B

description: 5after x-ray

value: primary ER+ breast carcinoma


title: 6B

description: 6after x-ray

source_name: breast tumour, LumB, after x-ray

value: 60 minutes


title: 6A

description: 6after excision

value: LumA

value: breast tumour


title: 3A

description: 3after excision


title: Cell line [SW756 Hyp]

description: SW756 Hyp.AVG_Signal

value: hypoxic (0.2% O2, 5% CO2) conditions for 24 h at 37°C


title: peripheral airway epithelial cells, smoker 27


title: Cell line [SW756 O2]

description: SW756 O2.AVG_Signal


title: Cell line [HT-3 O2]

description: HT-3 O2.AVG_Signal


title: peripheral airway epithelial cells, smoker 52


title: peripheral airway epithelial cells, smoker 29


title: Cell line [HeLa Hyp]

description: HeLa Hyp.AVG_Signal

value: HeLa


title: Cell line [ME-180 Hyp]

description: ME-180 Hyp.AVG_Signal


title: Cell line [HT-3 Hyp]

description: HT-3 Hyp.AVG_Signal


title: Cell line [C-33 A Hyp]

description: C-33 Hyp.AVG_Signal


title: Cell line [C-33 A O2]

description: C-33 O2.AVG_Signal


title: Cell line [C-41 Hyp]

description: C-41 Hyp.AVG_Signal


title: Tumor biopsy [P-538_re-analysis]

description: Reanalysis of GSM1668804

source_name: Cervical tumor

growth_protocol: 1-4 tumor samples wer collected from each patient at the time of diagnosis

extract_protocol: In cohort 1, RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. In cohort 2, RNA was extracted by use of the miRNeasy mini kit. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis.

tag: figo stage

tag: hypoxia classifier

value: Less hypoxic

tag: cohort

value: Cohort 2


title: Cell line [HeLa O2]

description: HeLa O2.AVG_Signal

tag: cell line


title: 18A

description: 18after excision

value: after excision

value: 40 minutes


title: Cell line [ME-180 O2]

description: ME-180 O2.AVG_Signal


title: Tumor biopsy [P-524_re-analysis]

description: Reanalysis of GSM1668793


title: Tumor biopsy [P-532_re-analysis]

description: Reanalysis of GSM1668799

value: More hypoxic


title: Tumor biopsy [P-537_re-analysis]

description: Reanalysis of GSM1668803


title: Tumor biopsy [P-535_re-analysis]

description: Reanalysis of GSM1668801


title: Tumor biopsy [P-536_re-analysis]

description: Reanalysis of GSM1668802


title: Tumor biopsy [P-518_re-analysis]

description: Reanalysis of GSM1668790


title: Tumor biopsy [P-533_re-analysis]

description: Reanalysis of GSM1668800


title: Tumor biopsy [P-531_re-analysis]

description: Reanalysis of GSM1668798


title: Tumor biopsy [P-488_re-analysis]

description: Reanalysis of GSM1668775


title: Tumor biopsy [P-496_re-analysis]

description: Reanalysis of GSM1668778


title: Tumor biopsy [P-503_re-analysis]

description: Reanalysis of GSM1668780


title: Tumor biopsy [P-510_re-analysis]

description: Reanalysis of GSM1668786


title: Tumor biopsy [P-529_re-analysis]

description: Reanalysis of GSM1668797


title: Tumor biopsy [P-526_re-analysis]

description: Reanalysis of GSM1668795


title: Tumor biopsy [P-525_re-analysis]

description: Reanalysis of GSM1668794


title: Tumor biopsy [P-493_re-analysis]

description: Reanalysis of GSM1668777


title: Tumor biopsy [P-527_re-analysis]

description: Reanalysis of GSM1668796


title: Tumor biopsy [P-513_re-analysis]

description: Reanalysis of GSM1668788


title: Tumor biopsy [P-505_re-analysis]

description: Reanalysis of GSM1668782


title: Tumor biopsy [P-516_re-analysis]

description: Reanalysis of GSM1668789


title: Tumor biopsy [P-500_re-analysis]

description: Reanalysis of GSM1668779


title: Tumor biopsy [P-509_re-analysis]

description: Reanalysis of GSM1668785


title: Tumor biopsy [P-512_re-analysis]

description: Reanalysis of GSM1668787


title: Tumor biopsy [P-520_re-analysis]

description: Reanalysis of GSM1668792


title: Tumor biopsy [P-507_re-analysis]

description: Reanalysis of GSM1668784


title: Tumor biopsy [P-519_re-analysis]

description: Reanalysis of GSM1668791


title: Tumor biopsy [P-491_re-analysis]

description: Reanalysis of GSM1668776


title: Tumor biopsy [P-506_re-analysis]

description: Reanalysis of GSM1668783


title: Tumor biopsy [P-487_re-analysis]

description: Reanalysis of GSM1668774


title: Tumor biopsy [P-504_re-analysis]

description: Reanalysis of GSM1668781


title: Tumor biopsy [P-484_re-analysis]

description: Reanalysis of GSM1668772


title: Tumor biopsy [P-468_re-analysis]

description: Reanalysis of GSM1668762


title: Tumor biopsy [P-479_re-analysis]

description: Reanalysis of GSM1668768


title: Tumor biopsy [P-482_re-analysis]

description: Reanalysis of GSM1668770


title: Tumor biopsy [P-475_re-analysis]

description: Reanalysis of GSM1668766


title: Tumor biopsy [P-485_re-analysis]

description: Reanalysis of GSM1668773


title: Tumor biopsy [P-478_re-analysis]

description: Reanalysis of GSM1668767


title: Tumor biopsy [P-471_re-analysis]

description: Reanalysis of GSM1668764


title: Tumor biopsy [P-474_re-analysis]

description: Reanalysis of GSM1668765


title: Tumor biopsy [P-462_re-analysis]

description: Reanalysis of GSM1668758


title: Tumor biopsy [P-460_re-analysis]

description: Reanalysis of GSM1668757


title: Tumor biopsy [P-483_re-analysis]

description: Reanalysis of GSM1668771


title: Tumor biopsy [P-466_re-analysis]

description: Reanalysis of GSM1668760


title: Tumor biopsy [P-455_re-analysis]

description: Reanalysis of GSM1668754


title: Mutant, biological rep37

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

institute: Fujita Health University

description: Gene expression data from the DG of mutant mouse (24-h LA: 54865.2)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000)

data_processing: The data were analyzed with Affymetrix Expression Cosole (version 1.1). The normalization used in RMA is quantile normalization.

source_name: DG of adult mutant mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

extract_protocol: Trizol extraction of total RNA and cleanup byRNeasy Micro kit (QIAGEN) was performed according to the manufacturer's instructions.

value: Dentate gyrus

value: Mutant

tag: backgrond


title: Tumor biopsy [P-443_re-analysis]

description: Reanalysis of GSM1668751


title: Tumor biopsy [P-469_re-analysis]

description: Reanalysis of GSM1668763


title: Tumor biopsy [P-464_re-analysis]

description: Reanalysis of GSM1668759


title: Mutant, biological rep33

description: Gene expression data from the DG of mutant mouse (24-h LA: 25590.06)

tag: genotype


title: Mutant, biological rep34

description: Gene expression data from the DG of mutant mouse (24-h LA: 121075.86)

tag: age


title: Tumor biopsy [P-445_re-analysis]

description: Reanalysis of GSM1668752


title: Tumor biopsy [P-456_re-analysis]

description: Reanalysis of GSM1668755


title: Tumor biopsy [P-467_re-analysis]

description: Reanalysis of GSM1668761


title: Tumor biopsy [P-442_re-analysis]

description: Reanalysis of GSM1668750


title: Tumor biopsy [P-457_re-analysis]

description: Reanalysis of GSM1668756


title: Mutant, biological rep36

description: Gene expression data from the DG of mutant mouse (24-h LA: 22211.46)


title: Mutant, biological rep32

description: Gene expression data from the DG of mutant mouse (24-h LA: 78306.12)


title: Tumor biopsy [P-438_re-analysis]

description: Reanalysis of GSM1668749


title: Tumor biopsy [P-434_re-analysis]

description: Reanalysis of GSM1668748


title: Mutant, biological rep31

description: Gene expression data from the DG of mutant mouse (24-h LA: 23889.42)


title: Mutant, biological rep30

description: Gene expression data from the DG of mutant mouse (24-h LA: 41603.46)


title: Tumor biopsy [P-423_re-analysis]

description: Reanalysis of GSM1668743


title: Tumor biopsy [P-481_re-analysis]

description: Reanalysis of GSM1668769


title: Tumor biopsy [P-426_re-analysis]

description: Reanalysis of GSM1668744


title: Mutant, biological rep26

description: Gene expression data from the DG of mutant mouse (24-h LA: 50378.7)


title: Tumor biopsy [P-422_re-analysis]

description: Reanalysis of GSM1668742


title: Tumor biopsy [P-416_re-analysis]

description: Reanalysis of GSM1668737


title: Mutant, biological rep29

description: Gene expression data from the DG of mutant mouse (24-h LA: 20966.82)


title: Tumor biopsy [P-433_re-analysis]

description: Reanalysis of GSM1668747


title: Mutant, biological rep28

description: Gene expression data from the DG of mutant mouse (24-h LA: 21910.56)


title: Tumor biopsy [P-421_re-analysis]

description: Reanalysis of GSM1668741


title: Tumor biopsy [P-429_re-analysis]

description: Reanalysis of GSM1668746


title: Tumor biopsy [P-418_re-analysis]

description: Reanalysis of GSM1668739


title: Mutant, biological rep35

description: Gene expression data from the DG of mutant mouse (24-h LA: 124392.12)


title: Tumor biopsy [P-420_re-analysis]

description: Reanalysis of GSM1668740


title: Mutant, biological rep24

description: Gene expression data from the DG of mutant mouse (24-h LA: 82113)


title: Tumor biopsy [P-417_re-analysis]

description: Reanalysis of GSM1668738


title: Tumor biopsy [P-413_re-analysis]

description: Reanalysis of GSM1668736


title: Tumor biopsy [P-412_re-analysis]

description: Reanalysis of GSM1668735


title: Tumor biopsy [P-409_re-analysis]

description: Reanalysis of GSM1668732


title: Tumor biopsy [P-454_re-analysis]

description: Reanalysis of GSM1668753


title: Wild-type, biological rep3

description: Gene expression data from the DG of wild-type mouse (24-h LA: 14301.12)

source_name: DG of adult wild-type mouse

value: Wild-type


title: Mutant, biological rep25

description: Gene expression data from the DG of mutant mouse (24-h LA: 101532.72)


title: Tumor biopsy [P-411_re-analysis]

description: Reanalysis of GSM1668734


title: Tumor biopsy [P-410_re-analysis]

description: Reanalysis of GSM1668733


title: Mutant, biological rep27

description: Gene expression data from the DG of mutant mouse (24-h LA: 46297.38)


title: Mutant, biological rep23

description: Gene expression data from the DG of mutant mouse (24-h LA: 19927.98)


title: Mutant, biological rep21

description: Gene expression data from the DG of mutant mouse (24-h LA: 20587.62)


title: Tumor biopsy [P-401_re-analysis]

description: Reanalysis of GSM1668729


title: Tumor biopsy [P-408_re-analysis]

description: Reanalysis of GSM1668731


title: Tumor biopsy [P-399_re-analysis]

description: Reanalysis of GSM1668728


title: Mutant, biological rep22

description: Gene expression data from the DG of mutant mouse (24-h LA: 18608.64)


title: Mutant, biological rep20

description: Gene expression data from the DG of mutant mouse (24-h LA: 74297.52)


title: Tumor biopsy [P-406_re-analysis]

description: Reanalysis of GSM1668730


title: Tumor biopsy [P-395_re-analysis]

description: Reanalysis of GSM1668726


title: Tumor biopsy [P-386_re-analysis]

description: Reanalysis of GSM1668725


title: Tumor biopsy [P-367_re-analysis]

description: Reanalysis of GSM1668723


title: Mutant, biological rep18

description: Gene expression data from the DG of mutant mouse (24-h LA: 19332.06)


title: Tumor biopsy [P-366_re-analysis]

description: Reanalysis of GSM1668722


title: Tumor biopsy [P-397_re-analysis]

description: Reanalysis of GSM1668727


title: Mutant, biological rep19

description: Gene expression data from the DG of mutant mouse (24-h LA: 19712.34)


title: Tumor biopsy [P-370_re-analysis]

description: Reanalysis of GSM1668724


title: Mutant, biological rep15

description: Gene expression data from the DG of mutant mouse (24-h LA: 63775.14)


title: Mutant, biological rep17

description: Gene expression data from the DG of mutant mouse (24-h LA: 43683.18)


title: Mutant, biological rep14

description: Gene expression data from the DG of mutant mouse (24-h LA: 66939.54)


title: Mutant, biological rep16

description: Gene expression data from the DG of mutant mouse (24-h LA: 59997)


title: Tumor biopsy [P-336_re-analysis]

description: Reanalysis of GSM1668717


title: Mutant, biological rep12

description: Gene expression data from the DG of mutant mouse (24-h LA: 71208.78)


title: Mutant, biological rep13

description: Gene expression data from the DG of mutant mouse (24-h LA: 17679)


title: Tumor biopsy [P-358_re-analysis]

description: Reanalysis of GSM1668721


title: Tumor biopsy [P-353_re-analysis]

description: Reanalysis of GSM1668719


title: Tumor biopsy [P-298_re-analysis]

description: Reanalysis of GSM1668713


title: Tumor biopsy [P-335_re-analysis]

description: Reanalysis of GSM1668716


title: Tumor biopsy [P-337_re-analysis]

description: Reanalysis of GSM1668718


title: Tumor biopsy [P-354_re-analysis]

description: Reanalysis of GSM1668720


title: Tumor biopsy [P-427_re-analysis]

description: Reanalysis of GSM1668745


title: Mutant, biological rep11

description: Gene expression data from the DG of mutant mouse (24-h LA: 16273.92)


title: Mutant, biological rep10

description: Gene expression data from the DG of mutant mouse (24-h LA: 59718.66)


title: Mutant, biological rep7

description: Gene expression data from the DG of mutant mouse (24-h LA: 69385.74)


title: Mutant, biological rep5

description: Gene expression data from the DG of mutant mouse (24-h LA: 97690.08)


title: Wild-type, biological rep1

description: Gene expression data from the DG of wild-type mouse (24-h LA: 20979.78)


title: Tumor biopsy [P-282_re-analysis]

description: Reanalysis of GSM1668711


title: 23A

description: 23after excision

value: female

value: 45 minutes


title: Wild-type, biological rep2

description: Gene expression data from the DG of wild-type mouse (24-h LA: 17522.94)


title: 11A

description: 11after excision

source_name: breast tumour, basal, after excision

value: Basal

value: 31 minutes


title: Mutant, biological rep6

description: Gene expression data from the DG of mutant mouse (24-h LA: 128827.08)


title: Mutant, biological rep1

description: Gene expression data from the DG of mutant mouse (24-h LA: 17827.56)


title: 10A

description: 10after excision

value: primary ER+ breast carcinoma

value: LumB

value: 30 minutes


title: 12B

description: 12after x-ray

value: LumA

value: breast tumour

value: after x-ray

value: 22 minutes


title: Tumor biopsy [P-277_re-analysis]

description: Reanalysis of GSM1668709

value: Squamous cell carcinoma

value: Less hypoxic

value: Cohort 2


title: 23B

description: 23after x-ray


title: 12A

description: 12after excision

value: after excision


title: Mutant, biological rep4

description: Gene expression data from the DG of mutant mouse (24-h LA: 94950.6)

value: Dentate gyrus

value: Mutant


title: 20B

description: 20after x-ray

value: female


title: Mutant, biological rep2

description: Gene expression data from the DG of mutant mouse (24-h LA: 18668.4)