title: 4 control a

source_name: Day:4 Treatment:control  Biorep:A


title: TAX577190

status: Public on Feb 29 2016

type: genomic

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Signal intensities were obtained from GenomeStudio (Illumina), converted to beta-values, filtered, and normalized to remove biases between Infinium I and II probes.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: breast tumor

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA was was isolated from fresh frozen breast tissues in a three-step procedure. Tumour cells were pre-treated with Proteinase K (20 mg/ml) at 55C over-night, DNA was further purified using the Promega Wizard Genomic DNA Purification kit (Promega Corporation, Madison, Wisconsin) and finally DNA was purified by phenol/chloroform treatment in phase-lock tubes.

tag: disease state

value: breast cancer


title: TAX577146


title: TAX577228


title: TAX577048


title: TAX577129


title: TAX577425


title: 8 control a

type: RNA

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

description: Randomized loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 216 slides were hybridized and scanned was Randomized to minimize the impact on differences between samples of any potential variation in the processing conditions. According to this Randomized experimental design combinations of labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Cy3 and Cy5 scans for each slide were combined and processed in ImaGene version 8.0 (BioDiscovery) to extract raw intensity and background corrected data values for each spot on the array
Quantified microarray data were Lowess normalied within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using a modified version of R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003).

label: Cy3 or Cy5

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Day:8 Treatment:control  Biorep:A

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis thaliana plants (Col-0, agl22-3 [SALK_141674], and agl22-4 [SAIL_583_C08]) were obtained from the European Arabidopsis Stock Centre, and were grown under a 8:16-h light:dark cycle at 23°C, 60% relative humidity, and light intensity of 150 µmol m-2 s-1. Arabidopsis seed was stratified for 3 d in 0.1% agarose at 4°C before sowing individual seeds onto a soil mix (Scotts Levingtons F2+S compost : fine grade vermiculite in a ratio of 6:1:). For the drought time course experiment, pots (7cm x 7cm x 9 cm) were filled with the same amount of soil mix. Control pots, to determine 100% and 0% soil water content, were set up at the same time. Plants were transferred into individual pots 2 weeks after the sowing date and were kept well watered until the beginning of the drying episode at 5 weeks after sowing.

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: Half the plants were maintained at well watered conditions, while for the remaining half, water was withdrawn and pot weight was determined daily. Relative soil water content was calculated for each day and pots were left to dry until 17% rSWC was reached. 5 week old plants were saturated in water to reach 95% rSWC, and watering was stopped in the treatment plants until ~17% rSWC was reached. The control plants were maintained under well-watered conditions at ~95% rSWC. Due to the early flowering phenotype of both agl22 mutant alleles, drought experiments were carried out on 20 day old plants to ensure the experiments were carried out at similar rosette developmental stages and prior to the onset of flowering, as indicated in Supplemental Figure 5A. The drying rate was determined as the slope of the decline in relative soil water content, measured daily throughout the drying period.

tag: treatment

value: control

tag: time (day)

tag: biological replicate

value: A


title: 0 zero a

source_name: Day:0 Treatment:zero  Biorep:A

value: zero


title: TAX577536


title: Whole blood sample, healthy individual, no treatment (01-01-013)

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

hyb_protocol: Labeled RNA was hybridized to GeneChip® HumanGenome U133 Plus 2.0 Arrays (Affymetrix).

scan_protocol: The slides were washed and stained on a GeneChip® Fluidics Station (Affymetrix) and scanned using a GeneChip® Scanner 3000 (Affymetrix).

data_processing: Fluorescence intensity data were normalized by robust multiarray analysis (RMA) using GeneSpring® (Agilent Technologies, Santa Clara, CA).

label: Biotin

source_name: Healthy individual, in the absence of any treatment

label_protocol: RNA was labeled using a One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA)

extract_protocol: RNA was extracted from blood samples using a Paxgene Blood RNA kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). All samples had a RNA integriti number (RIN) > 6

treatment_protocol:
28 patients with SLE (aged 18 - 50 years), according to the American College of Rheumatology criteria for SLE,[5] were recruited in a multicenter, randomized, double-blind placebo-controlled, phase I/II staggered dose-escalation trial of IFN-K (ClinicalTrials.gov registry number NCT01058343). Patients were randomized to receive 3 or 4 injections placebo (n=7), 30 microg (n=3), 60 microg (n=6), 120 microg (n=6) or 240 microg (n=6) IFN-K. Clinical and safety data, induction of anti-IFNalpha Ab, and gene expression profiling studies up to day 168 after the first IFN-K injection were reported previously (Lauwerys BR et al. Down-regulation of interferon signature in systemic lupus erythematosus patients by active immunization with interferon alpha-kinoid. Arthritis Rheum 2013; 65: 447-56)
In 6 patients, whole blood samples were collected in PAXgene Blood RNA tubes (Qiagen) every 6 months after completion of the initial study. RNA was extracted from these samples, and was also re-extracted from baseline (month 0) and day 168 (month 6) PAXgene tubes stored at -80° from the same patients, and from 10 healthy volunteers

tag: individual

value: Healthy

tag: gender

value: Female

tag: age at baseline

tag: anti-double stranded dna ab titers (farr units/ml)

value: ND

tag: serum c3 (mg/l)

tag: neutralizing anti-interferon alpha antibody titers-1 (100 = undetected)

tag: sledai

tag: physician global assessment (cm, range 0-10)

tag: global bilag score (each a = 9, each b = 3, each c = 1)

tag: agent

value: untreated

tag: tissue

value: whole blood


title: 12 drought d

source_name: Day:12 Treatment:drought  Biorep:D

value: drought

value: D


title: 1 control a

source_name: Day:1 Treatment:control  Biorep:A


title: Whole blood sample, healthy individual, no treatment (01-01-014)


title: Whole blood sample, healthy individual, no treatment (01-01-010)


title: TAX577067


title: 13 drought d

source_name: Day:13 Treatment:drought  Biorep:D


title: Whole blood sample, healthy individual, no treatment (01-01-004)


title: 2 control a

source_name: Day:2 Treatment:control  Biorep:A


title: Input Stress 1, biological replicate 1

city: Toronto

first: James

last: Rutka

state: Ontario

address: 686 Bay Street

department: Cell Biology

country: Canada

institute: Hospital for Sick Children

description: Input Stress 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. CHECK WITH FACILITY

scan_protocol: GeneChips were scanned at The Centre for Applied Genomics (TCAG), SickKids Hospital Toronto, Canada

data_processing: The data were normalized with Affymetrix Expression Console Software using RMA analysis.

label: biotin

source_name: Human Brain

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

growth_protocol: Cells were grown in DMEM media supplemented with 10% FBS

extract_protocol: RNA was extracted with the RNeasy Mini Kit (Qiagen, Cat#74104 ) using the manufacturer's protocol.

treatment_protocol: Cells were treated with 500uM aresenite to induce stress and RNA harvested after 30 minutes. Control cells (non stress) were treated with DMSO and RNA harvested from cells after 30 minutes.

tag: cell line

tag: cell type

value: astrocytoma


title: TAX577426

tag: disease state


title: Whole blood sample, healthy individual, no treatment (01-01-005)


title: 11 drought d

source_name: Day:11 Treatment:drought  Biorep:D

tag: treatment


title: 5 control a

source_name: Day:5 Treatment:control  Biorep:A

tag: time (day)


title: TAX577700


title: Whole blood sample, healthy individual, no treatment (01-01-003)

value: Male


title: 9 drought d

source_name: Day:9 Treatment:drought  Biorep:D

tag: biological replicate


title: TAX577782


title: TAX577181


title: 6 drought d

source_name: Day:6 Treatment:drought  Biorep:D


title: 8 drought d

source_name: Day:8 Treatment:drought  Biorep:D


title: Whole blood sample, SLE patient (060102 T12)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 12 months

tag: patient

value: SLE

value: IFN-K

tag: dose

value: 240 microgram

tag: protocol

value: 4 injections

tag: time

value: 12 months


title: 10 drought d

source_name: Day:10 Treatment:drought  Biorep:D


title: 5 drought d

source_name: Day:5 Treatment:drought  Biorep:D


title: 7 drought d

source_name: Day:7 Treatment:drought  Biorep:D


title: Whole blood sample, SLE patient (060102 T30)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 30 months

tag: gender

tag: age at baseline

tag: anti-double stranded dna ab titers (farr units/ml)

tag: serum c3 (mg/l)

value: 30 months


title: Whole blood sample, SLE patient (030401 T42)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, 42 months

tag: neutralizing anti-interferon alpha antibody titers-1 (100 = undetected)

tag: sledai

tag: physician global assessment (cm, range 0-10)

tag: global bilag score (each a = 9, each b = 3, each c = 1)

value: 120 microgram

value: 3 injections

value: 42 months


title: Whole blood sample, SLE patient (060102 T6)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 6 months

value: Female

tag: agent

value: 6 months

tag: tissue


title: 4 drought d

source_name: Day:4 Treatment:drought  Biorep:D

tag: treatment


title: 3 drought d

source_name: Day:3 Treatment:drought  Biorep:D

tag: time (day)


title: Whole blood sample, SLE patient (030401 T30)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, 30 months

tag: disease state


title: Whole blood sample, SLE patient (060102 T0)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, baseline

tag: patient

value: control

value: baseline (month 0)


title: TAX577365

source_name: breast tumor

value: breast cancer


title: TAX577049


title: TAX577116


title: Whole blood sample, healthy individual, no treatment (01-01-001)

source_name: Healthy individual, in the absence of any treatment

tag: individual

value: Healthy

value: ND

value: untreated

value: whole blood


title: 2 drought d

source_name: Day:2 Treatment:drought  Biorep:D

value: drought

tag: biological replicate

value: D


title: 1 drought d

source_name: Day:1 Treatment:drought  Biorep:D


title: Whole blood sample, SLE patient (030401 T36)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, 36 months

value: SLE

value: IFN-K

tag: dose

tag: protocol

tag: time

value: 36 months


title: TAX577222


title: 13 drought c

source_name: Day:13 Treatment:drought  Biorep:C

value: C


title: 12 drought c

source_name: Day:12 Treatment:drought  Biorep:C


title: Whole blood sample, SLE patient (030401 T0)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, baseline

tag: gender

tag: age at baseline

tag: anti-double stranded dna ab titers (farr units/ml)


title: Whole blood sample, SLE patient (030401 T18)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, 18 months

tag: serum c3 (mg/l)

tag: neutralizing anti-interferon alpha antibody titers-1 (100 = undetected)

tag: sledai

value: 120 microgram

value: 3 injections

value: 18 months


title: Whole blood sample, SLE patient (030401 T6)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, 6 months

value: Female

tag: physician global assessment (cm, range 0-10)

tag: global bilag score (each a = 9, each b = 3, each c = 1)

tag: agent

value: 6 months


title: 11 drought c

source_name: Day:11 Treatment:drought  Biorep:C

tag: treatment

tag: time (day)


title: 9 drought c

source_name: Day:9 Treatment:drought  Biorep:C


title: 8 drought c

source_name: Day:8 Treatment:drought  Biorep:C


title: 10 drought c

source_name: Day:10 Treatment:drought  Biorep:C


title: Whole blood sample, SLE patient (010101 T48)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, 48 months

tag: patient

tag: disease state

value: 30 microgram

value: 48 months

tag: tissue


title: Whole blood sample, SLE patient (030401 T12)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, 12 months

tag: dose

value: 12 months


title: Whole blood sample, SLE patient (010101 T42)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, 42 months

tag: protocol

value: 42 months


title: TAX577484

source_name: breast tumor

value: breast cancer


title: TAX577781


title: TAX577508


title: TAX577280


title: TAX577347


title: TAX577057


title: 7 drought c

source_name: Day:7 Treatment:drought  Biorep:C

tag: biological replicate


title: Whole blood sample, SLE patient (010101 T30)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, 30 months

tag: gender

tag: time

value: 30 months

value: whole blood


title: Whole blood sample, SLE patient (010101 T36)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, 36 months

tag: age at baseline

tag: anti-double stranded dna ab titers (farr units/ml)


title: 6 drought c

source_name: Day:6 Treatment:drought  Biorep:C

value: drought


title: TAX577064


title: 4 drought c

source_name: Day:4 Treatment:drought  Biorep:C


title: Whole blood sample, SLE patient (030401 T24)

source_name: SLE Patient, IFN-K 120 microgram, 3 injections, 24 months

value: SLE

tag: serum c3 (mg/l)

tag: neutralizing anti-interferon alpha antibody titers-1 (100 = undetected)

value: 24 months


title: Whole blood sample, SLE patient (010101 T24)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, 24 months

tag: sledai

tag: physician global assessment (cm, range 0-10)

value: IFN-K


title: Whole blood sample, SLE patient (010101 T18)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, 18 months

tag: global bilag score (each a = 9, each b = 3, each c = 1)

tag: agent


title: 5 drought c

source_name: Day:5 Treatment:drought  Biorep:C

tag: treatment

tag: time (day)

value: C


title: Whole blood sample, SLE patient (010101 T6)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, 6 months

tag: patient

tag: disease state


title: TAX577016


title: TAX577503


title: Whole blood sample, SLE patient (010101 T0)

source_name: SLE Patient, IFN-K 30 microgram, 3 injections, baseline

value: control

value: baseline (month 0)

tag: tissue


title: TAX577557


title: Whole blood sample, SLE patient (030402 T42)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 42 months

tag: dose

value: 240 microgram

tag: protocol

value: 4 injections


title: TAX577335


title: TAX577453


title: Whole blood sample, SLE patient (030402 T33)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 33 months

tag: gender

value: Female

value: 33 months


title: TAX577466


title: TAX577119


title: Whole blood sample, SLE patient (030402 T21)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 21 months

tag: time

value: 21 months


title: Whole blood sample, SLE patient (030402 T30)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 30 months

tag: age at baseline


title: 3 drought c

source_name: Day:3 Treatment:drought  Biorep:C

tag: biological replicate


title: Whole blood sample, SLE patient (030402 T0)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, baseline

tag: anti-double stranded dna ab titers (farr units/ml)

tag: serum c3 (mg/l)


title: TAX577378

source_name: breast tumor


title: Whole blood sample, SLE patient (030402 T12)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 12 months

tag: neutralizing anti-interferon alpha antibody titers-1 (100 = undetected)

tag: sledai

value: 12 months


title: Whole blood sample, SLE patient (030501 T36)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, 36 months

tag: physician global assessment (cm, range 0-10)

tag: global bilag score (each a = 9, each b = 3, each c = 1)

value: 120 microgram

value: 36 months


title: Whole blood sample, SLE patient (030402 T18)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 18 months

tag: agent

value: 18 months


title: Whole blood sample, SLE patient (030402 T6)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 6 months

value: 6 months

value: whole blood


title: TAX577780

value: breast cancer


title: Whole blood sample, SLE patient (030501 T33)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, 33 months

value: SLE


title: TAX577498


title: TAX577173


title: Whole blood sample, SLE patient (030501 T24)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, 24 months

value: IFN-K

value: 24 months


title: Whole blood sample, SLE patient (030501 T30)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, 30 months

value: 30 months


title: TAX577135


title: TAX577652


title: Whole blood sample, SLE patient (030501 T12)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, 12 months


title: TAX577376


title: Whole blood sample, SLE patient (030501 T6)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, 6 months


title: TAX577465


title: 2 drought c

source_name: Day:2 Treatment:drought  Biorep:C

tag: treatment

value: drought

tag: time (day)

value: C


title: Whole blood sample, SLE patient (060101 T36)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 36 months

tag: patient

tag: disease state

value: 240 microgram

value: 4 injections


title: Whole blood sample, SLE patient (060101 T30)

value: Female

tag: dose

tag: tissue


title: TAX577066


title: TAX577515


title: Whole blood sample, SLE patient (030501 T0)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, baseline

tag: gender

value: control

value: baseline (month 0)


title: TAX577073


title: Whole blood sample, SLE patient (060101 T24)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 24 months

tag: protocol

tag: time


title: Whole blood sample, SLE patient (060101 T6)

tag: age at baseline


title: TAX577193


title: TAX577145


title: Whole blood sample, SLE patient (060101 T0)

tag: anti-double stranded dna ab titers (farr units/ml)


title: TAX577476


title: Whole blood sample, lupus nephritis patient (SLE13 T0)

source_name: Lupus nephritis patient, prior to administration of immunosuppressive therapy

extract_protocol: RNA was extracted from blood samples using a Paxgene Blood RNA kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). All samples had a RNA integrity number > 6.

treatment_protocol: SLE patients with a renal BILAG A received conventional immunosuppressive therapy after collection of the baseline renal biopsy (induction with high-dose corticosteroids, IV cyclophosphamide or oral mycophenolate during the first 3 months, followed by maintenance with moderate- to low-dose corticosteroids, azathioprine or mycophenolate).

value: lupus nephritis

tag: date

tag: age

tag: glomerular filtration rate

tag: dsdna ab titers (u/l by farr assay)


title: Whole blood sample, lupus nephritis patient (SLE13 T24)

source_name: Lupus nephritis patient, 6 months after administration of immunosuppressive therapy

tag: sledai

value: immunosuppressive therapy


title: TAX577337


title: TAX577014


title: TAX577163


title: Whole blood sample, SLE patient (030501 T18)

source_name: SLE Patient, IFN-K 120 microgram, 4 injections, 18 months

tag: serum c3 (mg/l)

tag: neutralizing anti-interferon alpha antibody titers-1 (100 = undetected)

tag: physician global assessment (cm, range 0-10)

tag: global bilag score (each a = 9, each b = 3, each c = 1)

tag: agent

value: 120 microgram

value: 18 months


title: TAX577233

source_name: breast tumor

tag: disease state


title: Whole blood sample, lupus nephritis patient (SLE13 T12)

source_name: Lupus nephritis patient, 3 months after administration of immunosuppressive therapy

tag: patient

tag: treatment

value: 3 months

tag: tissue

value: whole blood


title: TAX577779

value: breast cancer


title: Whole blood sample, SLE patient (060101 T12)

source_name: SLE Patient, IFN-K 240 microgram, 4 injections, 12 months

value: SLE

tag: gender

value: IFN-K

tag: dose

tag: protocol

tag: time

value: 12 months


title: Whole blood sample, lupus nephritis patient (SLE12 T24)

tag: date

tag: age

value: 6 months


title: TAX577582


title: Whole blood sample, lupus nephritis patient (SLE12 T0)

tag: glomerular filtration rate

tag: dsdna ab titers (u/l by farr assay)

value: prior to administration of immunosuppressive therapy


title: TAX577277


title: TAX577474


title: TAX577214


title: TAX577281


title: TAX577386


title: Whole blood sample, lupus nephritis patient (SLE11 T0)

tag: sledai


title: TAX577047


title: TAX577245


title: Whole blood sample, lupus nephritis patient (SLE9 T12)


title: TAX577566


title: Whole blood sample, lupus nephritis patient (SLE6 T12)

value: Male


title: Whole blood sample, lupus nephritis patient (SLE6 T24)


title: Whole blood sample, lupus nephritis patient (SLE9 T24)


title: TAX577448


title: TAX577777


title: Whole blood sample, lupus nephritis patient (SLE9 T0)


title: Whole blood sample, lupus nephritis patient (SLE11 T12)


title: TAX577778


title: Whole blood sample, lupus nephritis patient (SLE6 T0)


title: Whole blood sample, lupus nephritis patient (SLE11 T24)


title: Whole blood sample, lupus nephritis patient (SLE5 T24)


title: TAX577597


title: TAX577033


title: TAX577505


title: Whole blood sample, lupus nephritis patient (SLE5 T12)


title: Whole blood sample, lupus nephritis patient (SLE5 T0)


title: TAX577543


title: TAX577018


title: Whole blood sample, lupus nephritis patient (SLE12 T12)


title: Whole blood sample, lupus nephritis patient (SLE3 T0)


title: Whole blood sample, lupus nephritis patient (SLE3 T12)


title: Whole blood sample, lupus nephritis patient (SLE4 T12)


title: Whole blood sample, lupus nephritis patient (SLE3 T24)


title: Whole blood sample, lupus nephritis patient (SLE4 T24)


title: TAX577390


title: TAX577776


title: TAX577752


title: TAX577371


title: Whole blood sample, lupus nephritis patient (SLE4 T0)


title: TAX577279


title: TAX577345


title: Whole blood sample, lupus nephritis patient (SLE2 T12)


title: TAX577331


title: TAX577042


title: TAX577478


title: Whole blood sample, lupus nephritis patient (SLE2 T0)


title: TAX577411


title: Whole blood sample, lupus nephritis patient (SLE2 T24)


title: TAX577775


title: TAX577348


title: ZML(412)

city: Shanghai

first: Zuguang

last: Xia

address: 270 Dong'an Road

country: China

institute: Shanghai Cancer Center

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) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The  processing algorithm used expression console

source_name: DLBCL tissue

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Two samples (CY and ZML) are from pathological tisuue of patients, and another two samples (ZML P1 and CY P1) are from the PDX model.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Stored in liquid nitrogen

value: DLBCL tissue

tag: subject

value: ZML


title: CY P1(CY_P4)

source_name: transplanted DLBCL tissue

value: transplanted DLBCL tissue

value: CY


title: CY(178)


title: Whole blood sample, lupus nephritis patient (SLE1 T0)

value: lupus nephritis

value: Female

value: control


title: TAX577529


title: Whole blood sample, lupus nephritis patient (SLE1 T24)

value: immunosuppressive therapy


title: TAX577412


title: TAX577774


title: KO-3

city: Mont-Saint-Aignan

first: Alain

last: Mareck

address: 2 rue tenieres

department: departement de biologie glycobiologie et matrice extracellulaire végétale

country: France

institute: université de rouen Haute Normandie

description: This sample is of mutant Arabidopsis thaliana. It is the third of five mutant biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.

hyb_protocol: Hybridization was performed overnight at 42°C using a 4-position NimbleGen hybridization system 4

scan_protocol: Slides were scanned using an Axon GenePix 4400 A scanner (molecular Devices Corporatiion, Sunnyvale, CA, USA) piloted by GenePiix pro software (Axon). Scanned images were then imported into Nimblescan software (NimbleGen Systems, Inc. Madison, WI, USA) for grid alignment and expression data analyses.

data_processing: Raw data (.par files)  were normalized using intra-array (RMA background correction) and inter-array (quantile) normalizations using  ANAIS software (Simon & Biot, 2010,  ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics 2010 Oct; 26(19):2468-9).

source_name: Arabidopsis thaliana 96-hours old etiolated hypocotyls, pme3 loss-of- function mutant

label_protocol: Labeling was performed following NimbleGen One-color labeling kit instructions (Roche)

growth_protocol: Etiolated 96-hour-old hypocotyls from wild type and atpme3-1 of Arabidopsis thaliana were used. Sterilized seeds were laid on 9 % agar, incubated for 3 days in the dark at 4°C, then transferred for 6 hours at 20°C in a phytotron with white light (200 µm.m-2.s-1). Finally, petri dishes were kept in the dark for 4 days.

extract_protocol: total RNA was extract using Ambion RNAqueous kit and DNA was removed using the Ambion TURBO-DNAfree kit. RNA was quantified using Nanodrop 1000 spectrophotometer (thermo scientific) and RNA quality was assessed using Eukaryote total RNA Standard Sensitivity chips  on the Experion system (Biorad). All extract protocols were performed at the Centre de Ressources Régionales en Biologie Moléculaire 5Université de picardie Jules Verne, Amiens). RNA concentration was determined using Nanodrop 1000 and RNA quality was assessed using Eukaryote Total RNA standard Sensitivity on the  Experion (Biorad) .

treatment_protocol: Arabidopsis thaliana (Columbia ecotype): wild type/atpme3-1 loss-of-function mutant

tag: ecotype

value: Columbia

tag: genotype

value: atpme3-1 loss-of-function mutant


title: TAX577191

value: breast cancer


title: ZML P1(ZML_P3)


title: TAX577450


title: WT-3

description: This sample is of wild-type Arabidopsis thaliana. It is the third of six wild-type biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.

source_name: Arabidopsis thaliana 96-hours old etiolated hypocotyls, wild type

value: wild-type


title: TAX577305


title: WT-2

description: This sample is of wild-type Arabidopsis thaliana. It is the second of six wild-type biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: A549_DON-treated_rep2

city: Obihiro

first: Takahito

last: Toyotome

state: Hokkaido

address: Nishi 2-11, Inada-cho

department: Diagnostic Center for Animal Health and Food Safety

country: Japan

institute: Obihiro University of Agriculture and Veterinary Medicine

description: Gene expression 24 hours after the treatment with 0.2 microg/mL deoxynivalenol

hyb_protocol: The target solution including 480 ng Cy3-labelled cRNA and blocking agent was used for hybridization. cRNA was hybridized at 65°C for 17 hours. The array slides were washed with Agilent Gene Expression Wash Buffer 1 in room temperature for 1min, and then washed with Agilent Gene Expression Wash Buffer 2 at 37°C for 1min. Finally, the slides were dried.

scan_protocol: The slides were scanned at a resolution of 3 micrometer by Agilent Technologies Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: A549 cells treated with 0.2 microg/mL DON for 24 hours

label_protocol: For labelling, Low Input Quick Amp Labeling Kit (Agilent Technologies) was used. And for purification of labelled cRNA Rneasy mini spin columns (Qiagen) was used.

growth_protocol: The lung epithelial cell line A549 derived from human lung adenocarcinoma was grown at 37°C in Dulbecco's Modified Eagle Medium containing 4.5 g/L glucose and supplemented with 5.958 g/L HEPES, 0.584 g/L L-glutamine, and 0.0159 g/L phenol red in the presence of 5 % CO2.

extract_protocol: Total RNA were recovered by TRI-Reagent using the Direct-zol RNA MiniPrep Kit purchased from Zymo Research Corp. (Irvine, CA).

treatment_protocol: A549 cells (5 × 103) were seeded and grown in DMEM for 24 h, and then treated or not with 0.2 microg/mL DON for another 24 h.

tag: cell line

tag: cell type

value: lung epithelial cells


title: WT-5

description: This sample is of wild-type Arabidopsis thaliana. It is the fifth of six wild-type biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: Whole blood sample, lupus nephritis patient (SLE1 T12)

tag: patient

tag: disease state

value: 3 months

value: whole blood


title: KO-5

description: This sample is of mutant Arabidopsis thaliana. It is the fourth of five mutant biological replicates used in this experiment. Each replicate was obtained separately from the others each and replicate represents about 300 hypocotyles.


title: WT-6

description: This sample is of wild-type Arabidopsis thaliana. It is the sixth of six wild-type biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: KO-2

description: This sample is of mutant Arabidopsis thaliana. It is the second of five mutant biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: A549_nontreated_rep2

source_name: A549 cells (control)


title: WT-4

description: This sample is of wild-type Arabidopsis thaliana. It is the fourth of six wild-type biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: TAX577409


title: TAX577002


title: TAX577773


title: TAX577393


title: A549_nontreated_rep1


title: B v.s. CTL replicate-3

status: Public on Feb 28 2016

city: Taipei

first: Yi-Ping

last: Wang

address: No.1, Changde St., Zhongzheng Dist.

department: Department of Dentistry

country: Taiwan

institute: National Taiwan University Hospital

description: Biological replicate 3 of 4, SAS-LYRIC shRNA (B) vs SAS-control (CTL)

hyb_protocol: The fluorochrome-labeled cDNAs were hybridized on Agilent human GE array 4x44 K using Agilent Gene Expression Hybridization Kit. After hybridization, sildes were washed sequential.

scan_protocol: Scanned on an Agilent G2565CA Microarray Scanner. Images were then quantified using Agilent Feature Extraction Software (version A.10.5.1.1, protocol GE2_105_Dec08)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and  Linear LOWESS normalization.

label: Alexa 647

source_name: B

label_protocol: The cDNAs of B and CTL were reverse transcribed from 15 ug of total RNAs and labeled with Alexa Fluor 647 and Alexa Flour 555, respectively, by SuperScript® Indirect cDNA Labeling System (Life Technologies) following manufacturer's instructions.

growth_protocol: SAS cells transfected with pLKO.1-LYRIC shRNA-B expression vector (desinaged as B) and control SAS cells (transfected with pLKO.1 vector, designated as CTL) were cultured in Dulbecco’s modiﬁed Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 2 μg/ml puromycin, and penicillin plus streptomycin (P/S, Gibco).

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

treatment_protocol: SAS cells were transfected with either lentiviral (packaging plasmid, dR8.91; envolope plasmid, pMG2.G) pLKO.1 vector (designated as CTL) or  transfected with lentiviral pLKO.1-LYRIC shRNA-B expression vector (desinaged as B). Selection of the stable clones were performed by treatment of the cells with 2 μg/ml puromycin for 14 days and were kept subsequently.

value: SAS

tag: transfection

value: pLKO.1-LYRIC shRNA-B

label: Alexa 555

source_name: CTL

value: pLKO.1 vector


title: KO-6

description: This sample is of mutant Arabidopsis thaliana. It is the sixth of five mutant biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: B v.s. CTL replicate-4

description: Biological replicate 4 of 4, SAS-LYRIC shRNA (B) vs SAS-control (CTL)


title: Human Sample 589

status: Public on Feb 27 2016

city: Nedlands

first: Ramesh

last: Ram

state: WA

address: 6 Verdun Street

department: Centre for Diabetes Research

country: Australia

institute: University of Western Australia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with lumi in R
The file Normalized_data.txt contains the log2 transformed and quantile normalized data.

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp 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.

tag: tissue

value: T

tag: condition

tag: Sex

tag: batchid


title: Human Sample 587


title: Human Sample 588


title: Human Sample 586


title: Human Sample 584


title: Human Sample 583


title: Human Sample 580


title: TAX577414


title: WT-1

description: This sample is of wild-type Arabidopsis thaliana. It is the first of six wild-type biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: TAX577302


title: TAX577530


title: B v.s. CTL replicate-1

description: Biological replicate 1 of 4, SAS-LYRIC shRNA (B) vs SAS-control (CTL)


title: Human Sample 577


title: Human Sample 590


title: Human Sample 585

value: DRxx


title: Human Sample 573


title: Human Sample 576


title: Human Sample 570


title: Human Sample 572


title: Human Sample 569


title: TAX577093


title: Human Sample 568


title: Human Sample 566


title: Human Sample 579


title: Human Sample 564


title: B v.s. CTL replicate-2

description: Biological replicate 2 of 4, SAS-LYRIC shRNA (B) vs SAS-control (CTL)


title: Human Sample 563


title: Human Sample 578


title: Human Sample 561


title: Human Sample 562


title: Human Sample 559


title: Human Sample 574


title: Human Sample 557


title: Human Sample 565


title: Human Sample 556


title: Human Sample 555


title: Human Sample 553


title: Human Sample 567


title: Human Sample 552


title: Human Sample 551


title: KO-1

description: This sample is of mutant Arabidopsis thaliana. It is the first of five mutant biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.


title: Human Sample 554


title: Human Sample 545


title: Human Sample 548


title: Human Sample 547


title: Human Sample 549


title: Human Sample 543


title: Human Sample 544


title: Human Sample 542


title: Human Sample 558


title: Human Sample 541


title: Human Sample 540


title: Human Sample 538


title: Human Sample 535


title: Human Sample 546


title: Human Sample 536


title: Human Sample 534


title: Human Sample 550


title: Human Sample 532


title: Human Sample 530


title: Human Sample 529


title: Human Sample 528


title: A549_DON-treated_rep1


title: Human Sample 531


title: Human Sample 527


title: Human Sample 522


title: Human Sample 525


title: Human Sample 523


title: Human Sample 524


title: Human Sample 533


title: Human Sample 521


title: Human Sample 520


title: Human Sample 537


title: Human Sample 519


title: Human Sample 518


title: Human Sample 517


title: Human Sample 516


title: Human Sample 515


title: Human Sample 560


title: Human Sample 513


title: Human Sample 539


title: Human Sample 512


title: Human Sample 511


title: Human Sample 508


title: Human Sample 504


title: Human Sample 509


title: Human Sample 506


title: Human Sample 500


title: Human Sample 526


title: Human Sample 501


title: Human Sample 514


title: Human Sample 505


title: Human Sample 503


title: Human Sample 502


title: Human Sample 507


title: Human Sample 499


title: Human Sample 495


title: Human Sample 496


title: Human Sample 498


title: Human Sample 494


title: Human Sample 493


title: Human Sample 497


title: Human Sample 492


title: Human Sample 491


title: Human Sample 490


title: Human Sample 489


title: Human Sample 488


title: Human Sample 510


title: Human Sample 582


title: Human Sample 486


title: Human Sample 487


title: Human Sample 483


title: Human Sample 480


title: Human Sample 478


title: Human Sample 484


title: Human Sample 485


title: Human Sample 481


title: Human Sample 476


title: Human Sample 474


title: Human Sample 479


title: Human Sample 571


title: Human Sample 472


title: Human Sample 467


title: Human Sample 473


title: Human Sample 575


title: Human Sample 469


title: Human Sample 470


title: Human Sample 471


title: Human Sample 468


title: Human Sample 464


title: Human Sample 465


title: Human Sample 463


title: Human Sample 462


title: Human Sample 482


title: Human Sample 475


title: Human Sample 477


title: Human Sample 459


title: Human Sample 460


title: Human Sample 466


title: Human Sample 456


title: Human Sample 455


title: Human Sample 458


title: Human Sample 452


title: Human Sample 457


title: Human Sample 453


title: Human Sample 451


title: Human Sample 450


title: Human Sample 454


title: Human Sample 446


title: Human Sample 445


title: Human Sample 449


title: Human Sample 444


title: Human Sample 447


title: Human Sample 443


title: Human Sample 440


title: Human Sample 442


title: Human Sample 438


title: Human Sample 441


title: Human Sample 439


title: Human Sample 461


title: Human Sample 437


title: Human Sample 435


title: Human Sample 436


title: Human Sample 432


title: Human Sample 433


title: Human Sample 429


title: Human Sample 430


title: Human Sample 426


title: Human Sample 428


title: Human Sample 581


title: Human Sample 431


title: Human Sample 424


title: Human Sample 423


title: Human Sample 448


title: Human Sample 425


title: Human Sample 422


title: Human Sample 427


title: Human Sample 420


title: Human Sample 421


title: Human Sample 417


title: Human Sample 415


title: Human Sample 418


title: Human Sample 416


title: Human Sample 414


title: Human Sample 413


title: Human Sample 412


title: Human Sample 409


title: Human Sample 410


title: Human Sample 407


title: Human Sample 405


title: Human Sample 404

source_name: whole blood

value: EBV-B

value: Basal


title: Human Sample 403


title: Human Sample 398

value: PMA 6h


title: Human Sample 399


title: Human Sample 400


title: Human Sample 419


title: Human Sample 396


title: Human Sample 402


title: Human Sample 392


title: Human Sample 391


title: Human Sample 394


title: Human Sample 395


title: Human Sample 393


title: Human Sample 411


title: Human Sample 390


title: Human Sample 389


title: Human Sample 401


title: Human Sample 387


title: Human Sample 386


title: Human Sample 408


title: Human Sample 382


title: Human Sample 385


title: Human Sample 384


title: Human Sample 406


title: Human Sample 383


title: Human Sample 381


title: Human Sample 378


title: Human Sample 379


title: Human Sample 380


title: Human Sample 397


title: Human Sample 377


title: Human Sample 376


title: Human Sample 373


title: Human Sample 374


title: Human Sample 371


title: Human Sample 388


title: Human Sample 370


title: Human Sample 369


title: Human Sample 365


title: Human Sample 366


title: Human Sample 367


title: Human Sample 364


title: Human Sample 360


title: Human Sample 362


title: Human Sample 355


title: Human Sample 357


title: Human Sample 361


title: Human Sample 359


title: Human Sample 356


title: Human Sample 358


title: Human Sample 354


title: Human Sample 352


title: Human Sample 375


title: Human Sample 351


title: Human Sample 350


title: Human Sample 372


title: Human Sample 349


title: Human Sample 348


title: Human Sample 368


title: Human Sample 347


title: Human Sample 346


title: Human Sample 345


title: Human Sample 363


title: Human Sample 344


title: Human Sample 342


title: Human Sample 341


title: Human Sample 338


title: Human Sample 340


title: Human Sample 337


title: Human Sample 336


title: Human Sample 335


title: Human Sample 334


title: Human Sample 332


title: Human Sample 333


title: Human Sample 330


title: Human Sample 353


title: Human Sample 329


title: Human Sample 331


title: Human Sample 328


title: Human Sample 327


title: Human Sample 326


title: Human Sample 324


title: Human Sample 325


title: Human Sample 322


title: Human Sample 323


title: Human Sample 321


title: Human Sample 343


title: Human Sample 319


title: Human Sample 339


title: Human Sample 316


title: Human Sample 315


title: Human Sample 317


title: Human Sample 320


title: Human Sample 318


title: Human Sample 314


title: Human Sample 312


title: Human Sample 311


title: Human Sample 313


title: Human Sample 309


title: Human Sample 310


title: Human Sample 307


title: Human Sample 308


title: Human Sample 306


title: Human Sample 305


title: Human Sample 304


title: Human Sample 303


title: Human Sample 302


title: Human Sample 300


title: Human Sample 298


title: Human Sample 299


title: Human Sample 297


title: Human Sample 434


title: Human Sample 294


title: Human Sample 293


title: Human Sample 292


title: Human Sample 290


title: Human Sample 288


title: Human Sample 286


title: Human Sample 291


title: Human Sample 284


title: Human Sample 287


title: Human Sample 283


title: Human Sample 282


title: Human Sample 281


title: Human Sample 279


title: Human Sample 277


title: Human Sample 276


title: Human Sample 278


title: Human Sample 275


title: Human Sample 301


title: Human Sample 274


title: Human Sample 273


title: Human Sample 272


title: Human Sample 271


title: Human Sample 296


title: Human Sample 295


title: Human Sample 269


title: Human Sample 267


title: Human Sample 268


title: Human Sample 266


title: Human Sample 289


title: Human Sample 265


title: Human Sample 285


title: Human Sample 264


title: Human Sample 260


title: Human Sample 261


title: Human Sample 280


title: Human Sample 258


title: Human Sample 257


title: Human Sample 256


title: Human Sample 259


title: Human Sample 252


title: Human Sample 250


title: Human Sample 263


title: Human Sample 249


title: Human Sample 270


title: Human Sample 248


title: Human Sample 247


title: Human Sample 246


title: Human Sample 251


title: Human Sample 255


title: Human Sample 244


title: Human Sample 241


title: Human Sample 242


title: Human Sample 245


title: Human Sample 238


title: Human Sample 243


title: Human Sample 239


title: Human Sample 237


title: Human Sample 240


title: Human Sample 262


title: Human Sample 235


title: Human Sample 234


title: Human Sample 254


title: Human Sample 236


title: Human Sample 233


title: Human Sample 229


title: Human Sample 232


title: Human Sample 253


title: Human Sample 227


title: Human Sample 230


title: Human Sample 226


title: Human Sample 225


title: Human Sample 224


title: Human Sample 222


title: Human Sample 223


title: Human Sample 219


title: Human Sample 220


title: Human Sample 221


title: Human Sample 216


title: Human Sample 218


title: Human Sample 214


title: Human Sample 212


title: Human Sample 217


title: Human Sample 215


title: Human Sample 231


title: Human Sample 213


title: Human Sample 210


title: Human Sample 228


title: Human Sample 211


title: Human Sample 209


title: Human Sample 205


title: Human Sample 208


title: Human Sample 206


title: Human Sample 203


title: Human Sample 202


title: Human Sample 204


title: Human Sample 207


title: Human Sample 198


title: Human Sample 200


title: Human Sample 197


title: Human Sample 201


title: Human Sample 195


title: Human Sample 196


title: Human Sample 194


title: Human Sample 193


title: Human Sample 191


title: Human Sample 192


title: Human Sample 189


title: Human Sample 190


title: Human Sample 187


title: Human Sample 188


title: Human Sample 186


title: Human Sample 184


title: Human Sample 183


title: Human Sample 182


title: Human Sample 185


title: Human Sample 181


title: Human Sample 179


title: Human Sample 180


title: Human Sample 176


title: Human Sample 177


title: Human Sample 175


title: Human Sample 172


title: Human Sample 173


title: Human Sample 171


title: Human Sample 174


title: Human Sample 168


title: Human Sample 167


title: Human Sample 166


title: Human Sample 165


title: Human Sample 164


title: Human Sample 158


title: Human Sample 159


title: Human Sample 157


title: Human Sample 161


title: Human Sample 160


title: Human Sample 178


title: Human Sample 156


title: Human Sample 199


title: Human Sample 154


title: Human Sample 155


title: Human Sample 162


title: Human Sample 152


title: Human Sample 150


title: Human Sample 149


title: Human Sample 151


title: Human Sample 147


title: Human Sample 153


title: Human Sample 148


title: Human Sample 163


title: Human Sample 145


title: Human Sample 170


title: Human Sample 143


title: Human Sample 144


title: Human Sample 169


title: Human Sample 146


title: Human Sample 141


title: Human Sample 142


title: Human Sample 140


title: Human Sample 139


title: Human Sample 137


title: Human Sample 131


title: Human Sample 136


title: Human Sample 134


title: Human Sample 133


title: Human Sample 135


title: Human Sample 132


title: Human Sample 130


title: Human Sample 128


title: Human Sample 125


title: Human Sample 126


title: Human Sample 121


title: Human Sample 129


title: Human Sample 120


title: Human Sample 123


title: Human Sample 127


title: Human Sample 114


title: Human Sample 119


title: Human Sample 116


title: Human Sample 124


title: Human Sample 113


title: Human Sample 117


title: Human Sample 138


title: Human Sample 111


title: Human Sample 110


title: Human Sample 112


title: Human Sample 115


title: Human Sample 118


title: Human Sample 109


title: Human Sample 105


title: Human Sample 106


title: Human Sample 104


title: Human Sample 107


title: Human Sample 102


title: Human Sample 101


title: Human Sample 103


title: Human Sample 100


title: Human Sample 97


title: Human Sample 122


title: Human Sample 99


title: Human Sample 96


title: Human Sample 94


title: Human Sample 93


title: Human Sample 98


title: Human Sample 88


title: Human Sample 91


title: Human Sample 92


title: Human Sample 89


title: Human Sample 87


title: Human Sample 83


title: Human Sample 84


title: Human Sample 81


title: Human Sample 86


title: Human Sample 85


title: Human Sample 108


title: Human Sample 78


title: Human Sample 82


title: Human Sample 79


title: Human Sample 76


title: Human Sample 77


title: Human Sample 75


title: Human Sample 74


title: Human Sample 73


title: Human Sample 95


title: Human Sample 71


title: Human Sample 69


title: Human Sample 70


title: Human Sample 68


title: Human Sample 67


title: Human Sample 90


title: Human Sample 65


title: Human Sample 63


title: Human Sample 64


title: Human Sample 66


title: Human Sample 61


title: Human Sample 62


title: Human Sample 60


title: Human Sample 80


title: Human Sample 57


title: Human Sample 58


title: Human Sample 72


title: Human Sample 56


title: Human Sample 53


title: Human Sample 55


title: Human Sample 52


title: Human Sample 51


title: Human Sample 50


title: Human Sample 59


title: Human Sample 49


title: Human Sample 47


title: Human Sample 46


title: Human Sample 45


title: Human Sample 54


title: Human Sample 43


title: Human Sample 42


title: Human Sample 44


title: Human Sample 48


title: Human Sample 41


title: Human Sample 40


title: Human Sample 38


title: Human Sample 37


title: Human Sample 36


title: Human Sample 35


title: Human Sample 39


title: Human Sample 34


title: Human Sample 33


title: Human Sample 32


title: Human Sample 31


title: Human Sample 30


title: L10_358

city: Amsterdam

first: Robin

last: Struijk

address: Meibergdreef 9-15

department: Center for Reproductive Medicine

country: Netherlands

institute: AMC Amsterdam

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

scan_protocol: BeadChip images were scanned using an Illumina iScan array scanner and data was extracted into the GenomeStudio using default analysis settings

data_processing: GenomeStudio v2011.1, Methylation Module v1.9.0. Raw data can be found in the idat files and in the file "Unmethylated_and_methylated_signal.txt" available on the series record.

source_name: Seminoma

label_protocol: Standard Illumina Protocol

growth_protocol: SSCs were isolated from testicular biopsies using a two step enzymatic digestion and cultured in StemPro34 medium in the presence of GDNF, FGF, LIF and EGF.

extract_protocol: Genomic DNA was isolated from ITGA6+ SSC fractions using the QIAamp DNA Mini Kit and eluted in low-TE buffer

tag: gender

value: m

value: seminoma

tag: batch


title: URO0034_sperm

source_name: eSPT

value: testicular elongated spermatids


title: L11_123


title: URO0179_d63

source_name: PTC, cultured, 63 days

value: primary testicular cells, itga6+


title: URO0246_d1

source_name: PTC, cultured, 1 day


title: Human Sample 29


title: URO0077_sperm


title: URO0179_d13

source_name: PTC, cultured, 13 days


title: URO0246_d13


title: L11_119


title: Human Sample 27


title: URO0246_sperm


title: URO0246_d63


title: URO0246_d3

source_name: PTC, cultured, 3 days


title: Human Sample 26


title: URO0034_d63_rep2


title: Human Sample 24


title: URO0246_d0.2

source_name: PTC, cultured, 4 hours


title: URO0246_d0

source_name: PTC, fresh isolation


title: URO0179_sperm


title: URO0179_d0


title: Human Sample 22


title: URO0077_d1


title: Human Sample 23


title: URO0179_d0.2


title: Human Sample 21


title: URO0179_d1


title: URO0179_d3


title: URO0077_d13


title: Human Sample 20


title: URO0034_d13


title: URO0034_d3


title: URO0077_d0.2


title: URO0034_d0.2


title: URO0077_d0_rep2


title: URO0077_d63_rep2


title: Human Sample 28


title: Human Sample 17


title: URO0077_d3


title: Human Sample 15


title: Human Sample 16


title: Human Sample 14


title: Human Sample 13


title: Human Sample 19


title: URO0034_d63_rep1


title: URO0034_d0_rep1


title: Human Sample 12


title: URO0034_d0_rep2


title: URO0034_d1


title: 60 min Au-NP 320 µM, rep 1

city: Halle/Saale

first: Cornelia

last: Große

department: Faculty of Biology/Microbiology

country: Germany

hyb_protocol: Hybridisation was done by the service provider IMGM Laboratories GmbH (Martinsried)

scan_protocol: Agilent DNA microarray Scanner were used by the service provider IMGM Laboratories GmbH (Martinsried)

data_processing: The mean intensity of the pixels of the surrounding area was subtracted from the mean density of the pixels of the spots to give the signal strength

organism: Cupriavidus metallidurans CH34

source_name: cells of C. metallidurans

label_protocol: Labeling was done by the service provider IMGM Laboratories GmbH (Martinsried)

growth_protocol: C. metallidurans cultures were grown in Mineral salts medium + 0.2 % Na-gluconate to a cell turbidity of 100 Klett, metal species added, incubated for 10-60 min, then harvest cells by centrifugation for 1' in 2.0 ml Tubes.

extract_protocol: RNeasy Mini Kit (Qiagen) was used according to the manufacturers manual including on-column DNase digestion. PCR were done to check for DNA contaminations, only RNA was used that did not generate products in the PCR reaction. RNA quality was checked on formamide gels and measured as RIN on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: genotype/variation

value: wild type


title: Human Sample 11


title: MKN28/STAT3c 2

city: Chia-Yi

first: Jora

middle: Meng-Ju

last: Lin

address: 168 UNiversity Road,Min Hsiung

institute: National Chung Cheng University

description: Gene expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MKN28 cells transfected with STAT3c

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MKN28 cells were maintained in RPMI-1640 medium supplemented with 10% FBS. Cells were incubated at 37C under a humidified atmosphere containing 5% CO2

extract_protocol: RNA extraction was performed using TriZol reagent (Invitrogen, Cat. no. 15596-026) according to the manufactuerer’s protocol. After removing the culture medium, cells were washed with 1×PBS twice following lysed by adding 1ml of Trizol reagent directly to the culture dish, the lysate was transfered to a 1.5ml micro centrifuge tube. 0.2 ml of chloroform was then added and the mixture was shaked vigorously for 20s and incubated them at room temperature for 3min. Sample was then centrifuged at 12,000×g for 10min at 4°C. After centrifugation, the mixture was separated into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase where RNA located. The aqueous phase was then transferred to a new 1.5ml micro centrifuge tube where RNA was precipitated by mixing with 0.5 ml isopropyl alcohol. Samples were then incubated at room temperature for 10 minutes and centrifuged at 12,000 × g for 10 min at 4°C. After removing the supernatant, RNA pellet was washed once with 1ml 75% ethanol, and centrifuged at 9,000 x g for 5 minutes at 4°C. Finally RNA was dried briefly, and dissolved in RNase-free water and stored at -70°C until further experiment.

treatment_protocol: MKN28 cells were either transfected with pcDNA3.1 (control) or plasmid overexpressing STAT3c. Stable clones were selected using medium containing 400ug/ml G418.

value: gastric cancer

value: plasmid overexpressing STAT3c


title: 10 min Pt(IV)chloride 50 µM, rep 3


title: MKN28/pcDNA3.1  2

description: Gene expression

source_name: MKN28 cells transfected with control

value: pcDNA3.1 (vector control)


title: Human Sample 25

value: whole blood


title: 10 min Pt(IV)chloride 50 µM, rep 2


title: MKN28/pcDNA3.1 1

description: Gene expression


title: MKN28/STAT3c 1

description: Gene expression


title: Human Sample 09


title: Human Sample 10


title: URO0077_d0_rep1


title: URO0077_d63_rep1


title: 10 min Pt(IV)chloride 50 µM, rep 1


title: 10 min cisplatin 50 µM, rep 2


title: URO0059_d0


title: 10 min cisplatin 50 µM, rep 3


title: Human Sample 05


title: Human Sample 07


title: Human Sample 04


title: 10 min cisplatin 50 µM, rep 1


title: Human Sample 03


title: Human Sample 01


title: Human Sample 06


title: Mel_12_1254_CD271+

city: Parkville

first: Vincent

middle: Dominique

last: Corbin

state: VIC

address: 1G Royal parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute

description: PDX melanoma tumor was SNP genotyped on an Illumina HumanOmni2.5-8v1.1 Genotyping BeadChips.

hyb_protocol: according to the Illumina protocol

scan_protocol: i-scan

data_processing: Genomic DNA extracted from purified human melanoma cells was genotyped using Infinium HD HumanOmni2.58 or HTS HumanOmniExpress (Illumina) beadchips and prepared for analysis using GenomeStudio data analysis software

label_protocol: according to the Illumina protocol

extract_protocol: Extraction of genomic DNA from snap-frozen purified cell pellets was performed using the Qiagen Dneasy Blood and Tissue kit, according to the manufacturer's instructions

tag: sample type

value: CD271+ purified cells

value: primary human melanoma (stage 3)


title: Mel_12_1254_CD271-

value: CD271- purified cells


title: URO0190_d0


title: URO0038_d63


title: Aichi H3N2

type: other

city: Potsdam

first: Henry

last: Memczak

address: Karl Liebknecht Straße 24/25

institute: University of Potsdam

hyb_protocol: Labeled analytes were incubated several hours or overnight at indicated concentrations using Femtotip buffer (FTP)30 (20 mM Tris, 30% glycerol, 3% polyvinylpyrrolidon 90, 0.1% Tween 20, pH 8.4) for dilution. The slides were washed twice in FTP and twice in ultrapure water and subsequently dried under a stream of nitrogen.

scan_protocol: Fluorescence measurements were performed using an Axon 4200A Laser Scanner (Molecular Devices) with 10 µm resolution.

data_processing: Fluorescence intensity was evaluated using GenePix Pro 6.0 software, contrasts were calculated using the formula C = (I_S - I_NC)/(I_S + I_NC), where I_S represents the relative fluorescence intensity (background substracted) of a sample spot and I_NC the relative fluorescence intensity of an appropriate negative control spot.

molecule: other

organism: unidentified influenza virus

source_name: virus isolate

label_protocol: For the labeling of proteins with a fluorescent dye, Dyomics DY-634 (λex = 635 nm, λem = 654 nm, Fluoro-spin 634 Kit (emp Biotech) was used, according to the manufacturer´s instructions.

growth_protocol: Influenza strain A/Aichi/2/68 H3N2 X31 (Aichi H3N2), reassorted with A/PuertoRico/8/1934 H1N1 were harvested from allantoic fluid of hen eggs.

extract_protocol: Virus isolates were clarified upon low speed centrifugation (300 x g, 10 min) and concentrated by ultracentrifugation (100 000 x g, 1 h). For safety reasons, viruses prepared for SPR experiments were inactivated by 5 min irradiation with UV-light on ice. Infectivity of inactivated virus was precluded using MDCK II based cell-assays, remaining binding ability of HA was proven using standard hemagglutination assay (HA) with human red blood cells.

tag: production

value: allantoic fluid from hen eggs

tag: deactivation

value: UV light

tag: manufacturer

value: DL, AH

tag: molecule subtype

value: virus and virus fragments


title: ST13_tumor

description: PDX melanoma tumor was SNP genotyped on an Illumina HumanOmniExpress-12v1 Genotyping BeadChips.

value: tumor

value: patient-derived xenograft


title: URO0038_d0

value: m


title: NewYork H3N2

source_name: monovalent split vaccine

value: formalin

value: GlaxoSmithKline


title: California H1N1


title: Victoria H3N2


title: Human Sample 02

value: EBV-B

value: Basal


title: URO0190_d63

value: primary testicular cells, itga6+


title: Mel_12_1036_CD271-


title: Mel_12_1036_CD271+


title: Mel_12_736_CD271+


title: ST11_tumor

source_name: M12-1254_CD271+_Quintana_10 cells


title: ST10_tumor


title: Mel_404_CD271-


title: ST12_tumor


title: Mel_12_736_CD271-


title: ST7_tumor


title: Human Sample 08

value: PMA 6h


title: Mel_13_609_CD271-


title: Mel_13_609_CD271+


title: ST6_tumor


title: URO0059_d63


title: ST4_tumor


title: Mel_404_CD271+


title: ST3_tumor


title: Human Sample 18

value: whole blood


title: Q0990.bdl vs Q0990.Col-6d-replicate 2

status: Public on Feb 26 2016

city: saskatoon

first: daoquan

last: xiang

state: SK

address: 110 Gymnasium Place

institute: NRC Saskatoon

description: aRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750).

hyb_protocol: Hybridized to these slides following the protocol described in http://ag.arizona.edu/microarry.

scan_protocol: ScanArray 4000 laser scanner

data_processing: The image analysis and signal quantification were performed using the QuantArray orogram (GSI Lumonics, Oxford, California)

source_name: 6days of Q0990.bdl

label_protocol: After purification of the aRNA, the NHS-ester dyes were coupled to the modified bases of aRNA in a chemical reaction. The aRNA samples representing four biological replicates from each experiment were labeled (2 cy3 and 2 cy5) following the protocol described inhttp://ag.arizona.edu/microarray.

growth_protocol: Plants were grown under 16h light / 8h dark photoperiod with constant temperature of 220C at 120 μE m-2 s-1 light intensity

extract_protocol: Total RNA extracted using RNAqueous-Micro kit  following manufacturer's instructions

treatment_protocol: embryos isolated from 6 days of pollination, Q0990 is female and bdl is male

tag: ecotype

tag: tissure

value: isolated embryo of Q0990Xbdl

tag: stock lines

value: Q0990 and bdl

source_name: 6 daysQ0990.Col-0

treatment_protocol: embryos isolated from 6 days of pollination, Q0990 is female and Col-0 is male

value: Q0990 and Col-0

value: embryo


title: Invasive Micropapillary Carcinoma [IMPC_82]

city: Paris

first: Nadège

last: GRUEL

address: 26 rue d'Ulm

department: Translational Research and U830 INSERM Unit

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: The array data were simultaneously normalised using the GC robust multiarray average (GCRMA) package 1.2 in the R environment (R Development Core Team) with Brainarray annotations (V.16.0.0, ENTREZG)

source_name: training set_IMPC

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

tag: sample source set

value: training set

value: Breast

tag: tissue subtype

value: Invasive Micropapillary Carcinoma


title: Q0990.bdl vs Q0990.Col-6d-replicate 1

tag: tissue


title: Q0990.bdl vs Q0990.Col-6d-replicate 3


title: Q0990.bdl vs Q0990.Col-3d-replicate 4

source_name: 3days of Q0990.bdl

treatment_protocol: embryos isolated from 3 days of pollination, Q0990 is female and bdl is male

source_name: 3 days Q0990.Col-0

treatment_protocol: embryos isolated from 3 days of pollination, Q0990 is female and Col-0 is male


title: Invasive Micropapillary Carcinoma [IMPC_85]


title: Invasive Micropapillary Carcinoma [IMPC_83]

source_name: validation set_IMPC

value: validation set


title: Invasive Micropapillary Carcinoma [IMPC_75]


title: Invasive Micropapillary Carcinoma [IMPC_74]


title: Invasive Micropapillary Carcinoma [IMPC_89]


title: Invasive Micropapillary Carcinoma [IMPC_86]


title: Invasive Micropapillary Carcinoma [IMPC_70]


title: Invasive Micropapillary Carcinoma [IMPC_08]


title: Q0990.bdl vs Q0990.Col-3d-replicate 3


title: Invasive Micropapillary Carcinoma [IMPC_84]


title: Invasive Micropapillary Carcinoma [IMPC_88]


title: Invasive Micropapillary Carcinoma [IMPC_81]


title: Invasive Micropapillary Carcinoma [IMPC_69]


title: Q0990.bdl vs Q0990.Col-3d-replicate 1


title: Q0990.bdl vs Q0990.Col-6d-replicate 4


title: Invasive Micropapillary Carcinoma [IMPC_90]


title: Invasive Micropapillary Carcinoma [IMPC_80]


title: Q0990.bdl vs Q0990.Col-3d-replicate 2


title: Invasive Micropapillary Carcinoma [IMPC_77]


title: Invasive Micropapillary Carcinoma [IMPC_78]


title: Invasive Micropapillary Carcinoma [IMPC_87]


title: Invasive Micropapillary Carcinoma [IMPC_72]


title: Invasive Micropapillary Carcinoma [IMPC_68]


title: Invasive Micropapillary Carcinoma [IMPC_66]


title: Invasive Micropapillary Carcinoma [IMPC_56]


title: Invasive Micropapillary Carcinoma [IMPC_55]


title: Invasive Micropapillary Carcinoma [IMPC_59]


title: Invasive Micropapillary Carcinoma [IMPC_65]


title: Invasive Micropapillary Carcinoma [IMPC_48]


title: Invasive Micropapillary Carcinoma [IMPC_60]


title: Invasive Micropapillary Carcinoma [IMPC_54]


title: Invasive Micropapillary Carcinoma [IMPC_43]


title: Invasive Micropapillary Carcinoma [IMPC_35]


title: Invasive Micropapillary Carcinoma [IMPC_36]


title: Invasive Micropapillary Carcinoma [IMPC_47]


title: Invasive Micropapillary Carcinoma [IMPC_42]


title: Invasive Micropapillary Carcinoma [IMPC_53]


title: Invasive Micropapillary Carcinoma [IMPC_46]


title: Invasive Micropapillary Carcinoma [IMPC_38]


title: Invasive Micropapillary Carcinoma [IMPC_41]


title: Invasive Micropapillary Carcinoma [IMPC_58]


title: Invasive Micropapillary Carcinoma [IMPC_45]


title: Invasive Micropapillary Carcinoma [IMPC_64]


title: Invasive Micropapillary Carcinoma [IMPC_57]


title: Invasive Micropapillary Carcinoma [IMPC_50]


title: Invasive Micropapillary Carcinoma [IMPC_39]


title: Invasive Micropapillary Carcinoma [IMPC_33]


title: Invasive Micropapillary Carcinoma [IMPC_61]


title: Invasive Micropapillary Carcinoma [IMPC_51]


title: Invasive Micropapillary Carcinoma [IMPC_32]


title: Invasive Micropapillary Carcinoma [IMPC_37]


title: Invasive Micropapillary Carcinoma [IMPC_49]


title: Invasive Micropapillary Carcinoma [IMPC_52]


title: Invasive Carcinoma No Special Type [ICNST_522408]

source_name: training set_ICNST

value: Invasive Carcinoma No Special Type


title: Invasive Micropapillary Carcinoma [IMPC_44]


title: Invasive Carcinoma No Special Type [ICNST_458869]

source_name: validation set_ICNST


title: Invasive Carcinoma No Special Type [ICNST_480143]


title: Invasive Carcinoma No Special Type [ICNST_437543]


title: Invasive Carcinoma No Special Type [ICNST_497927]


title: Invasive Carcinoma No Special Type [ICNST_495996]


title: Invasive Carcinoma No Special Type [ICNST_513970]


title: Invasive Micropapillary Carcinoma [ICNST_432564]


title: Invasive Carcinoma No Special Type [ICNST_492706]


title: Invasive Carcinoma No Special Type [ICNST_494274]


title: Invasive Carcinoma No Special Type [ICNST_497442]


title: Invasive Carcinoma No Special Type [ICNST_515202]


title: Invasive Carcinoma No Special Type [ICNST_455012]


title: Invasive Carcinoma No Special Type [ICNST_518119]


title: Invasive Carcinoma No Special Type [ICNST_488469]


title: Invasive Carcinoma No Special Type [ICNST_476155]


title: Invasive Carcinoma No Special Type [ICNST_473309]


title: Invasive Carcinoma No Special Type [ICNST_452610]


title: Invasive Carcinoma No Special Type [ICNST_504600]


title: Invasive Carcinoma No Special Type [ICNST_469625]


title: Invasive Carcinoma No Special Type [ICNST_515470]


title: Invasive Carcinoma No Special Type [ICNST_457330]


title: Invasive Carcinoma No Special Type [ICNST_488894]


title: Invasive Carcinoma No Special Type [ICNST_501669]


title: Invasive Carcinoma No Special Type [ICNST_513036]


title: Invasive Carcinoma No Special Type [ICNST_434364]


title: Invasive Carcinoma No Special Type [ICNST_472800]


title: Invasive Carcinoma No Special Type [ICNST_492789]


title: Invasive Carcinoma No Special Type [ICNST_482981]


title: Invasive Carcinoma No Special Type [ICNST_D30]


title: Invasive Carcinoma No Special Type [ICNST_D24]


title: Invasive Carcinoma No Special Type [ICNST_439455]


title: Invasive Carcinoma No Special Type [ICNST_D22]


title: Invasive Micropapillary Carcinoma [IMPC_31]


title: Invasive Carcinoma No Special Type [ICNST_C58]


title: Invasive Carcinoma No Special Type [ICNST_D18 ]


title: Invasive Micropapillary Carcinoma [IMPC_09]


title: Invasive Carcinoma No Special Type [ICNST_C40]


title: Invasive Micropapillary Carcinoma [IMPC_28]


title: Invasive Micropapillary Carcinoma [IMPC_06]


title: Invasive Micropapillary Carcinoma [IMPC_26]


title: Invasive Micropapillary Carcinoma [IMPC_21]


title: Invasive Micropapillary Carcinoma [IMPC_19]


title: Invasive Micropapillary Carcinoma [IMPC_27]


title: Invasive Carcinoma No Special Type [ICNST_D19]


title: Invasive Carcinoma No Special Type [ICNST_D17]


title: Invasive Carcinoma No Special Type [ICNST_D20]


title: Invasive Micropapillary Carcinoma [IMPC_29]


title: Invasive Micropapillary Carcinoma [IMPC_30]


title: Invasive Micropapillary Carcinoma [IMPC_20]


title: Invasive Carcinoma No Special Type [ICNST_D02]


title: Invasive Carcinoma No Special Type [ICNST_C57]


title: Invasive Carcinoma No Special Type [ICNST_C21]


title: Invasive Carcinoma No Special Type [ICNST_D39]


title: Invasive Carcinoma No Special Type [ICNST_C23]


title: Invasive Carcinoma No Special Type [ICNST_C34]


title: Invasive Carcinoma No Special Type [ICNST_D07]


title: Invasive Carcinoma No Special Type [ICNST_D01]


title: Invasive Carcinoma No Special Type [ICNST_C09]


title: Invasive Carcinoma No Special Type [ICNST_C51]


title: Invasive Carcinoma No Special Type [ICNST_C10]


title: Invasive Carcinoma No Special Type [ICNST_C14]


title: Invasive Micropapillary Carcinoma [IMPC_05]


title: Invasive Carcinoma No Special Type [ICNST_C02]


title: Invasive Micropapillary Carcinoma [IMPC_18]


title: Invasive Micropapillary Carcinoma [IMPC_12]


title: Invasive Micropapillary Carcinoma [IMPC_13]


title: Invasive Micropapillary Carcinoma [IMPC_01]


title: Invasive Micropapillary Carcinoma [IMPC_10]


title: Invasive Micropapillary Carcinoma [IMPC_14]


title: Invasive Micropapillary Carcinoma [IMPC_04]


title: c4.Pten&Tgfbr2KO-5

city: New York

first: Robert

middle: F

last: Schwabe

state: NY

address: 1150 st Nicholas Av

department: Medicine

country: USA

institute: Columbia University

hyb_protocol: 60 ul (25 ng/ul) of fragemented and labeled cDNA was hybridized to Mouse Genome 1.0ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm as implemented in Bioconductor/R.

organism: Mus musculus

source_name: Liver from hepatocyte-specific knockout of Pten and Tgfbr2 in C57Bl/6 genetic background

label_protocol: 150 ng RNA was amplified, biotin labeled and fragmented using the Ambion WT Expression kit and GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by column purification (Roche) and quantification by NanoDrop spectrophotometer.

treatment_protocol: AAV8-TBG-Cre was injected into PTEN floxed (PTEN ΔHep) mice and PTEN, Tgfbr2 double-floxed mice (TBR2/PTEN ΔHep). Mice were sacrficed ten months after AAV injection.

value: Male

tag: strain

value: Liver

value: hepatocyte-specific Pten-/- Tgfbr2-/-


title: Invasive Micropapillary Carcinoma [IMPC_16]


title: c3.Pten&Tgfbr2KO-4


title: Invasive Micropapillary Carcinoma [IMPC_17]


title: 0.02Gy (long-term effect)

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description: Low-dose irradiation of LT-HSC from mouse bone marrow.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomics Suite.

source_name: LT-HSC bone marrow, 0.02 Gy γ-irradiation, 6 month

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the Affymetrix GeneChip Whole Transcript (WT) Sense Target labelling assay kit).

extract_protocol: RNeasy-micro mRNA purification kit (QIAGEN), according to manufacturer's instruction.

treatment_protocol: Lin- ckit+ Sca+ cells were irradiated at 0Gy, 0.02Gy, 0.1Gy, and 0.5Gy and transplanted into lethally irradiated mice. Six months after transplantation, LT-HSCs (Lin- ckit+ Sca+ Flk2- CD48-CD150+) were sorted.

value: bone marrow

tag: cell type

value: long-term hematopoietic stem cells (Lin- ckit+ Sca+ Flk2- CD48-CD150+)

tag: irradiation dose

tag: time point

value: 6 months after transplantation


title: Ctrl (long-term effect)

description: No irradiation of LT-HSC from mouse bone marrow.

source_name: LT-HSC bone marrow, 0.00 Gy γ-irradiation, 6 month


title: b3.PtenKO-9

source_name: Liver from hepatocyte-specific knockout of Pten in C57Bl/6 genetic background

tag: gender

value: hepatocyte-specific Pten-/-


title: b4.PtenKO-12

tag: genotype/variation


title: 2.5Gy (immediate response)

description: High-dose irradiation of LT-HSC from mouse bone marrow.

source_name: LT-HSC bone marrow, 2.50 Gy γ-irradiation, 2 hr

growth_protocol: LT-HSCs (Lin- ckit+ Sca+ Flk2- CD48-CD150+) were sorted and incubated O.N. in Stemspan SFEM medium prior to irradiation.

treatment_protocol: LT-HSC were irradiated at 0Gy, 0.02Gy and 2.5Gy. Two hours after irradiation, mRNA was extracted.


title: a2.3-WT2_4

source_name: Normal liver from C57Bl/6 mice

value: WT


title: a3.WT-3


title: c2.Pten&Tgfbr2KO-2


title: 0.5Gy (long-term effect)

description: 0.5 Gy dose irradiation of LT-HSC from mouse bone marrow.

source_name: LT-HSC bone marrow, 0.50 Gy γ-irradiation, 6 month


title: Ctrl (immediate response)

source_name: LT-HSC bone marrow, 0.00 Gy γ-irradiation, 2 hr


title: 0.02Gy (immediate response)

source_name: LT-HSC bone marrow, 0.02 Gy γ-irradiation, 2 hr


title: c1.Pten&Tgfbr2KO-1


title: a1.WT-1


title: b2.PtenKO-6


title: b1.PtenKO-3


title: Pax7-/- ESCs day 21, biological rep 2

city: Warsaw

first: Areta

middle: Magda

last: Czerwinska

address: Krakowskie Przedmiescie 26/28

department: Faculty of Biology

country: Poland

institute: University of Warsaw

description: Gene expression data

hyb_protocol: According to manufacturer's protocol.

scan_protocol: The chips were scanned using the Affymetrix GeneAtlas scanner according to manufacturer's protocol.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

source_name: embryoid body outgrowths at day 21 of differentiation_Pax7-/-

label_protocol: According to manufacturer's protocol.

growth_protocol: ESCs were cultured under standard conditions, i.e. KO-DMEM containing all necessary supplements and LIF. Embryoid bodies and embryoid body outgrowths were cultured in KO-DMEM containing all necessary supplements, lacking LIF and supplemented with RA and ITS

extract_protocol: Total RNA was extracted using High Pure RNA isolation kit (Roche) according to manufacturer's protocol.

treatment_protocol: Material was callected at day 0 (undeifferentiated ESCs) and at day 7 and 21 of differentiation. Cells were washed with PBS and frozen in -80C.

tag: genotype

tag: cells

value: embryoid body outgrowths


title: Pax7-/- ESCs day 7, biological rep 3

description: Gene expression data

source_name: embryoid bodies at day 7 of differentiation_Pax7-/-

value: embryoid bodies


title: Pax7-/- ESCs day 21, biological rep 3

description: Gene expression data


title: Pax7-/- ESCs day 21, biological rep 1

description: Gene expression data


title: Pax7-/- ESCs day 0, biological rep 2

description: Gene expression data

source_name: undifferentiated ESCs_Pax7-/-

value: ESCs


title: Pax7-/- ESCs day 7, biological rep 2

description: Gene expression data


title: Pax7-/- ESCs day 0, biological rep 1

description: Gene expression data


title: Pax7-/- ESCs day 0, biological rep 3

description: Gene expression data


title: Pax7+/+ ESCs day 21, biological rep 2

description: Gene expression data

source_name: embryoid body outgrowths at day 21 of differentiation_wildtype


title: Pax7+/+ ESCs day 0, biological rep 3

description: Gene expression data

source_name: undifferentiated ESCs_wildtype


title: Pax7+/+ ESCs day 0, biological rep 2

description: Gene expression data


title: Pax7+/+ ESCs day 7, biological rep 2

description: Gene expression data

source_name: embryoid bodies at day 7 of differentiation_wildtype


title: Pax7+/+ ESCs day 7, biological rep 3

description: Gene expression data


title: Pax7+/+ ESCs day 21, biological rep 1

description: Gene expression data


title: Pax7+/+ ESCs day 0, biological rep 1

description: Gene expression data


title: Pax7+/+ ESCs day 7, biological rep 1

description: Gene expression data


title: Pax7-/- ESCs day 7, biological rep 1

description: Gene expression data


title: Pax7+/+ ESCs day 21, biological rep 3

description: Gene expression data


title: Patient 2 normal

city: Beijing

first: Chong

last: Li

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: The expression profiles of circRNA were compared between liver cancer and its adjacent normal tissues

hyb_protocol: The Cy3TM-labeled samples were hybridizedaccording to the manufacturer’s protocol (Arraystar Inc).

scan_protocol: The slides were scanned usingthe Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed.

source_name: Normal liver tissue

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer’s guideline for CircRNA labelling.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including CircRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: age

tag: Sex

value: Female

tag: tumor stage

tag: tissue type

value: normal liver tissue


title: Patient 3 normal


title: PER117 post Decitabine_2

city: Berlin

first: Lars

last: Fransecky

address: Hindenburgdamm 30

department: Hematology and Oncology

institute: Charité University Hospital Berlin

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization.

source_name: bone marrow mononuclear cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from bone marrow (BM) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using TRIzol (Life Technologies, Grand Island, NY, USA). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Pretreatment bone marrow mononuclear cells from cell lines derived from patients with acute T-cell lymphoblastic leukemia (T-ALL)

tag: all type

tag: decitabine

value: yes


title: RPMI8402_2

value: no


title: PER117 post Decitabine_1


title: PER117_1


title: PER117 post Decitabine_3


title: PER117_3


title: Patient 3 cancer

source_name: Liver cancer tissue

value: primary liver cancer tissue


title: PER117 post Decitabine_4


title: PER117_2


title: PER117 post Decitabine_5


title: Molt4_2


title: PER117 post Decitabine_6


title: Molt4_1


title: RPMI8402_1


title: Loucy_3


title: Loucy_2


title: T_ALL_patient_44 [GPL96]

treatment_protocol: Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute T-cell lymphoblastic leukemia (T-ALL)

tag: patient age at diagnosis

value: thymic T-ALL


title: Patient 1 normal

value: Male


title: Patient 2 cancer


title: T_ALL_patient_41 [GPL96]

value: pre-T-ALL


title: Patient 1 cancer


title: Loucy_1


title: T_ALL_patient_43 [GPL96]


title: T_ALL_patient_37 [GPL96]


title: T_ALL_patient_36 [GPL96]


title: T_ALL_patient_35 [GPL96]


title: T_ALL_patient_42 [GPL96]


title: T_ALL_patient_38 [GPL96]


title: T_ALL_patient_34 [GPL96]


title: T_ALL_patient_43 [GPL97]


title: Loucy post Decitabine_4


title: Loucy post Decitabine_5


title: T_ALL_patient_42 [GPL97]


title: Loucy post Decitabine_6


title: Loucy post Decitabine_2


title: T_ALL_patient_44 [GPL97]


title: T_ALL_patient_40 [GPL96]


title: Loucy post Decitabine_1


title: T_ALL_patient_31 [GPL96]


title: T_ALL_patient_33 [GPL96]


title: T_ALL_patient_32 [GPL96]


title: T_ALL_patient_30 [GPL96]


title: T_ALL_patient_40 [GPL97]


title: 0.1Gy (long-term effect)

description: 0.1 Gy dose irradiation of LT-HSC from mouse bone marrow.

source_name: LT-HSC bone marrow, 0.10 Gy γ-irradiation, 6 month


title: T_ALL_patient_41 [GPL97]


title: Loucy post Decitabine_3


title: Jurkat_1


title: T_ALL_patient_38 [GPL97]


title: T_ALL_patient_39 [GPL97]

value: mature T-ALL


title: T_ALL_patient_28 [GPL96]


title: T_ALL_patient_36 [GPL97]


title: T_ALL_patient_37 [GPL97]


title: Jurkat_2


title: BE13_1


title: T_ALL_patient_29 [GPL96]


title: T_ALL_patient_34 [GPL97]


title: T_ALL_patient_27 [GPL96]


title: T_ALL_patient_33 [GPL97]


title: T_ALL_patient_32 [GPL97]


title: T_ALL_patient_35 [GPL97]


title: T_ALL_patient_23 [GPL96]


title: BE13_2


title: T_ALL_patient_26 [GPL96]


title: T_ALL_patient_30 [GPL97]


title: T_ALL_patient_31 [GPL97]


title: T_ALL_patient_19 [GPL96]


title: T_ALL_patient_20 [GPL96]


title: T_ALL_patient_22 [GPL96]


title: T_ALL_patient_29 [GPL97]


title: T_ALL_patient_17 [GPL96]


title: T_ALL_patient_21 [GPL96]


title: T_ALL_patient_28 [GPL97]


title: T_ALL_patient_25 [GPL96]


title: T_ALL_patient_39 [GPL96]


title: T_ALL_patient_18 [GPL96]


title: T_ALL_patient_27 [GPL97]


title: T_ALL_patient_26 [GPL97]


title: T_ALL_patient_25 [GPL97]


title: T_ALL_patient_24 [GPL97]


title: T_ALL_patient_16 [GPL96]


title: T_ALL_patient_15 [GPL96]


title: T_ALL_patient_23 [GPL97]


title: T_ALL_patient_22 [GPL97]


title: T_ALL_patient_20 [GPL97]


title: T_ALL_patient_24 [GPL96]


title: Fresh frozen intrahepatic bile duct biopsy 18

city: Heidelberg

first: Dieter

last: Weichenhan

address: Im Neuenheimer Feld 280

department: C010 Epigenomics

institute: DKFZ Heidelberg

description:
ductal adenocarcinoma
ICC18

hyb_protocol: Agilent ChIP-on-chip protocol v9

scan_protocol: DNA Microarray scanner (Agilent, no G2565CA); Feature Extraction Software 10.5 (Agilent) and the standard ChIP protocol (Agilent)

data_processing: Feature extracted data was processed using the R statistical environment, version 2.13. (http://www.R-project.org) and bioconductor. Background correction and log2-ratio (M-value, test/reference) transformation were performed according to the NormExp method with offset=50 correction methods for two-color microarrays. To reduce variations between co-hybridized samples, intensity-based LOESS normalization on rank-invariant probes and negative controls was applied.

label: Alexa flour 5

source_name: Intrahepatic cholangiocarcinoma

label_protocol: BioPrime Total Genomic DNA Labeling System (Invitrogen)

extract_protocol: AllPrep DNA/RNA Mini kit (Qiagen)

value: female

value: Intrahepatic cholangiocarcinoma (ICC)

label: Alexa flour 3

source_name: matched normal

tag: sample type

value: normal control (reference)


title: Fresh frozen intrahepatic bile duct biopsy 16

description:
ductal adenocarcinoma
ICC16

value: male

source_name: common reference pool 1


title: T_ALL_patient_18 [GPL97]


title: Fresh frozen intrahepatic bile duct biopsy 15

description:
ductal adenocarcinoma
ICC15


title: T_ALL_patient_19 [GPL97]


title: T_ALL_patient_13 [GPL96]


title: T_ALL_patient_14 [GPL96]


title: Fresh frozen intrahepatic bile duct biopsy 17

description:
ductal adenocarcinoma
ICC17


title: T_ALL_patient_10 [GPL96]


title: T_ALL_patient_21 [GPL97]


title: T_ALL_patient_17 [GPL97]


title: T_ALL_patient_7 [GPL96]


title: T_ALL_patient_8 [GPL96]


title: Fresh frozen intrahepatic bile duct biopsy 14

description:
ductal adenocarcinoma
ICC14


title: T_ALL_patient_12 [GPL96]


title: Fresh frozen intrahepatic bile duct biopsy 12

description:
ductal adenocarcinoma
ICC12

source_name: common reference pool 2


title: Fresh frozen intrahepatic bile duct biopsy 10

description:
ductal adenocarcinoma
ICC10


title: T_ALL_patient_6 [GPL96]


title: T_ALL_patient_15 [GPL97]


title: Fresh frozen intrahepatic bile duct biopsy 13

description:
ductal adenocarcinoma
ICC13


title: T_ALL_patient_13 [GPL97]


title: T_ALL_patient_14 [GPL97]


title: T_ALL_patient_5 [GPL96]


title: T_ALL_patient_11 [GPL96]


title: T_ALL_patient_16 [GPL97]


title: T_ALL_patient_3 [GPL96]


title: T_ALL_patient_9 [GPL96]


title: Fresh frozen extrahepatic bile duct biopsy 7

description:
ductal adenocarcinoma
ECC7

source_name: Extrahepatic cholangiocarcinoma

value: Extrahepatic cholangiocarcinoma (ECC)


title: Fresh frozen intrahepatic bile duct biopsy 11

description:
ductal adenocarcinoma
ICC11


title: T_ALL_patient_4 [GPL96]


title: Fresh frozen extrahepatic bile duct biopsy 6

description:
ductal adenocarcinoma
ECC6


title: T_ALL_patient_12 [GPL97]


title: T_ALL_patient_2 [GPL96]


title: Fresh frozen intrahepatic bile duct biopsy 9

description:
ductal adenocarcinoma
ICC9


title: T_ALL_patient_9 [GPL97]


title: Fresh frozen extrahepatic bile duct biopsy 3

description:
ductal adenocarcinoma
ECC3


title: Fresh frozen extrahepatic bile duct biopsy 8

description:
ductal adenocarcinoma
ECC8


title: T_ALL_patient_8 [GPL97]


title: Fresh frozen extrahepatic bile duct biopsy 2

description:
ductal adenocarcinoma
ECC2


title: Fresh frozen extrahepatic bile duct biopsy 5

description:
ductal adenocarcinoma
ECC5


title: spermatids like cells, biological rep2

city: Nanjing

first: Quan

last: Zhou

state: Jiangsu

address: NO. 140, Hanzhong Road

institute: Nanjing Medical University

description: Gene expression data from in vitro differentiated spermatids like cells

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) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: spermatids like cells

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.

growth_protocol: cells were collected by FACS  at room temperature (RT)

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: cells were suspended in the TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) on ice.

tag: derivation

value: in vitro differentiation


title: spermatids like cells, biological rep3


title: T_ALL_patient_10 [GPL97]


title: Fresh frozen extrahepatic bile duct biopsy 1

description:
ductal adenocarcinoma
ECC1


title: Fresh frozen extrahepatic bile duct biopsy 4

description:
ductal adenocarcinoma
ECC4


title: T_ALL_patient_2 [GPL97]


title: T_ALL_patient_1 [GPL97]


title: T_ALL_patient_11 [GPL97]


title: T_ALL_patient_3 [GPL97]


title: T_ALL_patient_45 [GPL570]


title: T_ALL_patient_5 [GPL97]


title: T_ALL_patient_4 [GPL97]


title: spermatids, biological rep1

description: Gene expression data from round spermatids from 3-week mouse testis

value: BDF1 male mouse testis


title: day 6 PGCLCs,  biological rep2

description: Gene expression data from in vitro differentiated day 6 PGCLCs

source_name: day 6 PGCLCs


title: day 6 PGCLCs,  biological rep1


title: E12.5 male PGCs, biological rep2

description: Gene expression data from PGCs of E12.5 male fetal genital ridge

source_name: PGCs of E12.5 male fetal genital ridge

value: BDF1 male fatel genital ridge


title: E12.5 male PGCs, biological rep3


title: spermatids, biological rep2

source_name: round spermatids from 3-week mouse testis


title: E12.5 male PGCs, biological rep1


status: Public on Feb 25 2016

city: Seville

first: Ricardo

last: Pardal

address: Avda. Manuel Siurot, s/n.

department: Medical Physiology and Biophysics

country: Spain

institute: University of Seville

description: Gene expression data from Spheres from NB14t Adherent Primary Cells cultured in NC medium + ET1 (1,5% FBS)

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeViewTM Human Gene Expression Array (Affymetrix). 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 GeneChip® Command Console Software (AGCC) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Adherent primary cells cultured from NB tumor samples.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: Primary cells were cultured for 7 days in neural crest medium (1,5% FBS) at 37ºC in ultra-low 6-well plates for the formation of spheres.

extract_protocol: Total RNA was extracted using a commercial kit (RNeasy MICRO kit; QIAGEN), according to manufacturer's instruction guidelines.

treatment_protocol: Spheres were cultured in NC medium with low serum (1,5%) and treated daily with 25 ng/mL ET-1 (Sigma-Aldrich) during 7 days

tag: tissue

value: neuroblastoma


description: Gene expression data from Spheres from NB27t Adherent Primary Cells cultured in NC medium (1,5% FBS)

value: Adherent primary cells cultured from NB tumor samples

tag: cell type


description: Gene expression data from Spheres from NB14t Adherent Primary Cells cultured in NC medium (1,5% FBS)


description: Gene expression data from Spheres from NB5t Adherent Primary Cells cultured in NC medium + ET1 (1,5% FBS)


description: Gene expression data from Spheres from NB5t Adherent Primary Cells cultured in NC medium (1,5% FBS)


description: Gene expression data from Spheres from NB27t Adherent Primary Cells cultured in NC medium + ET1 (1,5% FBS)


title: T_ALL_patient_1 [GPL96]


title: spermatids like cells, biological rep1


title: T_ALL_patient_7 [GPL97]


title: day 6 PGCLCs,  biological rep3


title: T_ALL_patient_6 [GPL97]


title: spermatids, biological rep3


title: 9934987142_R04C02

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

hyb_protocol: Illumina Methylation protocol

scan_protocol: Scan was performed using Illumina HiScan system

data_processing: Genome Studio Methylaton module

label: Cy3 and Cy5

source_name: Saliva

label_protocol: EZ96 DNA methylation kit

extract_protocol: DNA extraction was performed as per DNA Genotek's recommendations using the PrepIT L2P reagent. Extracted DNA was stored in individually barcoded cryovials at –80 degrees Fahrenheit. Child saliva was obtained using the “baby brush” approach, in which small sponges attached to plastic handles are inserted between cheek and gumline to absorb saliva using the Oragene DNA saliva kit.

tag: adult age

tag: adult bmi

tag: adult waist

tag: child gender

value: M

tag: child age

tag: child bmi

tag: child waist


title: 9934987142_R05C02

value: F


title: 9934987142_R06C01


title: 9934987142_R05C01


title: 9934987142_R03C01


title: 9934987106_R05C01


title: 9934987106_R06C02


title: 9934987142_R04C01


title: 9934987142_R06C02


title: 9934987106_R03C01


title: 9934987106_R02C02


title: 9934987106_R05C02


title: 9934987142_R02C02


title: 9934987106_R03C02


title: 9934987142_R01C02