title: AML80

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

country: Denmark

institute: Copenhagen University

description: Gene expression data from purified cell from the hematopoietic system

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol

scan_protocol: arrays were scanned in the Affymetrix Genearray 2500 scanner to generate flourescent images, as described in Affymetrix GeneChip protocol.

data_processing: Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA)

source_name: Granulocyte Macrophage Progenitors

label_protocol: 2.5ug amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

growth_protocol: Mononuclear bone marrow cells  from heathly donors were enriched for 34+ and hematopoietic stem and progenitor cells were sorted by FACS.

extract_protocol: RNeasy from Qiagen. According to manufaturer protocol.  Followed by amplification with NuGEN's WT Ovation Pico kit. Again according to manufacturer protocol.

tag: karyotype

value: AML with t(8;21)

tag: cell type

value: Granulocyte Macrophage Progenitors


title: MEF+KOSM_19d_1

status: Public on Mar 23 2015

type: RNA

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized using GenomeStudio Gene Expression Module v1.0 and the report was created using GEO Data Submission Report Plug-in v2.0.0

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: iPSC intermediate

label_protocol: cRNA was prepared by reverse-transcription and labeling using Illumina TotalPrep RNA Amplification Kit (Life Technologies).

extract_protocol: Total RNA was purified by ReliaPrep RNA Cell Miniprep System (Promega).

tag: vector infection

value: Day 19

tag: shield1 addition


title: HCC0019_VI-

city: Rochester

first: Kuang-Hsiang

last: Chuang

state: NY

address: 601 Elmwood Ave

department: Wilmot Cancer Institute

country: USA

institute: University of Rochester

hyb_protocol: miRNAs were hybridized to Affymetrix GeneChip miRNA 1.0 microarrays (Affymetrix, Santa Clara, CA, USA). These arrays are comprised of 46,228 probe sets representing over 6703 miRNA sequences (71 organisms) from the Sanger miRNA database (V.11) and an additional 922 sequences of human snoRNA and scaRNA from the Ensemble database and snoRNABase.

scan_protocol: Arrays were scanned with a GeneChip Scanner 7G Plus. Data files (.cel files) were generated using the miRNA-1_0_2X gain library file.

data_processing: Array signal intensities and present calls were produced by using AffyMetrix miRNA QCTool program (version 1.0.33.0, Affymetrix, Santa Clara, CA, USA). The normalization algorithm used was the default setting in AffyMetrix miRNA QCTool program, which is background adjustment, BC-CG Adjust; normalization, Quantile; summarization, median polish. The data processing was carried out on all 46,228 probe sets, after which non-human probe sets were removed leaving 847 human miRNA probe sets.

label: biotin

organism: Homo sapiens

source_name: HCC tumor

label_protocol: miRNAs were labeled using the FlashTag Biotin RNA labeling kit (Affymetrix, Santa Clara, CA, USA) by following the manufacture’s protocol

extract_protocol: miRNA was isolated from FFPE HCC tumors using the Roche High Pure miRNA isolation kit (Roche Diagnostics, Mannheim, Germany). miRNA extraction was carried out from individual tissue blocks using seven sections of 10 microns each. One to four extractions were carried out for each tumor to generate sufficient miRNA for microarray analysis

tag: tumor vascular invasion/invasiveness

value: No


title: AML92


title: MEF+KOSM_4d_1

description: replicate 1

value: Day 4


title: HCC0023_VI-


title: genomic DNA from young sun protected dermis 1

type: genomic

city: Baltimore

first: Andrew

last: Feinberg

state: Maryland

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

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

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Minfi Package

label: Cy5 and Cy3

molecule: genomic DNA

source_name: young sun protected dermis

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was purified using EpiCentre MasterPure kit according to manufactuerer's instructions.

treatment_protocol: Overnight incubation in dispase at 4 degrees C followed by seperation of epidermal and dermal layers.

tag: gender

value: male

tag: age

tag: exposure

value: sun protected

tag: tissue

value: dermis


title: MEF+KOSM_8d_1

description: replicate 1

value: Day 8


title: AML77


title: HCC0018_VI-


title: AML79


title: MEF_2

description: replicate 2

source_name: Somatic cell

value: Day 0


title: MEF+KOSM_4d_2

description: replicate 2


title: AML76

value: AML with inv(3)/t(3;3)


title: HCC0016_VI-


title: HCC0017_VI-


title: AML75


title: HCC0014_VI-


title: HCC0013_VI-


title: mutant,t=60 min, biological replicate 1

city: Grenoble

first: Thomas

last: Pfannschmidt

address: 17 rue des Martyrs

department: Institut de Recherches en Technologies et Sciences pour le Vivant

country: France

institute: CNRS/UJF/INRA/CEA Grenoble

description:
stn_7_I-II_60-1
gene expression of stn7 at t=60 min shifted from PSI-light to PSII-light

hyb_protocol: carried out according to Affymetrix GeneChip® 3’ IVT Express Kit User Manual (P/N 702646 Rev. 1)

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Gene Chip Operating  System (GCOS) 1.4 and Expression console 1.1 software, Robust Multi-chip Analysis (RMA)

organism: Arabidopsis thaliana

source_name: mutant shifted from PSI to PSII-light for 60 min

growth_protocol: Arabidopsis were precultivated for 20 days on potting soil/vermicullite mixture under 35 µE continous white light at 22 °C and 60% humidity. After 20 days plants were subjected for 3 d to continuous PSI-light (According to Wagner et al. Planta, 2008)

extract_protocol: Basically, total RNA was prepared as described in Logemann et al., Analytical Biochemistry 1987

treatment_protocol: Col-0 and stn7 were shifted to PSII light for either 30 or 60 min, rosette were harvested directly under the light sources and frozen in liq. N2

value: rosette leaves

value: 23d after germination

tag: line/ecotype

value: stn7 KO (SALK_073254) Col-0 background

tag: treatment protocol

value: shifted from PSI-light to PSII-light

tag: time

value: 60 min


title: mutant,t=60 min, biological replicate 2

description:
stn_7_I-II_60-2
gene expression of stn7 at t=60 min shifted from PSI-light to PSII-light

label_protocol: carried out according to Affymetrix GeneChip® 3’ IVT Express Kit User Manual (P/N 702646 Rev. 1)


title: AML74


title: mutant,t=60 min, biological replicate 3

description:
stn_7_I-II_60-3
gene expression of stn7 at t=60 min shifted from PSI-light to PSII-light


title: HCC0015_VI-


title: HCC0012_VI-


title: AML70

value: AML with t(15;17)


title: MEF_1

description: replicate 1


title: HCC0011_VI-


title: AML69


title: mutant,t=30 min, biological replicate 1

description:
stn_7_I-II_30-1
gene expression of stn7 at t=30 min shifted from PSI-light to PSII-light

source_name: mutant shifted from PSI to PSII-light for 30 min

value: 30 min


title: AML61

value: Granulocyte Macrophage Progenitors


title: HCC0010_VI-


title: mutant,t=30 min, biological replicate 3

description:
stn_7_I-II_30-3
gene expression of stn7 at t=30 min shifted from PSI-light to PSII-light


title: mutant,t=0 min, biological replicate 3

description:
stn_7_I_5
gene expression of stn7 at t=0 under continous PSI-light

source_name: mutant acclimated for 3 d to PSI light

value: under continous PSI-light

value: 0 min


title: mutant,t=0 min, biological replicate 2

description:
stn_7_I_2
gene expression of stn7 at t=0 under continous PSI-light


title: WT,t=60 min, biological replicate 3

description:
Col_I-II_60-3
gene expression of Col-0 at t=60 min shifted from PSI-light to PSII-light

source_name: Col-0 shifted from PSI to PSII-light for 60 min


title: AML59


title: AML43

value: AML with del(7q)/-7


title: AML73


title: AML40


title: mutant,t=0 min, biological replicate 1

description:
stn_7_I_1
gene expression of stn7 at t=0 under continous PSI-light


title: mutant,t=30 min, biological replicate 2

description:
stn_7_I-II_30-2
gene expression of stn7 at t=30 min shifted from PSI-light to PSII-light


title: AML60


title: AML36


title: HCC0009_VI-

value: No


title: HCC0008_VI-


title: AML68


title: HCC0005_VI-


title: HCC0006_VI-


title: HCC0004_VI-


title: HCC0003_VI-


title: AML23

value: AML with t(8;21)


title: HCC0001_VI-


title: WT,t=60 min, biological replicate 2

description:
Col_I-II_60-2
gene expression of Col-0 at t=60 min shifted from PSI-light to PSII-light


title: WT,t=30 min, biological replicate 3

description:
Col_I-II_30-3
gene expression of Col-0 at t=30 min shifted from PSI-light to PSII-light

source_name: Col-0 shifted from PSI to PSII-light for 30 min


title: WT,t=30 min, biological replicate 1

description:
Col_I-II_30-1
gene expression of Col-0 at t=30 min shifted from PSI-light to PSII-light


title: HCC0007_VI-


title: AML8

source_name: Common myeloid progenitors

value: Common myeloid progenitors


title: WT,t=30 min, biological replicate 2

description:
Col_I-II_30-2
gene expression of Col-0 at t=30 min shifted from PSI-light to PSII-light


title: HCC0002_VI-


title: WT,t=0 min, biological replicate 2

description:
Col_I_2
gene expression of Col-0 at t=0 under continous PSI-light

source_name: Col-0 acclimated for 3 d to PSI light


title: WT,t=60 min, biological replicate 1

description:
Col_I-II_60-1
gene expression of Col-0 at t=60 min shifted from PSI-light to PSII-light


title: WT,t=0 min, biological replicate 3

description:
Col_I_4
gene expression of Col-0 at t=0 under continous PSI-light


title: BR0172DTTA01_AD09-134T

status: Public on Mar 22 2015

city: Chuo-ku

first: Motonobu

last: Saito

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center

description: Gene expression data from primary lung ADC

hyb_protocol: Hybridization was performed following the Agilent protocols

scan_protocol: Slides were scanned immediately after washing on the G25052C DNA microarray scanner (Agilent) following the manufacturer's protocol, using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters.The data were normalized by the GeneSpring GX software.

source_name: frozen tissue of primary lung tumors

label_protocol: Approximately 100 ng of total RNA was Cy3 labeled using miRNA Complete Labeling and Hyb Kit (Agilent) following the manufacturer's protocols.

extract_protocol: Trizol extraction according to the manufacturer's instructions.

tag: Sex

value: female

tag: smoking

value: Never-smoker

tag: bi

tag: pathological stage

value: ⅡA

tag: gene alteration status

value: EGFR/KRAS/HER2/BRAF/ROS/RET/ALK -

tag: regimen

value: CBDCA+PTX

tag: recist

value: SD

tag: response

value: Non-responder


title: BR0171DTTA01_AD08_343T

value: male

value: Ever-smoker


title: WT,t=0 min, biological replicate 1

description:
Col_I_1
gene expression of Col-0 at t=0 under continous PSI-light

value: rosette leaves

value: 23d after germination


title: AML14

description: Gene expression data from purified cell from the hematopoietic system

tag: karyotype

tag: cell type

value: Granulocyte Macrophage Progenitors


title: BR0151DTTA01_AD09-487T

value: ⅢA

value: PR

value: Responder


title: AML9

value: AML with t(8;21)


title: BR0144DTTA01_AD09-447T

value: KRAS mutation +


title: Blood, Subject 29876571, hours since injury 131.3

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

description: Please notice that this sample with low RNA quality.

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station FS 4500, and used the standard solutions recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: Affymetrix Power Tools version 1.8.6 RMA model

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug RNA (Expression Analysis Technical Manual rev 3, 2002, Affymetrix)

extract_protocol: Total RNA was purified using the Rneasy RNA Isolation kit standard protocol (Qiagen, Valencia, CA)

treatment_protocol: White blood cells were separated using a modified buffy coat isolation and red blood cell lysis method. This protocol recovers the plasma fraction, lyses RBCs, and allows recovery of the white blood cell fraction, eliminating the need to recover the buffy coat interfacial layer.

value: White Blood Cells

value: F


title: BR0149DTTA01_AD09-472T

value: ALK-fusion +


title: BR0143DTTA01_AD09-442T

value: female

value: ⅠA

value: EGFR mutation +


title: Blood, Subject 30335589, hours since injury 176.9

description: Sample from patients with incomplete time points.


title: Blood, Subject 30335589, hours since injury 107.3


title: Blood, Subject 29876571, hours since injury 35.4


title: BR0142DTTA01_AD09-429T

value: ⅡB

value: CBDCA+PTX


title: Blood, Subject 25964909, hours since injury 23.8

value: M


title: Blood, Subject 27166716, hours since injury 181.3


title: BR0128DTTA01_AD09-193T

value: male

value: Ever-smoker


title: BR0125DTTA01_AD09-144T

value: Never-smoker

value: ⅠB

value: SD

value: Non-responder


title: BR0137DTTA01_AD09-330T

value: ⅢA

value: CDDP+GEM

value: PR

value: Responder


title: BR0138DTTA01_AD09-340T


title: Blood, Subject 28634107, hours since injury 103.8

value: White Blood Cells


title: Blood, Subject 30335589, hours since injury 32.8

value: F


title: Blood, Subject 25499319, hours since injury 110.3


title: Blood, Subject 25499319, hours since injury 157.5


title: Blood, Subject 33132122, hours since injury 33.7


title: BR0139DTTA01_AD09-383T

value: ⅢB

value: EGFR/KRAS/HER2/BRAF/ROS/RET/ALK -

value: CBDCA+GEM


title: Blood, Subject 22920269, hours since injury 349


title: BR0119DTTA01_AD09-003T

value: ⅠA

value: KRAS mutation +

value: CBDCA+PTX


title: BR0120DTTA01_AD09-034T

value: male

value: Ever-smoker

value: EGFR mutation +


title: BR0107DTTA01_AD08_170T

value: SD


title: BR0108DTTA01_AD08_178T

value: female

value: Never-smoker

value: Non-responder


title: BR0109DTTA01_AD08_181T

value: ⅡA

value: PD


title: Blood, Subject 22934880, hours since injury 30.8

value: White Blood Cells


title: BR0112DTTA01_AD08_220T

value: ⅡB


title: Blood, Subject 22920269, hours since injury 127.2

value: M


title: BR0101DTTA01_AD08_101T

value: ⅢA

value: PR

value: Responder


title: Blood, Subject 20997140, hours since injury 37.2


title: BR0100DTTA01_AD08_096T

value: EGFR/KRAS/HER2/BRAF/ROS/RET/ALK -

value: CBDCA+GEM


title: Blood, Subject 20435061, hours since injury 37.7

value: F


title: BR0097DTTA01_AD08_060T

value: male

value: Ever-smoker

value: CBDCA+PTX


title: BR0096DTTA01_AD08_047T

value: female

value: ⅠA

value: ROS fusion +

value: CDDP+GEM

value: SD


title: Blood, Subject 20435061, hours since injury 207.6

value: White Blood Cells


title: BR0095DTTA01_AD08_046T

value: Never-smoker


title: Blood, Subject 16832704, hours since injury 332.1


title: Blood, Subject 22934880, hours since injury 107.8


title: Blood, Subject 22920269, hours since injury 177

value: M


title: Blood, Subject 25499319, hours since injury 326.7


title: Blood, Subject 15628834, hours since injury 179.7


title: Blood, Subject 20435061, hours since injury 111.1


title: Blood, Subject 15629307, hours since injury 197.8


title: Blood, Subject 15938658, hours since injury 114.3


title: BR0092DTTA01_AD08_028T

value: ⅢA

value: BRAF mutation +

value: Non-responder


title: BR0090DTTA01_AD08_024T

value: EGFR mutation +


title: BR0089DTTA01_AD08_009T


title: Blood, Subject 15628834, hours since injury 107.3


title: WT with 7 days T-treatment Replicate 2

city: Mississauga

first: Ashley

last: Monks

state: Ontario

address: 3359 Mississauga Road

department: Dept. of Psychology

country: Canada

institute: University of Toronto

description: Biological replicate 2 of 3, compared a sample from 7 days T-Treated female WT  with RNA reference

hyb_protocol: The labelled cDNA was combined with 75 µL of hybridization solution composed of 20:1:1 volume fraction DIG EasyHyb (Roche Diagnostics, Laval, Que.), 10 mg yeast tRNA/mL, and 10 mgsalmon sperm DNA/mL. Target cDNAs were denatured at 65 °C (5 min), allowed to cool slightly, and applied to the microarrays. The arrays were sealed in hybridization chambers (Corning) before incubation in a 37 °C water bath for 18 h. Coverslips were removed after submerging the slides in plastic Coplin jars containing 1× SSC/0.1% SDS at 50 °C. The slides were washed (three times for 15 min each) in Coplin jars containing fresh 1× SSC/ 0.1% SDS in a 50 °C water bath, with occasional swirling. Slides were then repeatedly dipped in 1× SSC and then 0.1× SSC, both at room temperature. Liquid was quickly removed from the slide surface by blowing compressed air at a downward angle onto the vertically held slide.

scan_protocol: Microarrays were scanned at a 10-µm resolution with a ScanArray 4000 system (GSI Lumonics/Perkin Elmer), using both blue and red lasers. The 16-bit TIFF images were saved and pre-processed and quantified with GenePix 5 software (Axon Instruments, Inc., CA). The adaptive quantification algorithm was used.

data_processing: Data analysis was performed with GeneTraffic Duo 2.5 (Iobion Informatics LLC, La Jolla, Calif.). The data were normalized using the Lowess algorithm at the subgrid level while ignoring flagged values. After normalization of data, average values were taken for statistical analysis. Gene lists were filtered in GeneTraffic to include only those genes that displayed at least 2-fold difference and whose coefficient of variance was less than 100% and p-value small than 0.05. Hierarchical cluster analysis and significant analysis of microarrays were performed in GeneTraffic DUO using the Pearson algorithm and average linkage.

source_name: RNA reference from wild type mice

label_protocol: Cyanine (Cy) dyes were directly incorporated into cDNA synthesized from 40 µg of total RNA. RNA was mixed with 1x SuperScript II first-strand buffer (Invitrogen); 10 mmol/L DTT; 150 pmol dT20VN primer; 50 µmol/L dCTP (Amersham Biosciences); 25 µmol/L Cy3- or Cy5-dCTP (Perkin Elmer); and  RNase-free water, up to a volume of 38 µL. The reactions were heated to 65 °C for 5 min, then 42 °C for 5 min, and SuperScript II reverse transcriptase (400 U, Invitrogen) was added, and cDNA synthesis was carried out for 3 h at 42 °C.

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

tag: muscles

value: Limb Muscles

tag: strain

tag: gender

value: Male and Female

source_name: Total RNA from WT with 7 days T-treatment 2

value: Female


title: WT with 7 days T-treatment Replicate 3

description: Biological replicate 3 of 3, compared a sample from 7 days T-Treated female WT  with RNA reference

source_name: Total RNA from WT with 7 days T-treatment 3


title: BR0085DTTA01_404T

tag: age

value: Ⅳ


title: WT with 7 days T-treatment Replicate 1

description: Biological replicate 1 of 3, compared a sample from 7 days T-Treated female WT  with RNA reference

source_name: Total RNA from WT with 7 days T-treatment 1


title: BR0084DTTA01_336T

value: CBDCA+PTX


title: ATHB15 BL 2

city: Bellaterra

first: Ana

last: Cano-Delgado

state: Barcelona

address: Edificio CRAG- Bellaterra (Cerdanyola del Vallés)

country: Spain

institute: CRAG

description: Gene expression data from protoplasts

hyb_protocol: Samples were submited to Expression Analysis Inc, (Durham, NC) for hybriditzation to Affymetrix ATH1 microarrays

data_processing:
Software described in Levesque et al. (2006), PLoS Biology, 4:e143 was used for normalization. This uses the global normalization/linear modeling approach described in Chu et al. (2001). This method simultaneously considers the perfect match probeset data across all chips in an experiment. Normalization across all chips was performed as follows: [Log2(IntensityPROBE, ARRAY) = logarithmic meanALLARRAY INTENSITY VALUES + residualsPROBE, ARRAY]. For each array, all probes were removed that were greater than two standard deviations from the probeset mean. For all remaining probe values across replicates in a treatment, expression indices are calculated as: 2^r1 + 2^r2 + 2^rN/N
Normalized gene expression mean values were used to prepare input files for the GiTools analysis. For each gene at different points in WOL or 2 hr in ATHB15, the mean expression value was compared with the mean value of the untreated control and a p value was calculated in accordance. GiTools input files for up- and downregulated genes were prepared in the binomial format. When the ratio of the mean expression values between treated and untreated control was higher or lower than 1 and the p value was smaller than 0.05 or 0.01, then the gene was considered as up- or downregulated, respectively, at the specific point and assigned the value of ‘‘1’’ (presence). When the difference between gene expression mean value at a specific point versus the untreated control was not statistically significant (p > 0.05), then the gene was assigned a value of ‘‘0’’ (absence) for the specific point

source_name: Protoplasts from 6 day old roots

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix

growth_protocol: Six-day-old roots grown in vertical plates were transferred to plates with half MS media supplemented with 10 nM BL at different times (0, 0.5, 1, 2, and 4 hr). Protoplasts were extracted in a Petri dish containing 0.5 mM CaCl2, 0.5 mM MgCl2, 5 mM MES, 1.5% Cellulase RS, 0.03% Pectolyase Y23, 0.25% BSA, at pH 5.5 with gentle agitation for 2 hr at room temperature until root cell protoplasts were released. Osmolarity was adjusted to 550 mmol/kg by the addition of D-sorbitol. The protoplast suspension was filtered through a nylon mesh (30 mm), washed several times, and resuspended with basic medium at 70 revolutions per minute. Subsequently, cells were purified with a multiparameter cell sorter. GFP fluorescent (530/30 nm) plots were com- pared to red autofluorescent (580/30 nm) to set gates around GFP-positive (GFP+) and GFP-negative (GFP) cells. Sorted cells were resuspended into lysis buffer for RNA isolation.

extract_protocol: RNA extraction was performed using Rneasy Micro Kit (Qiagen GMbH), Qiagen cat nº 74004, following manufactures instructions

treatment_protocol: Six-day-old roots grown in vertical plates were transferred to plates with half MS media supplemented with 10 nM BL (Wako ref. 635_00811) at different times (0, 0.5, 1, 2, and 4 hr)

tag: tissue

value: primary root

tag: agent

value: BL

tag: cell sorting

value: protoplasts were sorted by FACS using pAtHB15:YFP markers

value: provascular cells


title: WT with 3 days T-treatment Replicate 2

description: Biological replicate 2 of 3, compared a sample from 3 days T-Treated female WT  with RNA reference

source_name: Total RNA from WT with 3 days T-treatment 2


title: BR0082DTTA01_260T

tag: Sex

value: male

value: Ever-smoker

value: EGFR/KRAS/HER2/BRAF/ROS/RET/ALK -

value: CBDCA+GEM

value: CR

value: Responder


title: Blood, Subject 34043374, hours since injury 108.9

value: White Blood Cells

value: F


title: WT with 3 days T-treatment Replicate 1

description: Biological replicate 1 of 3, compared a sample from 3 days T-Treated female WT  with RNA reference

value: Limb Muscles

source_name: Total RNA from WT with 3 days T-treatment 1


title: Blood, Subject 14298862, hours since injury 185.6


title: WT untreated Replicate 3

description: Biological replicate 3 of 3, compared a sample from untreated female WT  with RNA reference

value: Male and Female

source_name: Total RNA from WT untreated 3


title: Blood, Subject 15628834, hours since injury 348.5

value: M


title: ATHB15 BL 1

description: Gene expression data from protoplasts

scan_protocol: Samples were submited to Expression Analysis Inc, (Durham, NC) for hybriditzation to Affymetrix ATH1 microarrays

tag: time


title: WT with 3 days T-treatment Replicate 3

description: Biological replicate 3 of 3, compared a sample from 3 days T-Treated female WT  with RNA reference

source_name: Total RNA from WT with 3 days T-treatment 3

value: Female


title: WT untreated Replicate 2

description: Biological replicate 2 of 3, compared a sample from untreated female WT  with RNA reference

source_name: Total RNA from WT untreated 2


title: Blood, Subject 15628834, hours since injury 34.8


title: ATHB15 CTL 3

description: Gene expression data from protoplasts

value: CTRL

value: control


title: Tg with 7 days T-treatment Replicate 3

description: Biological replicate 3 of 3, compared a sample from 7 days T-Treated female Tg  with RNA reference

source_name: Total RNA from HSA-AR transgenic (Tg) mouse model with 7 days T-treatment 3


title: Blood, Subject 13807517, hours since injury 178.4


title: BR0081DTTA01_255T

value: female

tag: smoking

value: Never-smoker

tag: bi

value: ⅢA

value: ALK-fusion +

value: CBDCA+PTX

value: SD

value: Non-responder


title: Blood, Subject 13230417, hours since injury 102.7


title: WT untreated Replicate 1

description: Biological replicate 1 of 3, compared a sample from untreated female WT  with RNA reference

source_name: Total RNA from WT untreated 1


title: ATHB15 CTL 2

description: Gene expression data from protoplasts

value: primary root

value: protoplasts were sorted by FACS using pAtHB15:YFP markers

value: provascular cells


title: Blood, Subject 12040372, hours since injury 107.5

value: White Blood Cells


title: BR0079DTTA01_223T

tag: pathological stage

value: ⅠB

tag: gene alteration status

value: EGFR mutation +


title: BR0074DTTA01_119T

value: male

value: HER2 mutation +

tag: regimen

tag: recist

value: PR

value: Responder


title: WOL 4h BL B

description: Gene expression data from protoplasts

value: BL

value: protoplasts were sorted by FACS using pWOL:GFP

value: stele cells


title: Tg with 7 days T-treatment Replicate 2

description: Biological replicate 2 of 3, compared a sample from 7 days T-Treated female Tg  with RNA reference

value: Limb Muscles

value: Male and Female

source_name: Total RNA from HSA-AR transgenic (Tg) mouse model with 7 days T-treatment 2

value: Female


title: Blood, Subject 13230417, hours since injury 42

source_name: Subject 13230417, hours since injury 42

value: M


title: Blood, Subject 11941840, hours since injury 35.3


title: BR0073DTTA01_106T

value: female

value: Never-smoker

value: Ⅳ

value: CBDCA+GEM

value: SD

tag: response

value: Non-responder


title: Blood, Subject 10341675, hours since injury 40.2

value: White Blood Cells


title: BR0076DTTA01_151T

value: ⅢA

value: EGFR mutation +

value: CBDCA+PTX


title: Blood, Subject 12040372, hours since injury 35.6


title: WOL 2h BL B

description: Gene expression data from protoplasts

value: primary root

value: BL

tag: cell type


title: WOL 4h BL A

description: Gene expression data from protoplasts

value: protoplasts were sorted by FACS using pWOL:GFP

value: stele cells


title: BR0069DTTA01_50T

value: ⅢB

value: CDDP+GEM

value: PD


title: Tg with 7 days T-treatment Replicate 1

description: Biological replicate 1 of 3, compared a sample from 7 days T-Treated female Tg  with RNA reference

tag: muscles

value: Limb Muscles

value: Male and Female

source_name: Total RNA from HSA-AR transgenic (Tg) mouse model with 7 days T-treatment 1

value: Female


title: Tg with 3 days T-treatment Replicate 3

description: Biological replicate 3 of 3, compared a sample from 3 days T-Treated female Tg  with RNA reference

tag: strain

source_name: Total RNA from HSA-AR transgenic (Tg) mouse model with 3 days T-treatment 3


title: Blood, Subject 9558988, hours since injury 103.9

value: F


title: BR0059DTTA01_AD09-108T

description: Gene expression data from primary lung ADC

source_name: frozen tissue of primary lung tumors

value: female

value: Never-smoker

value: ⅠB

value: HER2 mutation +

value: PR

value: Responder


title: ATHB15 CTL 1

description: Gene expression data from protoplasts

value: primary root

value: CTRL

value: control

value: protoplasts were sorted by FACS using pAtHB15:YFP markers

value: provascular cells


title: Blood, Subject 9558988, hours since injury 35.3

value: White Blood Cells


title: WOL 2h BL A

description: Gene expression data from protoplasts

value: BL

value: protoplasts were sorted by FACS using pWOL:GFP

value: stele cells


title: Tg with 3 days T-treatment Replicate 2

description: Biological replicate 2 of 3, compared a sample from 3 days T-Treated female Tg  with RNA reference

source_name: RNA reference from wild type mice

value: Limb Muscles

tag: gender

value: Male and Female

source_name: Total RNA from HSA-AR transgenic (Tg) mouse model with 3 days T-treatment 2

value: Female


title: WOL 1h BL B

description: Gene expression data from protoplasts


title: Blood, Subject 9558988, hours since injury 346.5

description: Please notice that this sample with low RNA quality.

value: F

tag: age


title: BR0049DTTA01_AD08_295T

value: male

value: Ever-smoker

value: ⅠB

value: EGFR/KRAS/HER2/BRAF/ROS/RET/ALK -

value: CBDCA+PTX


title: BR0036DTTA01_AD08_151T

value: CDDP+GEM

value: PR

value: Responder


title: heart-a2a-rep2

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description:
Gene expression data from the heart of transgenic mouse
A2a_TAC2

hyb_protocol: Labelled single-stranded cDNA were hybridized for 17 hours at 45°C and 60 rpm on GeneChip® Mouse Gene ST Arrays.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G

data_processing: Microarray data was processed with Partek Genomics Suite using RMA with GC correction and quantile normalisation. Probesets were summarised with mean values for one transcript cluster.

source_name: heart, Adenosine transgenic

label_protocol: The single-stranded cDNAs were labelled according to standard Affymetrix GeneChip® WT Terminal Labeling Kit from 100 ng total RNA

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

tag: tissue

value: heart

tag: genotype/variation

value: A2a-R transgenic

tag: stress

value: transverse aortic constriction (TAC)


title: WOL 1h BL A

description: Gene expression data from protoplasts

value: primary root

tag: agent

value: BL

tag: cell sorting

value: protoplasts were sorted by FACS using pWOL:GFP


title: heart-a2a-rep1

description:
Gene expression data from the heart of transgenic mouse
A2a_TAC1


title: Tg with 3 days T-treatment Replicate 1

description: Biological replicate 1 of 3, compared a sample from 3 days T-Treated female Tg  with RNA reference

value: Limb Muscles

value: Male and Female

source_name: Total RNA from HSA-AR transgenic (Tg) mouse model with 3 days T-treatment 1


title: BR0034DTTA01_AD08_132T

tag: Sex

tag: smoking

value: ⅠA

value: HER2 mutation +

value: SD

value: Non-responder


title: BR0026DTTA01_AD08_056T

value: male

value: Ever-smoker

tag: bi

tag: pathological stage

value: ⅡA

value: EGFR/KRAS/HER2/BRAF/ROS/RET/ALK -

value: CDDP+VNR


title: heart-a2a-rep3

description:
Gene expression data from the heart of transgenic mouse
A2a_TAC3

value: heart


title: Blood, Subject 9289610, hours since injury 33

source_name: Subject 9289610, hours since injury 33

value: White Blood Cells

value: F


title: WOL 30min BL A

description: Gene expression data from protoplasts

source_name: Protoplasts from 6 day old roots

value: primary root

tag: time

value: stele cells


title: heart-wt-rep3

description:
Gene expression data from the heart of wild type mouse
WT_TAC5

source_name: heart, wild type

value: wild type

value: transverse aortic constriction (TAC)


title: WOL 30min BL B

description: Gene expression data from protoplasts

value: BL

value: protoplasts were sorted by FACS using pWOL:GFP


title: heart-wt-rep2

description:
Gene expression data from the heart of wild type mouse
WT_TAC4


title: WOL CTL B

description: Gene expression data from protoplasts

value: CTRL

value: control


title: Blood, Subject 9289610, hours since injury 105

source_name: Subject 9289610, hours since injury 105


title: Blood, Subject 9289610, hours since injury 201.2


title: Paired non-neoplastic tissue P181N

status: Public on Mar 21 2015

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: Control

data_processing:
Raw data were processed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.
For the normalization it uses the average of four housekeeping genes: EIF2B1, MRPL19, IPO8, and UBB
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_HKG)

label: FAM

source_name: Paired non-neoplastic tissue

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in RotorGene 6000 produced by Corbett Research (Sydney, Australia) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. cDNA was preamplified using TaqMan PreAmp Master Mix (Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated from frozen tissues using Trizol reagent according to manufacturers protocol (Invitrogen, Carlsbad, CA, USA)

tag: age (years)

tag: menopause

tag: histology (1=idc, 0=other)

tag: grade

tag: size (mm)

tag: Stage

tag: pt

tag: pn

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)

tag: her2 (0=negative, 1= positive)

tag: neo-anthracycline

tag: neo-taxane

tag: response (0=sd/pd, 1=pr)

tag: relapse

tag: dfs (months)

value: Paired non-neoplastic tissue


title: WOL CTL A

description: Gene expression data from protoplasts

tag: tissue

tag: agent

tag: time

tag: cell sorting

tag: cell type


title: Breast tumor P166T

description: Tumor

source_name: Breast tumor

tag: age (years)

tag: menopause

value: post

tag: histology (1=idc, 0=other)

tag: grade

tag: size (mm)

value: IIA

value: no

value: unknown

value: Breast tumor


title: Paired non-neoplastic tissue P198N

description: Control

tag: Stage

tag: pt

tag: pn

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)


title: Breast tumor P181T

description: Tumor

value: I

tag: her2 (0=negative, 1= positive)

tag: neo-anthracycline

tag: neo-taxane

tag: response (0=sd/pd, 1=pr)

tag: relapse


title: heart-wt-rep1

description:
Gene expression data from the heart of wild type mouse
WT_TAC3

tag: tissue

value: heart

tag: genotype/variation

tag: stress


title: Breast tumor P198T

description: Tumor

tag: age (years)

tag: menopause

tag: dfs (months)


title: Blood, Subject 6221614, hours since injury 35.4

value: White Blood Cells

tag: Sex

value: M

tag: age


title: G-CSF treated CAR cells biological replicate 5

city: St. Louis

first: Daniel

middle: C

last: Link

state: MO

address: 660 S. Euclid, Campus Box 8007

institute: Washington University

hyb_protocol: Samples were hybridized to Mouse Gene 1.0 ST arrays (Affymetrix) at the Genome Technology Access Center (Washington University in St. Louis)

scan_protocol: Samples were scanned at the Genome Technology Access Center (Washington University in St. Louis)

data_processing: RMA-summarized gene-level expression values computed using Affymetrix Expression Console.

source_name: CFU-PreB colonies Hspa9+/-

label_protocol: Nugen Encore Biotin kit protocol

extract_protocol: CXCL12-GFP-bright, lineage- cells were sorted directly into TRIzol LS (Life Technologies) and RNA was extracted using standard protocols. cDNA was prepared using the PicoSL Ovation system (NuGen). Samples were hybridized to Mouse Gene 1.0 ST arrays.

treatment_protocol: Mice were treated with G-CSF (250 µg/kg/d) or phosphate-buffered saline alone for 5 days.

tag: genotpe/variation

tag: treatment

value: G-CSF (250 µg/kg/d)


title: SK-N-AS + GSK461364 biol repl 02

city: Essen

first: Sven

last: Lindner

address: Hufelandstraße 55

country: Germany

institute: University Hospital Essen

hyb_protocol: Hybridisation to human arrays was performed according to the manufacturers recommendations (Affymetrix)

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent)

data_processing: Data were summarized to gene levels and normalized using gcRMA from the Bioconductor repository of statistical tools [30]. Only probes with the highest mean expression for each gene and with a log2 expression >5 were included in the analysis for differential expression using the Rank Product analysis package v 2.36.0 in R [31]. Samples were clustered by applying hierarchical clustering and dissimilarity based on Manhattan distance

molecule: polyA RNA

source_name: Human neuroblastoma cell line SK-N-AS

label_protocol: Biotin labelling was performed according the manufacturers recommendations (Affymetrix)

growth_protocol: SK-N-AS cells were seeded onto 6-well plates (1 x 10^5 cells/well). Tweleve hours after seeding cells were treated

extract_protocol: Total RNA was extracted using the RNeasyMini kit (Qiagen, Hilden, Germany)

treatment_protocol: Cells were incubated with 5nM GSK461364 or DMSO 0.1% for 24h

tag: cell line

value: SK-N-AS

tag: cell type

value: neuroblastoma

value: GSK461364 biol repl 02


title: G-CSF treated CAR cells biological replicate 4


title: G-CSF treated CAR cells biological replicate 3


title: SK-N-AS + GSK461364 biol repl 03

value: GSK461364 biol repl 03


title: PBS treated CAR cells biological replicate 3

source_name: CFU-PreB colonies Wildtype littermate

value: phosphate-buffered saline alone for 5 days


title: Blood, Subject 9007070, hours since injury 179.4


title: G-CSF treated CAR cells biological replicate 1


title: SK-N-AS + GSK461364 biol repl 01

value: GSK461364 biol repl 01


title: PBS treated CAR cells biological replicate 4


title: SK-N-AS + DMSO biol repl 02

value: DMSO biol repl 02


title: SK-N-AS + DMSO biol repl 03

value: DMSO biol repl 03


title: with SR1, with ZFN HT22

city: Houston

first: Jianliang

last: Dai

address: 1400 Pressler St

institute: MD Anderson Cancer Center

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

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

extract_protocol: Total RNA from fresh HSCs or  cultured HSCs was isolated by by Allprep DNA/RNA Micro Kit (Qiagen). Integrity of RNA was validated by Bioanalyzer (2100 Expert, Agilent). Gene expression analysis was undertaken using the HumanHT-12 v4 Expression BeadChip (illumina).

tag: subject

value: with SR1, with ZFN

value: hematopoietic stem cells


title: G-CSF treated CAR cells biological replicate 2


title: SK-N-AS + DMSO biol repl 01

value: DMSO biol repl 01


title: PBS treated CAR cells biological replicate 2


title: Log-phase Cghog1∆ cells grown in YNB supplemented with FeCl3 for 2 h biological replicate 2

city: Hyderabad

first: Rupinder

last: Kaur

state: Telangana

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

description: Gene expresion after 2 h growth in YNB supplemented with FeCl3

hyb_protocol: The labeled cRNA samples were hybridized on to Slides used: Agilent Platform Custom Candida  glabrata 8x15k designed by Genotypic Technology Private Limited.(AMADID: 049117).600ng of cy3 labeled samples were  fragmented and hybridized .Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 11.5)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX

organism: Nakaseomyces glabratus CBS 138

source_name: Yeast cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Log phase wild-type and Cghog1∆  were grown in YNB, YNB supplemented with BPS (50 µM) and YNB supplemented with FeCl3 (500 µM) for 2 h, cells were collected and washed twice with nuclease free water, total RNA was isolated using acid phenol method and stored in nuclease free water.

extract_protocol: Total RNA was isolated using acid phenol method and resuspended in nuclease free water.

treatment_protocol: Log phase wild-type and Cghog1∆  were grown in YNB, YNB supplemented with BPS (50 µM) and YNB supplemented with FeCl3 (500 µM) for 2 h, cells were collected and washed twice with nuclease free water.

value: Cghog1∆ cells

value: grown in YNB supplemented with FeCl3


title: Log-phase Cghog1∆ cells grown in YNB supplemented with BPS for 2 h biological replicate 2

description: Gene expresion after 2 h growth in YNB supplemented with BPS

value: grown in YNB supplemented with BPS


title: Log-phase Cghog1∆ cells grown in YNB for 2 h biological replicate 2

description: Gene expresion after 2 h growth in YNB

value: grown in YNB


title: with SR1, with ZFN HT17


title: with SR1, without ZFN HT20

value: with SR1, without ZFN


title: without SR1, without ZFN HT19

value: without SR1, without ZFN


title: Log-phase Cghog1∆ cells grown in YNB for 2 h biological replicate 1

description: Gene expresion after 2 h growth in YNB


title: Log-phase wild-type cells grown in YNB supplemented with BPS for 2 h biological replicate 2

value: wild-type cells


title: Log-phase Cghog1∆ cells grown in YNB supplemented with BPS for 2 h biological replicate 1


title: Pre-expansion HT18

value: Pre-expansion


title: Log-phase wild-type cells grown in YNB supplemented with FeCl3 for 2 h biological replicate 2


title: Log-phase Cghog1∆ cells grown in YNB supplemented with FeCl3 for 2 h biological replicate 1


title: without SR1, with ZFN HT16

value: without SR1, with ZFN


title: without SR1, without ZFN HT14


title: Pre-expansion HT13


title: Log-phase wild-type cells grown in YNB for 2 h biological replicate 1

description: Gene expresion after 2 h growth in YNB


title: Log-phase wild-type cells grown in YNB supplemented with BPS for 2 h biological replicate 1


title: Log-phase wild-type cells grown in YNB supplemented with FeCl3 for 2 h biological replicate 1


title: without SR1, with ZFN HT_09


title: with SR1, without ZFN HT15


title: with SR1, with ZFN HT_10


title: with SR1, without ZFN HT_08


title: Pre-expansion HT_12


title: KSL cells from FLT3/ITD-SmoM2 mouse bone marrow

first: Yiting

last: Lim

state: MD

address: 1650 Orleans Street

description: Gene expression data from KSL cells of FLT3/ITD-SmoM2 mouse bone marrow

hyb_protocol: 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip arrays for 16hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA.  The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix 3000 GeneArray Scanner with G7 upgrade and image analysis of each GeneChip was done through the Affymetrix GeneChip Command Console 3.4.1 (AGCC) software from Affymetrix, using the standard default settings.

data_processing:
Affymetrix Expression Console (v 1.2.0.20) was used to analyze the data to generate normalized expression values.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.2.0.20

source_name: FLT3/ITD-SmoM2 KSL

label_protocol: 100 nanograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, biotinilated anti-sense cRNA was generated through in vitro transcription using the T7 RNA polymerase.

growth_protocol: C57BL/6 wild-type and transgenic FLT3/ITD and SmoM2; FLT3/ITD mice were bred in the animal facility. Poly(I:C) was administered via intraperitoneal injections upon weaning.

extract_protocol: RNA from sorted mouse bone marrow cells (KSL and GMP populations) was extracted using the Qiagen Rneasy Micro kit and processed using the RNA amplification protocol described by Affymetrix (Affymetrix 3’ IVT Express Manual).

treatment_protocol: Mouse bone marrow cells were harvested by flushing the tibia and femur bones with PBS, stained with antibodies and sorted for KSL and GMP cells.

tag: strain background

value: bone marrow

value: KSL cells


title: Pre-expansion HT_11


title: without SR1, without ZFN HT_07


title: GMP cells from FLT3/ITD-SmoM2 mouse bone marrow

description: Gene expression data from GMP cells of FLT3/ITD-SmoM2 mouse bone marrow

source_name: FLT3/ITD-SmoM2 GMP

value: GMP cells


title: KSL cells from FLT3/ITD bone marrow

description: Gene expression data from KSL cells of FLT3/ITD mouse bone marrow

source_name: FLT3/ITD KSL


title: GMP cells from FLT3/ITD mouse bone marrow

description: Gene expression data from GMP cells of FLT3/ITD mouse bone marrow

source_name: FLT3/ITD GMP


title: Pre-expansion HT_06


title: GMP cells from wild type mouse bone marrow

description: Gene expression data from GMP cells of wild type mouse bone marrow

source_name: WT GMP

value: wild type


title: KSL cells from wild type bone marrow

description: Gene expression data from KSL cells of wild type mouse bone marrow

source_name: WT KSL


title: with SR1, without ZFN HT-3-1


title: Log-phase wild-type cells grown in YNB for 2 h biological replicate 2

description: Gene expresion after 2 h growth in YNB


title: with SR1, with ZFN HT-5-1


title: Pre-expansion HT-1-1


title: Expt 26 - atopic 5

status: Public on Mar 20 2015

first: Donald

middle: Welton

last: MacGlashan

address: 5501 Hopkins Bayview Circle

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

description: dma11: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

data_processing: Genome Studio was used for generating the data. Due to the way data was processed in the published description of these results (no global normalization but local normalization in specific comparative analyses), the matrix of results that is normally entered as normalized is not normalized but instead a replicate of the non-normalized data.

source_name: peripheral blood

growth_protocol: peripheral blood basophils (source was residual cells from leukopheresis or venipuncture) were isolated by a combination of elutriation, two-step Percoll gradients and Miltenyi columns with StemSep basophil isolation reagents for a final average purity of 99%; where appropriate, purified basophils were cultured in RPMI-1640 medium supplemented with 20 µg/ml gentamycin, 0.03% human serum albumin and glutamine

extract_protocol: mRNA was isolated by miRNEasy kit extractions and contained both mRNA and miRNA, RIN values > 6 (lower allowed because of presence of miRNA)

treatment_protocol: the title of each sample identifies the treatment; D0 = day 0, D1 = day 1, D3 = day 3; IL-3 = interleukin-3, anti-IgE Ab = a monoclonal 6061P (Hybridoma Labs, Baltimore, MD) anti-IgE antibody (where 0.5 µg/ml is considered optimal); IL-5 = interleukin-5, NGF = nerve growth factor, IL-33 = interleukin-33, IL-2 = interleukin-2, FMLP = formyl-met-leu-phe (tripeptide)

value: basophils (purified to average of 99%)


title: Expt 26 - atopic 6

description: dma12: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: without SR1, with ZFN HT-4-1


title: HNSCC_HPV-_HN.8

city: Detroit

first: Maria

last: Worsham

state: MI

address: 1 Ford Place

department: Otolaryngology

institute: Henry Ford Health System

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1

extract_protocol: genomic DNA was extracted and purified fromhead and neck tumor samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: hpv status

value: HPV negative

tag: disease state

value: oropharyngeal HNSCC


title: without SR1, without ZFN HT-2-1

tag: tissue

value: hematopoietic stem cells


title: Expt 26 - non-atopic 3

description: dma3: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - atopic 4

description: dma10: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - atopic 1

description: dma7: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - non-atopic 5

description: dma5: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 25 - Releaser 2

description: DM-146: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - non-atopic 2

description: dma2: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - non-atopic 6

description: dma6: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - atopic 2

description: dma8: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - atopic 3

description: dma9: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 25 - Non-releaser 1

description: DM-147: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 25 - Non-releaser 2

description: DM-148: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: PBS treated CAR cells biological replicate 1

value: phosphate-buffered saline alone for 5 days


title: Expt 24 - D1 (24hr IL- 33 @ 20 ng/ml)

description: DM-178: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - non-atopic 1

description: dma1: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 25 - Releaser 1

description: DM-145: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 24 - D0 (4hr IL-33 @ 20 ng/ml)

description: DM-176: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 26 - non-atopic 4

description: dma4: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: HNSCC_HPV-_HN.6

value: Male

value: Laryngeal HNSCC


title: HNSCC_HPV+_HN.1

value: HPV positive


title: without SR1, with ZFN HT21


title: Expt 24 - D1 (24hr IL3 @ 10 ng/ml)

description: DM-177: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: HNSCC_HPV-_HN.7

value: Tongue HNSCC


title: HNSCC_HPV+_HN.2


title: Expt 24 - D0 (4hr IL-3 @ 10 ng/ml)

description: DM-175: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 24 - D0 (4hr control)

description: DM-174: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D0 (4hr control)


title: HNSCC_HPV-_HN.5


title: Expt 22 - D2 (24hr IL-3 @ 10 ng/ml, then IL-2 @ 20 ng/ml for 24hrs)

description: DM-154: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 24 - D0

description: DM-173: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 23 - D2 (48hr IL-3 @ 10 ng/ml)

description: DM-167: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 23 - D2 (24hr IL-3 @ 10 ng/ml, then IL-2 @ 20 ng/ml for 24hrs)

description: DM-168: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 22 - D0

description: DM-149: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 22 - D2 (24hr IL-3 @ 10 ng/ml, then IL-33 @ 20 ng/ml for 24hrs)

description: DM-153: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: HNSCC_HPV+_HN.3


title: Expt 21 - D2 (48hr IL-3 @ 10 ng/ml)

description: DM-143: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 21 - D2 (24hr IL-3 @ 10 ng/ml, then IL-33 @ 20 ng/ml for 24hrs)

description: DM-144: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 22 - D2 (48hr IL-3 @ 10 ng/ml)

description: DM-152: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: HNSCC_HPV+_HN.4

value: Tonsillar HNSCC


title: Expt 21 - D1 (24hr IL-5 @ 10 ng/ml)

description: DM-141: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 21 - D1 (24hr IL-33 @ 20 ng/ml)

description: DM-142: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 21 - D1 (24hr IL-3 @ 0.2 ng/ml)

description: DM-140: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 20 - D1 (24hr IL-3 @ 0.2 ng/ml)

description: DM-134: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 22 - D1 (24hr IL-33 @ 20 ng/ml)

description: DM-151: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 21 - D1 (24hr IL-3 @ 2 ng/ml)

description: DM-139: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 20 - D1 (24hr IL-3 @ 2 ng/ml)

description: DM-133: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 22 - D1 (24hr IL-3 @ 10 ng/ml)

description: DM-150: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 20 - D1 (24hr IL-5 @ 10 ng/ml)

description: DM-135: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 21 - D1 (24hr IL-3 @ 10 ng/ml)

description: DM-138: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 19 - D1 (24hr NGF @ 10 ng/ml)

description: DM-130: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D1 (24hr NGF @ 10 ng/ml)


title: Expt 20 - D0

description: DM-131: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 19 - D1 (24hr IL-3 @ 0.2 ng/ml)

description: DM-127: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 19 - D1 (24hr IL-3 @ 2 ng/ml)

description: DM-126: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 20 - D1 (24hr IL-3 @ 10 ng/ml)

description: DM-132: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 18 - D1 (24hr IL3 @ 0.06 ng/ml)

description: DM-110: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 19 - D1 (24hr IL-5 @ 10 ng/ml)

description: DM-129: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 18 - D1 (24hr IL-5 @ 10 ng/ml)

description: DM-111: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 17 - D1 (24hr IL-5 @ 10 ng/ml)

description: DM-172: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 18 - D1 (24hr NGF @ 10 ng/ml)

description: DM-112: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 18 - D1 (24hr IL-3 @ 0.2 ng/ml)

description: DM-109: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 16 - D2 (48hr IL-3 @ 2 ng/ml)

description: DM-117: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 17 - D1 (15hr FMLP @ 100 nM)

description: DM-170: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D1 (15hr FMLP @ 100 nM)


title: Expt 16 - D2 (24hr IL-3 @ 2 ng/ml, then aIgE @ 0.5 µg/ml for 24hrs)

description: DM-115: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 18 - D0

description: DM-107: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 19 - D1 (24hr IL3 @ 0.06 ng/ml)

description: DM-128: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 18 - D1 (24hr IL-3 @ 2 ng/ml)

description: DM-108: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 17 - D0

description: DM-169: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 21 - D0

description: DM-137: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 16 - D2 (24hr IL-3 @ 2 ng/ml, then IL-33 @ 10 ng/ml for 24hrs)

description: DM-118: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D2 (24hr IL-3 @ 2 ng/ml, then IL-33 @ 10/ml for 24hrs)


title: Expt 19 - D0

description: DM-125: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 16 - D0

description: DM-113: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 14 - D0 (2hr FMLP @ 100 nM)

description: DM-157: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D0 (2hr FMLP @ 100 nM)


title: Expt 16 - D1 (15hr aIgE @ 0.5 µg/ml)

description: DM-114: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D1 (15hr aIgE @ 0.5 µg/ml)


title: Expt 14 - D1 (24hr IL-3 @ 10 ng/ml)

description: DM-161: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: basophils (purified to average of 99%)


title: Expt 14 - D1 (15hr aIgE @ 0.5 µg/ml)

description: DM-159: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 14 - D1 (15hr FMLP @ 100 nM)

description: DM-160: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 14 - D1 (24hr IL-33 @ 20 ng/ml)

description: DM-162: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 16 - D1 (24hr IL-3 @ 2 ng/ml)

description: DM-116: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 14 - D0 (2hr aIgE @ 0.5 µg/ml)

description: DM-156: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D0 (2hr aIgE @ 0.5 µg/ml)


title: Expt 17 - D1 (24hr IL-5 @ 30 ng/ml)

description: DM-171: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 4 - D1 (IL3 @ 10 ng/ml)

description: DM-96: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 4 - D1 (no IL3)

description: DM-95: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D1 (no IL3)


title: Expt 3 - D1 (no IL3)

description: DM-92: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 4 - D0

description: DM-94: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 3 - D1 (IL3 @ 10 ng/ml)

description: DM-93: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 14 - D0 (2hr ctrl)

description: DM-155: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D0 (2hr ctrl)


title: K562, scrambled shRNA control, rep3

city: London

first: Andrea

last: Kuehnl

address: Great Maze Pond

country: United Kingdom

institute: King's College London

description: lentiviral pLKO scrambled shRNA control

hyb_protocol: 10ug of biotinylated and fragmented cRNA were hybridized unto the GeneChip® Human Genome U133A 2.0 array, incubated in the GeneChip® Hybridization Oven 645 at 60 RPM and 45°C for approximately 16h; arrays were washed and stained using the GeneChip® Fluidics Station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (P/N 900720).

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G

data_processing: Upon generation of cel files, these were loaded on the Expression Console software from Affymetrix to observe data quality parameters and generate chp files under gene rma level analysis. Chp files were then imported into Glucore and a q score of 0.1 was used as as stringency.

source_name: K562 after Wnt3a stimulation, scrambled shRNA control

label_protocol: 500ng total RNA spiked with Poly-A controls was processed into biotinylated cRNA following the GeneChip® 3' IVT PLUS Reagent Kit instructions (P/N 902416) supplied by Affymetrix

growth_protocol: K562 were cultured under standard conditions after transient transfection of EGFP-CXXC5 vector (samples 1-6) or stable lentiviral infection of  CXXC5 shRNA (pLKO.1; clone TRCN0000144558 and TRCN0000142729 (samples 7-12)

extract_protocol: Total RNA was harvested after 8h using the RNeasy Midi Kit (Qiagen)

treatment_protocol: K562 cells were incubated in serum-free medium with 100ng/ml Wnt3a protein

value: AML cell line


title: K562, CXXC5 shRNA, rep1

description: lentiviral pLKO CXXC5 shRNA (clone TRCN0000144558 and TRCN0000142729)

source_name: K562 after Wnt3a stimulation, CXXC5 knockdown


title: Expt 3 - D0

description: DM-91: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: K562, pEGFP-CXXC5, rep2

description: Human CXXC5 inserted into pEGFP-C2 vector transfected using the Lonza Nucleofector II

source_name: K562 after Wnt3a stimulation, CXXC5 overexpression


title: K562, pEGFP-C2 empty vector control, rep1

description: empty pEGFP-C2 vector transfected using the Lonza Nucleofector II

source_name: K562 after Wnt3a stimulation, vector control


title: K562, pEGFP-CXXC5, rep1


title: K562, pEGFP-C2 empty vector control, rep3


title: K562, CXXC5 shRNA, rep3


title: K562, scrambled shRNA control, rep2

description: lentiviral pLKO scrambled shRNA control


title: K562, CXXC5 shRNA, rep2


title: K562, pEGFP-C2 empty vector control, rep2


title: T98G-untreated, biological replicate 1

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description: Gene expression data from a Glioblastoma cell line

hyb_protocol: The labeled aRNAs were then mixed with hybridization master mix, and the hybridization mixtures were then denatured at 95 °C for 5 min, followed by 45 °C for 5 min, and then kept at 45 °C until applied to the hybridization tray (GeneAtlas System; 120 μL hybridization mixture of a cell culture was transferred into a well of a four-well hybridization tray). The array strip was immerse into hybridization mixture and incubated in theHybridization Station at 45 °C for 16 h.

scan_protocol: The intensity of each hybridized probe was generated using the GeneAtlas Imaging Station.

data_processing: The raw .CEL files were normalized and summarized using RMA method in R Bioconductor.

source_name: Glioblastoma cell line

label_protocol: Biotinylated antisense RNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using an GeneCHip 3′ IVT Express kit (Affymetrix), as described by the manufacturer.

growth_protocol: GSCs were cultured in DMEM/F12 (Invitrogen) supplemented with B27 (1:50), heparin (5 mg/mL), basic FGF (bFGF) (20 ng/mL), and EGF (20 ng/mL). LN428 cells were cultured in alpha MEM supplemented with 10% heat inactivated FBS, L-glutamine antibiotic/antimycotic and gentamycin. T98G and U87 glioblastoma cells were cultured in EMEM supplemented with 10% heat inactivated FBS,Sodium Pyruvate,MEM Non Essential Amino acids, antibiotic/antimycotic and Gentamycin. U373 glioblastoma cells were cultured DMEM containing 10% heat inactivated FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin.  LN444 and LN44-AA cells were cultured in DMEM with high glucose (Invitrogen) containing 10% (vol/vol) FBS (HyClone-Thermo Fisher), 100 units/mL penicillin, and 100 μg/mL streptomycin (Invitrogen). All the cells were maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol: Cells were collected in the exponential phase of growth by 500 rpm centrifigation and then washed twice with 1x PBS. Followed, the cells were lysed with 1 mL Qiazol lysis reagent.Total RNA was then extracted and purified using the Qiagen RNeasy Mini kit (catalog no. 217004) according to the manufacturer’s instructions.

value: Glioblastoma cell line

value: Brain

tag: stem cell

value: No


title: U373


title: U87


title: K562, scrambled shRNA control, rep1

description: lentiviral pLKO scrambled shRNA control


title: T98G-untreated, biological replicate 2


title: K562, pEGFP-CXXC5, rep3


title: MD13, biological replicate 1

description: Gene expression data from Mesenchymal glioma stem cells (Mes-GSC)

source_name: Mesenchymal glioma stem cells (Mes-GSC)

value: Mesenchymal glioma stem cells (Mes-GSC)

value: Yes


title: MD30, biological replicate 1


title: T98G-untreated, biological replicate 3


title: LN444-AA


title: MD13, biological replicate 3


title: MD30, biological replicate 3


title: LN444


title: MD13, biological replicate 2


title: LN428, biological replicate 1


title: MD30, biological replicate 2


title: LN428, biological replicate 2


title: LN428, biological replicate 3


title: F298_MS

city: Rotterdam

first: Esther

last: Korpershoek

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC University Medical Center Rotterdam

hyb_protocol: The hybridization was pêrformed in the Tecan HS4800 PRO (Tecan Group Ltd., Mannedorf, Switzerland),

scan_protocol: The arrays were scanned with the Tecan Scanner (Tecan Group Ltd.)).

data_processing: Raw mRNA data were analyzed using R according to Affymetrixs instructions and an Affymetrix script from the Bioconductor website. Background correction was performed according to the RMA background correction method. The statistical analyses were perfomed through the freely available software: Pomelo II

source_name: human pheochromocytoma

label_protocol: labeling was performed by One-Cycle Target Labeling using the 3IVT Espress kit according manufacturers instructions (Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was isolated using RNA-Bee according manufacturers instructions (Amsbio, Abingdon, United Kingdom). cDNA was generated with oligo-dT primer and Superscript TM II Reverse Transcriptase (Invitrogen Life Technologies, Carlsbad, USA), according to the manufacturers protocol.

tag: tissue type

value: Primary tumor tissue

value: malignant

tag: mutation type

value: SPORADIC


title: ASTROCYTE, biological relicate 5

description: Gene expression data from Norman human astrocytes

source_name: Norman human astrocyte

value: Norman human astrocyte


title: ASTROCYTE, biological relicate 1


title: ASTROCYTE, biological relicate 3


title: F376_MB

source_name: human sympathetic paraganglioma

value: SDHB


title: AC20, biological replicate 2

description: Gene expression data from Proneural glioma stem cellsl (PN-GSC)

source_name: Proneural glioma stem cells (PN-GSC)

value: Proneural glioma stem cells (PN-GSC)


title: PGL65_BS

value: benign


title: ASTROCYTE, biological relicate 2


title: ASTROCYTE, biological relicate 4


title: F303_MS


title: F228_MS


title: AC20, biological replicate 3


title: PGL167_MS


title: PGL28_BS


title: F418_MS


title: F207_MS


title: F170_MS


title: F318_BS


title: PGL172_BS


title: PGL30_MS


title: PGL95_BS


title: F233_BV

value: VHL


title: PGL114_BS


title: F245_MS


title: AC17, biological replicate 3


title: AC20, biological replicate 1


title: Expt 14 - D0

description: DM-158: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

value: basophils (purified to average of 99%)


title: AC17, biological replicate 2


title: 84, biological replicate 3


title: F305_BS


title: 83, biological replicate 3


title: 84, biological replicate 1


title: F296_BS


title: F331_BS


title: F121_BS


title: F285_BS


title: F112_BS


title: PLG29_BS


title: 816, biological replicate 2


title: 84, biological replicate 2


title: F343_BS


title: F277_BS


title: F134_BS


title: F246_BS


title: 83, biological replicate 2


title: F122_BS


title: 816, biological replicate 3


title: 816, biological replicate 1


title: F202_MS


title: F234_BS


title: F281_BS


title: 83, biological replicate 1


title: F108_BS


title: F320_BS


title: F321_BS


title: F106_BS


title: AC17, biological replicate 1


title: F99_BS


title: F323_BD

value: SDHD


title: 528, biological replicate 3


title: 528, biological replicate 1


title: F100_BN


title: F239_BD


title: F103_BS


title: F237_BD


title: F322_BD


title: 16WF, biological replicate 3

description: Gene expression data from Normal neurospheres

source_name: Normal  neurosphere

value: Normal  neurosphere


title: F419_BS

value: RET


title: F330_BR


title: 16WF, biological replicate 1


title: 16WF, biological replicate 2


title: L12

city: Dublin

first: Sinead

middle: T

last: Aherne

address: Glasvevin

country: Ireland

institute: Dublin City University

description: Test

data_processing: Each miRNA was normalised by the ΔΔCt method using the average within sample Ct value. This technique involves the use of the mean expression value of all expressed microRNAs in a given sample as a normalisation factor for microRNA real-time quantitative PCR data. Thus the average within sample Ct value for each card is calculated by averaging all miRNA Ct values for each individual sample. This was performed using the Bioconductor package HTqPCR (www.bioconductor.org). The non-parametric Kruskal-Wallis test was used to determine between group variations by rank as the data was not normally distributed. A Wilcoxon rank sum test was subsequently used to perform pair-wise comparisons between the 5 groups for the significant miRNAs identified by the Kruskal-Wallis test. The file "fold_change_data.txt" is available on the series record and reports test/control (i.e., polyp/control) ratios.

source_name: blood plasma

label_protocol: Reverse transcription and quantitative PCR (qPCR) were performed on equal volumes of RNA from each sample according to the manufacturer's instructions using TaqMan® MicroRNA Reverse Transcription Kit (Cat no 4366596, Applied Biosystems) and Megaplex RT Primers to convert the miRNAs to cDNA, TaqMan® PreAmp Master Mix (Cat no 4391128, Applied Biosystems) and Megaplex PreAmp Primers for a preamplification step before real-time analysis. qPCR was performed using TaqMan® Universal Master Mix II, no UNG (Cat no 4440048, Applied Biosystems) on the 7900HT Fast Real-Time PCR system (Applied Biosystems).

extract_protocol: Total RNA was isolated from 60µl of each plasma sample using the miRNeasy mini kit (Cat no 217004, Qiagen). The Qiagen supplementary protocol (Purification of total RNA, including small RNAs, from serum or plasma) was utilised with the following modifications: thawed plasma samples were centrifuged at 1000 x g for 5 minutes at 4ºC to remove excess debris from samples, RNA was extracted from the upper 50µl of each sample. To elute the RNA, 50µl of nuclease-free water was added to each spin column and incubated for 1 minute at room temperature before centrifuging into non-stick RNase-free microfuge tubes (Cat no AM12350, Ambion) to elute the RNA.

treatment_protocol: Plasma samples were collected according to standard phlebotomy procedures. 10 ml of blood sample was collected into EDTA plasma tubes and immediately placed in ice. The tubes were centrifuged at 1000 x g for 10 minutes at 4ºC. Plasma was denuded by pipette from the cellular material, aliquoted in the cryovial tubes, labelled and stored at -80ºC until time of analysis. The time from sample procurement to storage at -80°C was less than 3 hours. Each plasma sample underwent no more than 3 freeze / thaw cycles prior to analysis.

tag: disease status

value: Late Stage CRC (III & IV)

value: blood plasma


title: L10

description: Test


title: F304_BR


title: L8

description: Test


title: L7

description: Test


title: 157, biological replicate 3

value: Brain


title: L4

description: Test


title: L3

description: Test


title: 528, biological replicate 2


title: Loop-2: C2 vs. B3

city: Hsinchu

first: Chaang Ray

last: Chen

address: 101, Section 2, Kuang-Fu Road

department: Biomedical Engineering and Environmental Sciences

country: Taiwan

institute: National Tsing Hua University

hyb_protocol: Hybridization was performed at 65℃ in a water bath for16 to 18 hours, and arrays were washed following the manufacturer’sprotocol (Corning Life Sciences, New York, NY, USA).

scan_protocol: The arrays were scanned using the GenePix 4000B scanner (AxonInstruments, Foster City, CA, USA)

data_processing: Microarray data preprocessing, normalization, and statistical analysis was performed using a bioinformatics software suite called THEME (http://metadb.bmes.nthu.edu.tw/theme).

source_name: Loop-2: C2 patient

label_protocol: Fluorescence-labeled (Cy3, Cy5-3DNA Capture Reagent) cDNA was conducted using 3DNA Array 900 labeling kit, following the manufacturer’s protocols (Genisphere, Hatfield, PA, USA). Reverse transcription was performed using SuperScript II (Invitrogen, Carlsbad, CA, USA).

extract_protocol: We extracted total RNA using RNeasy mini kit following manufacturer’s protocol (Qiagen, Valencia, CA, USA). Total RNA quantity and quality was assessed by spectrophotometer UV absorption at 260nm and 280nm. then α- and β-globin mRNA were reduced from a portion of the total RNA samples using the GLOBINclear™ human kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions, with the recommended start quantity of 10 μg of total RNA. The quality of total RNA was evaluated using the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA)

value: Human red blood cell

source_name: Loop-2: B3 patient


title: L2

description: Test


title: F307_BR


title: Loop-2: C3 vs. B1

source_name: Loop-2: C3 patient

source_name: Loop-2: B1 patient


title: Loop-2: D2 vs. B3

source_name: Loop-2: D2 patient


title: F342_BR


title: Loop-2: D2 vs. C3


title: 1123, biological replicate 1

value: Mesenchymal glioma stem cells (Mes-GSC)

value: Yes


title: Loop-2: C1 vs. B2

source_name: Loop-2: C1 patient

source_name: Loop-2: B2 patient


title: 157, biological replicate 2


title: L1

description: Test


title: Loop-2: B1 vs. D1

source_name: Loop-2: D1 patient


title: 2792 liver-aggressive explant

city: Montreal

first: Peter

middle: M

last: Siegel

state: Quebec

address: 1160 Pine avenue West

department: Medicine

institute: McGill University

hyb_protocol: Hybridization to 44K whole mouse genome microarray gene expression chips (Agilent Technologies) was conducted following manufacturer’s protocol (Agilent Technologies).

scan_protocol: Microarray chips were then washed and immediately scanned using a DNA Microarray Scanner (Model G2565BA, Agilent Technologies).

data_processing: Microarray data were feature extracted using Feature Extraction Software (v. 9.5.3.1) available from Agilent, using the default variables. Microarray expression data were normalized and analyzed using GeneSpring software (V7.3, Agilent Technologies). Each group (parental cell line and the explants derived form mammary fat pad, bone, lung and liver metastasis) was individually compared to all the other groups. A two-fold change cut off was determined and differentially expressed genes were selected using a non-parametric test coupled with a false discovery rate of 0.05.

source_name: 2792 liver-aggressive explant

label_protocol: Purified total RNA (40 ng) was subjected to two consecutive rounds of T7-based amplification using Amino Allyl MessageAmp II kits (Applied Biosystems, Streetsville, ON, Canada) and the resulting aRNA was conjugated to Cy5 dyes (GE Healthcare Bio-sciences, Bair d’Urfe, QC, Canada).

growth_protocol: All cell lines were grown in DMEM supplemented with 10% fetal bovine serum, 10 mmol/L HEPES, 1 mmol/L sodium pyruvate, 1.5 g/L sodium bicarbonate, penicillin/streptomycin, and fungizone.

extract_protocol: RNA was extracted from 4T1 parental and individual in vivo selected metastatic sub-populations using RNeasy Mini Kits and QIAshredder columns (Qiagen, Mississauga, ON, Canada).

value: liver-aggressive explant


title: E8

description: Test

value: Early Stage CRC (I & II)


title: Loop-2: B2 vs. A3

source_name: Loop-2: A3 patient


title: Loop-2: C3 vs. A1

source_name: Loop-2: A1 patient


title: F284_BR

source_name: human pheochromocytoma

value: Primary tumor tissue


title: 157, biological replicate 1


title: F325_BN


title: 2869 liver-aggressive explant

source_name: 2869 liver-aggressive explant


title: 1123, biological replicate 2

source_name: Mesenchymal glioma stem cells (Mes-GSC)


title: 1123, biological replicate 3


title: Loop-2: A3 vs. D3

source_name: Loop-2: D3 patient


title: Loop-2: C2 vs. A3


title: Loop-2: D1 vs. C2


title: E7

description: Test


title: 593 bone-aggressive explant

source_name: 593 bone-aggressive explant

value: bone-aggressive explant


title: Loop-2: B3 vs. D3


title: 2776 liver-aggressive explant

source_name: 2776 liver-aggressive explant


title: F130_BS

value: SPORADIC


title: E3

description: Test

source_name: blood plasma


title: E4

description: Test


title: E2

description: Test


title: Loop-2: B3 vs. A1

source_name: Loop-2: B3 patient


title: Loop-2: A1 vs. C1


title: E1

description: Test


title: E6

description: Test


title: Loop-1: A3 vs. C3

source_name: Loop-1: A3 patient

source_name: Loop-1: C3 patient


title: Loop-2: D1 vs. B2


title: Loop-2: A1 vs. D1


title: 533 lung-aggressive explant

source_name: 533 lung-aggressive explant

value: lung-aggressive explant


title: HD14

description: Test

value: Advanced Adenoma


title: 590 bone-aggressive explant

source_name: 590 bone-aggressive explant


title: Loop-1: D2 vs. C3

source_name: Loop-1: D2 patient


title: 537 lung-aggressive explant

source_name: 537 lung-aggressive explant


title: E5

description: Test


title: HD13

description: Test


title: 154 primary tumor explant

source_name: 154 primary tumor explant

value: primary tumor explant


title: Loop-1: B2 vs. A3

source_name: Loop-1: B2 patient


title: Loop-1: C2 vs. B3

source_name: Loop-1: C2 patient

source_name: Loop-1: B3 patient


title: Loop-1: C2 vs. A3


title: 148 primary tumor explant

source_name: 148 primary tumor explant


title: 152 primary tumor explant

source_name: 152 primary tumor explant


title: HD12

description: Test


title: Loop-1: D2 vs. B3


title: Loop-1: B3 vs. D3

source_name: Loop-1: D3 patient


title: 526 lung-aggressive explant

source_name: 526 lung-aggressive explant


title: HD11

description: Test


title: Loop-1: A2 vs. C2

source_name: Loop-1: A2 patient


title: 592 bone-aggressive explant

source_name: 592 bone-aggressive explant


title: 4T1 parental rep E

source_name: 4T1 parental rep E

value: 4T1 parental


title: HD9

description: Test

source_name: blood plasma


title: HD8

description: Test


title: Expt 15 - D1 (15hr anti-IgE Ab @ 0.5 µg/ml)

city: Baltimore

description: DM-29: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

data_processing: Illumina Bead Studio was used for generating the data. Due to the way data was processed in the published description of these results (no global normalization), the matrix of results that is normally entered as normalized is not normalized but instead a replicate of the non-normalized data.

source_name: peripheral blood

growth_protocol: purified basophils were cultured in RPMI-1640 medium supplemented with 20 µg/ml gentamycin, 0.03% human serum albumin and glutamine

treatment_protocol: the title of each sample identifies the treatment; D0 = day 0, D1 = day 1, D3 = day 3; IL-3 = interleukin-3, anti-IgE Ab = a monoclonal 6061P (Hybridoma Labs, Baltimore, MD) anti-IgE antibody (where 0.5 µg/ml is considered optimal)

value: basophils (purified to average of 99%)

value: D1 (15 hr anti-IgE Ab @ 0.5 µg/ml)


title: HD2

description: Test


title: HD1

description: Test


title: 4T1 parental rep D

source_name: 4T1 parental rep D


title: AA20

description: Test


title: AA19

description: Test


title: Expt 13 - D0 (2hr anti-IgE Ab @ 0.5 µg/ml)

description: DM-33: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D0 (2hr anti-IgE Ab @ 0.5 µg/ml)


title: Expt 15 - D1 (15hr control)

description: DM-28: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D1 (15hr control)


title: AA16

description: Test

value: blood plasma


title: Loop-1: D1 vs. C2

source_name: Loop-1: D1 patient

value: Human red blood cell


title: Loop-1: D3 vs. B1

source_name: Loop-1: B1 patient


title: Loop-1: C3 vs. B1

source_name: Loop-1: C3 patient


title: Loop-1: B3 vs. A1

source_name: Loop-1: A1 patient


title: YDFR.SL3, Vemurafenib, rep 1

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Gene expression of YDFR, micro-metastasis to lung

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: Onlyl gene-level analyses was performed. RMA normalization and summarization by mean were performed by Partek Genomics suite ((version 6.6) Copyright © 2012).

source_name: YDFR-human melanoma cells micro-metastasis to lung

growth_protocol: All human melanoma cells (YDFR.CB3, YDFR.SB3, YDFR.CB3CSL3) were grown in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mmol/ml L-glutamine, 100 units/ml penicillin, 0.1 mg/ml streptomycin, 12.5 units/ml nystatin and 1% Hepes (Biological Industries, Beit-Haemek, Israel).

extract_protocol: total RNA was isolated using the EZ-RNA Total RNA Isolation Kit (Biological Industries). RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.

treatment_protocol: Medium of melanoma cells resistant to Vemurafenib was supplemented with 1 µM PLX-4032 (Vemurafenib) (Selleck, Houston, TX) dissolved in Dimethyl Sulfoxide (DMSO) (Sigma-Aldrich, St. Louis, MO). Medium of the non-resistant melanoma cells was supplemented with the same amount of DMSO.

value: 1 µM PLX-4032 (Vemurafenib)

tag: malignancy stage

value: lung micro-metastasis


title: Expt 12 - D0 (2hr control)

description: DM-30: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

value: D0 (2hr control)


title: Expt 12 - D0 (2hr anti-IgE Ab @ 0.5 µg/ml)

description: DM-31: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 11 - D3 (IL3@10 ng/ml + anti-IgE Ab @ 0.5 µg/ml)

description: DM-10: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Loop-2: B2 vs. D2

source_name: Loop-2: B2 patient

source_name: Loop-2: D2 patient


title: Expt 15 - D0

description: DM-27: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: YDFR.SB3, DMSO, rep 1

description: Gene expression of YDFR, micro-metastasis to brain

scan_protocol: according to the instruction manual, as described in the Affymetrix website

source_name: YDFR-human melanoma cells micro-metastasis to brain

value: 1 µM DMSO

value: brain micro-metastasis


title: Loop-1: C3 vs. A1


title: 4T1 parental rep F

source_name: 4T1 parental rep F


title: YDFR.SL3, DMSO, rep 1

label_protocol: according to the instruction manual, as described in the Affymetrix website


title: YDFR.CB3, DMSO, rep 1

description: Gene expression of YDFR, macro-metastasis to brain

source_name: YDFR-human melanoma cells macro-metastasis to brain

value: brain macro-metastasis


title: Loop-1: D1 vs. B2

source_name: Loop-1: B2 patient


title: Expt 13 - D0 (2hr control)

description: DM-32: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Loop-1: D3 vs. C1

source_name: Loop-1: D3 patient

source_name: Loop-1: C1 patient


title: AA15

description: Test


title: YDFR.SB3, Vemurafenib, rep 1


title: YDFR.CB3, Vemurafenib, rep1


title: Expt 11 - D3 (IL3@10 ng/ml)

description: DM-9: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: AA14

description: Test


title: Loop-2: A2 vs. D2

source_name: Loop-2: A2 patient


title: AA13

description: Test

source_name: blood plasma


title: AA12

description: Test


title: Loop-2: A3 vs. C3

source_name: Loop-2: A3 patient

source_name: Loop-2: C3 patient


title: Loop-2: D3 vs. C1

source_name: Loop-2: D3 patient

source_name: Loop-2: C1 patient


title: AA11

description: Test


title: P15

description: Test

value: Polyp


title: P16

description: Test


title: Loop-2: C1 vs. A2


title: P14

description: Test


title: Expt 10 - D0

description: DM-5: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report

source_name: peripheral blood


title: Expt 10 - D3 (IL3@10 ng/ml)

description: DM-6: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: P13

description: Test


title: Expt 10 - D3 (IL3@10 ng/ml + anti-IgE Ab @ 0.5 µg/ml)

description: DM-7: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: P12

description: Test


title: Loop-2: B1 vs. A2

source_name: Loop-2: B1 patient


title: Loop-2: D3 vs. B1


title: P1

description: Test


title: Loop-1: B1 vs. A2

source_name: Loop-1: B1 patient

source_name: Loop-1: A2 patient


title: Loop-1: A3 vs. D3

source_name: Loop-1: A3 patient


title: Loop-1: B2 vs. D2

source_name: Loop-1: D2 patient


title: Expt 9 - D0

description: DM-14: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Loop-1: C1 vs. A2


title: Loop-1: A2 vs. D2


title: Expt 9 - D3 (IL3@10 ng/ml + anti-IgE Ab @ 0.5 µg/ml)

description: DM-16: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 9 - D3 (IL3@10 ng/ml)

description: DM-15: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 7 - D1 (IL3@10 ng/ml)

description: DM-40: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: C18

description: Control

value: Control


title: C17

description: Control


title: Expt 8 - D3 (IL3@10 ng/ml + anti-IgE Ab @ 0.5 µg/ml)

description: DM-13: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Loop-1: C1 vs. B2


title: P5

description: Test


title: P11

description: Test


title: Expt 8 - D3 (IL3@10 ng/ml)

description: DM-12: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 8 - D0

description: DM-11: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Loop-1: A1 vs. D1

source_name: Loop-1: A1 patient

source_name: Loop-1: D1 patient


title: Loop-2: A2 vs. C2

source_name: Loop-2: C2 patient


title: Expt 7 - D0

description: DM-39: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: C16

description: Control


title: Loop-1: B1 vs. D1


title: Loop-1: A1 vs. C1


title: Expt 6 - D1 (IL3@10 ng/ml)

description: DM-25: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 7 - D3 (IL3@10 ng/ml)

description: DM-41: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 6 - D3 (IL3@10 ng/ml)

description: DM-26: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: Expt 6 - D0

description: DM-24: the sample title describes a preparation of basophils (Expt xx) and the conditions of treatment and follow naming consistent with the published report


title: C15

description: Control


title: C13

description: Control


title: OV202SH1_3

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: replicate 3

source_name: primary OV202 cell line

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.

value: ovarian carcinoma

tag: group


title: C14

description: Control


title: C12

description: Control


title: OV202SH1_2

description: replicate 2


title: C11

description: Control