title: NHEK_vehicle_rep2

status: Public on Dec 31 2015

type: RNA

city: Berlin

first: Annabell

last: Plauth

state: Berlin

address: Ihnestrasse 63-73

department: OWL

country: Germany

institute: MPI Molgen

description:
7680504041_J
replicate 2

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data were normalised using cubic spline normalisation with Illumina GenomeStudio

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: skin

label_protocol: standard Illumina protocol

extract_protocol: RNA was by clean-up and treated with DNase I using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: NHEK treated for 16h with 50µM RSV or vehicle

tag: treatment

value: vehicle

tag: cell type

value: primary neonatal normal human epidermal keratinocytes (NHEK)


title: NHEK_vehicle_rep3

description:
7680504041_K
replicate 3


title: NHEK_50uM_RSV_rep1

description:
7680504041_E
replicate 1

value: 16 hours 50 µM resveratrol


title: siRNA against Sat III  transfection, heat shock treatment followed by recovery, replicate 4

city: Turku

first: Lea

last: Sistonen

address: Tykistökatu 6 B

department: Department of Biosciences

country: Finland

institute: Åbo Akademi

description:
siRNA III 1h HS 6hR 4
Replicate 4

hyb_protocol: From each sample, 750 ng cRNA was hybridized to Illumina's HumanHT-12 Expression BeadChip, version 3 (cat no BD-103-0203) at 58°C overnight (19 h) according to Illumina Whole-Genome Gene Expression Direct Hybridization protocol, revision A.

scan_protocol: The chips were scanned with Illumina BeadArray Reader, BeadScan software version 3.5, and numerical results were extracted with Illumina's GenomeStudio v1.0 software without any normalization.

data_processing:
The gene expression microarray data was analyzed using R and Bioconductor softwares. The data was quantile normalized.
The Sample data table and non-normalized data matrix do not include values for the control probes.

label: Biotin

source_name: HEK293T cells, siRNA against Sat III, heat shock followed by recovery

label_protocol: To synthesize the biotinylated cRNA, 300 ng of total RNA was amplified using Ambion's Illumina TotalPrep RNA Amplification kit (cat #AMIL1791).

growth_protocol: Human HEK293T cells were cultured in Dulbecco's Modified Eagle's medium. The media were supplemented with 10% fetal calf serum, 2 mM L-glutamine and antibiotics (penicillin and streptomycin), and the cells were cultured in a humidified 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was isolated from HEK293T cells using the RNeasy kit (Qiagen).

treatment_protocol: Heat shocks were performed for 1 h at 42 °C by submersion in a water bath. Recovery was for 6 h.

tag: cell line

tag: sirna

value: against Sat III

value: heat shock followed by recovery


title: scrambled transfection, heat shock treatment, replicate 4

description:
Scrambled 1h HS 4
Replicate 4

source_name: HEK293T cells, scrambled siRNA, heat shock

value: scrambled

value: heat shock


title: scrambled transfection, heat shock treatment followed by recovery, replicate 4

description:
Scrambled 1h HS 6hR 4
Replicate 4

source_name: HEK293T cells, scrambled siRNA, heat shock followed by recovery


title: NHEK_vehicle_rep4

description:
7680504041_L
replicate 4


title: siRNA against Sat III transfection, heat shock treatment, replicate 4

description:
siRNA III 1h HS 4
Replicate 4

source_name: HEK293T cells, siRNA against Sat III, heat shock


title: siRNA against Sat III transfection, replicate 2

description:
siRNA III Control 2
Replicate 2

source_name: HEK293T cells, siRNA against Sat III, untreated


title: scrambled transfection, heat shock treatment, replicate 3

description:
Scrambled 1h HS 3
Replicate 3


title: NHEK_50uM_RSV_rep2

description:
7680504041_F
replicate 2


title: siRNA against Sat III transfection, replicate 4

description:
siRNA III Control 4
Replicate 4


title: NHEK_50uM_RSV_rep3

description:
7680504041_H
replicate 3


title: siRNA against Sat III  transfection, heat shock treatment followed by recovery, replicate 2

description:
siRNA III 1h HS 6hR 2
Replicate 2


title: scrambled transfection, heat shock treatment followed by recovery, replicate 2

description:
Scrambled 1h HS 6hR 2
Replicate 2


title: siRNA against Sat III  transfection, heat shock treatment followed by recovery, replicate 1

description:
siRNA III 1h HS 6hR 1
Replicate 1


title: siRNA against Sat III transfection, heat shock treatment, replicate 2

description:
siRNA III 1h HS 2
Replicate 2


title: scrambled transfection, heat shock treatment, replicate 2

description:
Scrambled 1h HS 2
Replicate 2


title: siRNA against Sat III transfection, heat shock treatment, replicate 1

description:
siRNA III 1h HS 1
Replicate 1


title: siRNA against Sat III  transfection, heat shock treatment followed by recovery, replicate 3

description:
siRNA III 1h HS 6hR 3
Replicate 3


title: NHEK_vehicle_rep1

description:
7680504041_I
replicate 1


title: scrambled transfection, heat shock treatment followed by recovery, replicate 1

description:
Scrambled 1h HS 6hR 1
Replicate 1


title: scrambled transfection, replicate 3

description:
Scrambled Control 3
Replicate 3

source_name: HEK293T cells, scrambled siRNA, untreated


title: scrambled transfection, replicate 4

description:
Scrambled Control 4
Replicate 4


title: scrambled transfection, heat shock treatment followed by recovery, replicate 3

description:
Scrambled 1h HS 6hR 3
Replicate 3


title: scrambled transfection, replicate 2

description:
Scrambled Control 2
Replicate 2


title: siRNA against Sat III transfection, replicate 1

description:
siRNA III Control 1
Replicate 1


title: EXPERIMENT 02, nodules, XTR-278#17

city: Evry

first: stefano

last: cairo

address: 4 rue Pierre Fontaine

country: France

institute: Xentech

description: tumor fragment

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: residual nodules post-treatment

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

extract_protocol: RNA was extracted from microdissected areas using the RNeasy Mini kit (Qiagen, Valencia, CA). This approach allowed isolating foci of human tumor cells from the murine stroma. Gene expression analysis was performed with Affymetrix Exon 1.0 ST microarrays. Hybridization, data normalization and statistical analysis were outsourced to GenoSplice Technology (Paris, France).

treatment_protocol: Female Swiss nude mice, 10-week old, were purchased from Charles River (Les Arbresles, France). PDXs with tumors in a range between 60 and 200 mm3 received one dose of adriamycin (DOX, Doxorubicin, Teva Pharmaceuticals, Paris, France) and cyclophosphamide (Endoxan, Baxter, Maurepas, France) at the doses of 2 mg/kg, 6 mg/kg and 100 mg/kg

tag: tissue

value: human breast cancer xenograft

tag: sample type

value: residual nodules post-treatment


title: EXPERIMENT 03, nodules, XTR-240#06

description: tumor fragment


title: EXPERIMENT 03, control, XTR-240#03

description: tumor fragment

source_name: control tumor

value: control tumor


title: EXPERIMENT 02, nodules, XTR-278#5

description: tumor fragment


title: EXPERIMENT 03, nodules, XTR-240#12

description: tumor fragment


title: EXPERIMENT 02, control, XTR-278#12

description: tumor fragment


title: EXPERIMENT 03, control, XTR-240#10

description: tumor fragment


title: EXPERIMENT 03, nodules, XTR-240#13

description: tumor fragment


title: EXPERIMENT 03, control, XTR-240#26

description: tumor fragment


title: EXPERIMENT 02, control, XTR-278#11

description: tumor fragment


title: EXPERIMENT 03, nodules, XTR-240#04

description: tumor fragment


title: scrambled transfection, heat shock treatment, replicate 1

description:
Scrambled 1h HS 1
Replicate 1


title: EXPERIMENT 03, nodules, XTR-240#31

description: tumor fragment


title: UCC2003 versus UCC2003-luxS

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown in MRS supplemented with 0.05% cysteine

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 or UCC2003-luxS were grown in (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960), supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5

extract_protocol: Method for cell disruption, RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) BMC.Genomics 6: 77).

tag: genotype/variation

source_name: Bifidobacterium breve UCC2003-luxS grown in MRS supplemented with 0.05% cysteine


title: EXPERIMENT 02, control, XTR-278#7

description: tumor fragment


title: EXPERIMENT 01, nodules, XTR-299#15

description: tumor fragment


title: EXPERIMENT 02, nodules, XTR-278#32

description: tumor fragment


title: Bortezomib resistant KAS-6/1 multiple myeloma cells

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

country: USA

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing:
The non-normalized data were generated by GenomeStudio with background correction.
.txt files contain bead level data and each have 4 columns which are Code, Grn, GrnX, GrnY.
Code, the Array_Address_Id in illumina annotation file, is another kind of identifier corresponding to unique illumina probeid.
Grn, the intensity values of beads.
GrnX and GrnY matrices give the coordinates of each bead centre on the original TIFF image.
.csv files contain probe level and each have 4 columns which are Illumicode, N, Mean GRN, Dev GRN.
Illumicode, the Code in .txt file or Array_Address_Id in illumina annotation file, is another kind of identifier corresponding to unique illumina probeid.
N, is number of beads
Mean GRN and Dev GRN are robust means and standard deviations of the individual channel intensities.
The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Human multiple myeloma

label_protocol: 200 ng total RNA was amplified and biotin-labeled through a Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: KAS-6/1, ANBL-6 and bortezomib-resistant (BR) cells were cultured in RPMI 1640 (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Sigma; St Louis, MO), 100 U/mL penicillin, and 100 μg/mL streptomycin (Tissue Culture Facility, University of North Carolina), and maintained in 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using the TRIzol reagent according to the manufactory's guideline. Then the RNA was purified by the Qiagen RNeasy Mini Kit column.

treatment_protocol: Bortezomib-resistant (BR) cells were developed by exposing parental cells to serially increased drug concentrations.

value: KAS-6/1 multiple myeloma cells

value: Bortezomib resistant


title: EXPERIMENT 03, control, XTR-240#02

description: tumor fragment


title: EXPERIMENT 03, control, XTR-240#15

description: tumor fragment


title: Bortezomib resistant ANBL-6 multiple myeloma cells

value: ANBL-6 multiple myeloma cells


title: Wild type ANBL-6 multiple myeloma cells

value: Wild type


title: EXPERIMENT 02, nodules, XTR-278#b34

description: tumor fragment


title: Wild type KAS-6/1 multiple myeloma cells


title: scrambled transfection, replicate 1

description:
Scrambled Control 1
Replicate 1


title: EXPERIMENT 01, nodules, XTR-299#13

description: tumor fragment


title: EXPERIMENT 01, nodules, XTR-299#72

description: tumor fragment


title: EXPERIMENT 01, nodules, XTR-299#22

description: tumor fragment


title: EXPERIMENT 02, control, XTR-278#b2

description: tumor fragment


title: EXPERIMENT 01, control, XTR-299#34

description: tumor fragment


title: EXPERIMENT 01, control, XTR-299#35

description: tumor fragment


title: EXPERIMENT 01, control, XTR-299#33

description: tumor fragment


title: MO2058 1000 nM JQ1 treated replicate 1

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

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

scan_protocol: Scanning of the chip is conducted using an Affymetrix GeneChip® Scanner 3000 7G with autoloader.

data_processing: All microarray expression analysis was performed using R. The R package “affy” was used to read in probe intensity data, and the Robust Multi-Array Average (RMA) procedure from the “affy” package was used for background correction, quantile normalisation and probeset summarization.

source_name: Mantle Cell Lymphoma JQ1 treated

label_protocol: Cy3 labeled cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MO2058 cells were maintained in RPMI-1640 media with 10% FBS.

extract_protocol: Roche High Pure RNA isolation kit with on-column DNAse I digestion. Elution in RNAse free water.

treatment_protocol: Cells were treated with JQ1, as indicated,  for 8 hours prior to RNA isolation.

value: lymphocyte


title: EXPERIMENT 01, nodules, XTR-299#4

description: tumor fragment


title: MO2058 1000 nM JQ1 treated replicate 2


title: MO2058 250 nM JQ1 treated replicate 1

value: 250 nM JQ1


title: EXPERIMENT 01, control, XTR-299#31

description: tumor fragment


title: HCLE_WT serratia 1

city: Pittsburgh

first: Stephen

middle: Alan Kenneth

last: Harvey

state: PA

address: 203 Lothrop St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

description: WT serratia 1

hyb_protocol: Following fragmentation, 20 ug of cRNA was hybridized for 16 hr at 45 'C on GeneChip Mouse 430 2.0 microarrays. GeneChips were washed and stained in a Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing:
Data were analyzed with GCOS 1.4 (MAS 5.0 algorithm) using Affymetrix default analysis settings and global scaling as normalization method. The 2% trimmed mean target intensity of each array was arbitrarily set to 150.
GCOS 1.4 signal intensity. Presence/Absence flags for all 6 samples, and Increase/Decrease/No Change flags for all 15 pairwise comparisons were also provided (available in the 'complete_processed_data.txt).

source_name: HCLE_WT serratia

label_protocol: Biotinylated cRNAs (aRNAs) were prepared from 500 ng of total RNA using an Affymetrix 3'-IVT Express  kit, following the manufacturer's instructions

growth_protocol:
HCLE (Gipson lab): Human corneal limbal epithelial (HCLE) cells (Gipson et al., 2003 PMID:12766048) were cultured at 37°C (5% CO2) in keratinocyte serum free medium (KSFM) containing penicillin, streptomycin, 0.2 ng/ml embryonic growth factor (EGF), and 25 ug/ml bovine pituitary extract.
Serratia marcescens PIC3611: Overnight bacterial cultures were prepared by inoculating a single colony of bacteria into 5 ml LB broth (0.5% yeast extract, 1% tryptone, 0.5% NaCl) with shaking incubation for 18-20 h at 30 C.   Bacterial cultures were normalized by dilution to O.D.600 = 2.0 with LB broth, and bacteria were removed by centrifugation for 2 min at 16,000 x g. Supernatant was filtered  (0.22 um PVDF filter) prior to use.

extract_protocol: Cells were then treated with Sigma RNA later and RNA was extracted using a Sigma GenElute Mammalian total RNA miniprep kit followed by a Zymo RNA clean up kit according to manufacturer’s protocols

treatment_protocol: HCLE cells  in KSFM were seeded into 12 well dishes at a density of 1.2 x 10^4 cells per well. After 24h in culture,  KSFM was removed from the confluent cells and replaced with fresh medium containing 500 uL filtered bacterial supernatant or with 500 uL LB medium.  After 5h medium was removed and the cells washed once with PBS.

value: immortalized human corneal-limbal epithelial (HCLE) cells

tag: culture medium

value: KSFM+filtered bacterial supernatant

tag: s. marcescens genotype/variation

value: wild type


title: HCLE_WT serratia 2

description: WT serratia 2


title: EXPERIMENT 01, control, XTR-299#32

description: tumor fragment


title: Colorectal Cancer, Patient_29

city: Fuzhou

first: Xingrong

last: Lu

address: No. 29, Xinquan Road, Gulou District

country: China

institute: Affiliated Union Hospital of Fujian Medical University

description:
post-chemotherapy
481363

hyb_protocol: Microarray hybrid iza tion was performed at 45°C with rotation lasting 16 h using the Affymetrix GeneChip Hybridization Oven 640. The arrays were washed and stained (streptavidin –phycoerythrin) by Affymetrix GeneChip Fluidics Station 450 and then scanned on the Affymetrix GeneChip Scanner 3000 in order to analyze the hybridization data.

scan_protocol: The obtained scanned images were assessed firstly by visual inspection and then analyzed by the Affymetrix GeneChip Operating Software (GCOS 1.4).

data_processing: dChip software was used in the global scaling procedures. Signal log ratio and the gene symbol of differentially expressed genes were input into the MAS3.0 software for gene ontology and pathway analyses.

source_name: tumor sample of patients undergone neoadjuvant FOLFOX4   chemotherapy

label_protocol: Total RNA was used to synthesize double-stranded cDNA, which was subsequently transcribed into biotin-tagged cRNA using the MessageAmp™ II aRNA Amplification Kit (Ambion, TX, USA). The cRNA was then fragmented to produce strands of 35–200 bases in length in accordance with protocols (Affymetrix, CA, USA). The fragmented cRNA was hybridized to the Affymetrix GeneChip®Human Genome U133 Plus 2.0 Array containing 47,000 transcripts.

growth_protocol: Each sample was divided in half: one half was fixed in formalin and embedded in paraffin; the other half floated in ice-cold phosphate-buffered saline and was stored in liquid nitrogen until total RNA extraction.

extract_protocol: Tissue homogenization and isolation of total RNA were performed according to the manufacturer’s instructions using the Macherey–Nagel NucleoSpin®RNA II kit (Macherey–Nagel, Duren, Germany); this RNA isolation kit has significantly reduced contamination by both genome DNA and proteins. The RNA, extracted with ribosomal 28S and 18S RNA with a ratio of intensities of 1.0:1.0–1.5:1.0, was used in subsequent microarray assays.

tag: gender

value: Male

tag: age

tag: tumor stage

tag: chemoresponse

value: noresponder

value: colorectal tumor


title: HaCaT cells under negative pressure, biological rep3

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

label_protocol: Standard Affymetrix protocol

growth_protocol: HaCaT cell line, (Cell Lines Service GmbH, Eppelheim, Deutschland) were cultured in DMEM (Sigma-Aldrich Corporation, St. Louis, MO, USA) and contained 10% FBS and 100 mg/mL streptomycin-penicillin.

extract_protocol: HaCaT treated with NP (or AP) were washed twice with ice-cold PBS immediately after NP treatment. Total RNA was extracted with TRIsure (bioline) by following manufacturer's instructions.

treatment_protocol: A negative-pressure incubator (NPI1500, Linston Advanced Technology Corporation, Longtan, Taoyuan, Taiwan) was used to create a negative pressure (AP) gradient for incubated cells. AP (control) and NP (intervention) were used to treat cells for 12 hours.

value: HaCaT

value: skin keratinocyte

tag: protocol

value: negative pressure


title: HaCaT cells under negative pressure, biological rep1


title: Colorectal Cancer, Patient_27

description:
post-chemotherapy
498294

value: Female


title: HCLE_eepR mutant 1

description: eepR mutant 1

source_name: HCLE_eepR mutant

value: eepR mutant


title: MO2058 Control replicate 2

source_name: Mantle Cell Lymphoma untreated

value: untreated


title: HCLE_eepR mutant 2

description: eepR mutant 2


title: Colorectal Cancer, Patient_23

description:
post-chemotherapy
497052

value: responder


title: Colorectal Cancer, Patient_28

description:
post-chemotherapy
479084


title: Colorectal Cancer, Patient_30

description:
post-chemotherapy
493013


title: MO2058 250 nM JQ1 treated replicate 2


title: HaCaT cells under ambient pressure, biological rep1

value: Control


title: Colorectal Cancer, Patient_26

description:
post-chemotherapy
483258


title: HaCaT cells under ambient pressure, biological rep3


title: HaCaT cells under ambient pressure, biological rep2


title: HaCaT cells under negative pressure, biological rep2


title: Colorectal Cancer, Patient_24

description:
post-chemotherapy
497673


title: Colorectal Cancer, Patient_22

description:
post-chemotherapy
507925


title: Colorectal Cancer, Patient_25

description:
post-chemotherapy
T-237


title: Colorectal Cancer, Patient_21

description:
post-chemotherapy
503556


title: MO2058 Control replicate 1


title: Colorectal Cancer, Patient_20

description:
post-chemotherapy
501406


title: Colorectal Cancer, Patient_14

description:
post-chemotherapy
547476


title: Colorectal Cancer, Patient_11

description:
post-chemotherapy
546174


title: Colorectal Cancer, Patient_16

description:
post-chemotherapy
549756


title: Colorectal Cancer, Patient_8

description:
post-chemotherapy
539865


title: Colorectal Cancer, Patient_13

description:
post-chemotherapy
547441


title: Colorectal Cancer, Patient_15

description:
post-chemotherapy
548584


title: Colorectal Cancer, Patient_18

description:
post-chemotherapy
499809


title: Colorectal Cancer, Patient_5

description:
post-chemotherapy
527198


title: Colorectal Cancer, Patient_19

description:
post-chemotherapy
500034


title: Colorectal Cancer, Patient_6

description:
post-chemotherapy
529242


title: Colorectal Cancer, Patient_10

description:
post-chemotherapy
544822


title: Colorectal Cancer, Patient_9

description:
post-chemotherapy
543548


title: Colorectal Cancer, Patient_3

description:
post-chemotherapy
519119


title: Colorectal Cancer, Patient_17

description:
post-chemotherapy
494013


title: AML patient #12

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
Gene expression data from AML patient sample with BCOR mutation
MLL_00129

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

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed using RMA in the bioconducter and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 8 (3 in log2 scale).

source_name: mononuclear cells after Ficoll purification

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: blood samples

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: untreated samples

tag: disease state

value: AML

value: BCOR Gly1376IlefsX65

value: mononuclear cell


title: AML patient #5

description:
Gene expression data from AML patient sample with BCOR WT
MLL_00115

value: BCOR WT


title: Colorectal Cancer, Patient_2

description:
post-chemotherapy
518087


title: AML patient #6

description:
Gene expression data from AML patient sample with BCOR WT
MLL_00238


title: Colorectal Cancer, Patient_1

description:
post-chemotherapy
550651


title: AML patient #9

description:
Gene expression data from AML patient sample with BCOR mutation
MLL_00124

value: BCOR Asp975GlyfsX2


title: AML patient #4

description:
Gene expression data from AML patient sample with BCOR WT
MLL_00114


title: AML patient #11

description:
Gene expression data from AML patient sample with BCOR mutation
MLL_00126

value: BCOR Arg1547X


title: AML patient #8

description:
Gene expression data from AML patient sample with BCOR mutation
MLL_00122

value: BCOR Arg1661X


title: AML patient #10

description:
Gene expression data from AML patient sample with BCOR mutation
MLL_00125

value: BCOR Ser369TrpfsX12


title: Colorectal Cancer, Patient_7

description:
post-chemotherapy
530890

value: Male

value: noresponder

value: colorectal tumor


title: Colorectal Cancer, Patient_4

description:
post-chemotherapy
524736


title: Colorectal Cancer, Patient_12

description:
post-chemotherapy
547100


title: AML patient #3

description:
Gene expression data from AML patient sample with BCOR WT
MLL_00112


title: AML patient #1

description:
Gene expression data from AML patient sample with BCOR WT
MLL_00106


title: AML patient #7

description:
Gene expression data from AML patient sample with BCOR mutation
MLL_00120

value: BCOR Arg342X


title: BM-CD138+, diagnosis, rep1 [MM 95; re-analysis]

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

description: re-analysis of GSM1401629

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Array Scanner 7G

data_processing: Samples were overall normalized with CG-RMA procedure by Affymetrix Power Tools software (v.1.17.0).

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient

label_protocol: Samples with at least 30ng/uL RNA were labelled for gene expression profiling, using the Affymetrix One-cycle Gene Chip microarray system, according to the standard Affymetrix procedures.

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

treatment_protocol: Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). CD138+ cell fractions were than stored at -80°C in guanidium thiocyanate, until use.

value: Multiple Myeloma

value: BM-CD138+ cells

tag: response to vtd therapy

value: VGPR


title: AML patient #2

description:
Gene expression data from AML patient sample with BCOR WT
MLL_00107


title: BM-CD138+, diagnosis, rep1 [MM 96; re-analysis]

description: re-analysis of GSM1401630

value: SD


title: BM-CD138+, diagnosis, rep1 [MM 97; re-analysis]

description: re-analysis of GSM1401631

value: PR


title: BM-CD138+, diagnosis, rep1 [MM 91; re-analysis]

description: re-analysis of GSM1401625

value: CR


title: BM-CD138+, diagnosis, rep1 [MM 92; re-analysis]

description: re-analysis of GSM1401626

value: nCR


title: BM-CD138+, diagnosis, rep1 [MM 94; re-analysis]

description: re-analysis of GSM1401628


title: BM-CD138+, diagnosis, rep1 [MM 90; re-analysis]

description: re-analysis of GSM1401624


title: BM-CD138+, diagnosis, rep1 [MM 88; re-analysis]

description: re-analysis of GSM1401622


title: BM-CD138+, diagnosis, rep1 [MM 86; re-analysis]

description: re-analysis of GSM1401621


title: BM-CD138+, diagnosis, rep1 [MM 93; re-analysis]

description: re-analysis of GSM1401627


title: BM-CD138+, diagnosis, rep1 [MM 83; re-analysis]

description: re-analysis of GSM1401619


title: BM-CD138+, diagnosis, rep1 [MM 85; re-analysis]

description: re-analysis of GSM1401620


title: BM-CD138+, diagnosis, rep1 [MM 55; re-analysis]

description: re-analysis of GSM1401613


title: BM-CD138+, diagnosis, rep1 [MM 56; re-analysis]

description: re-analysis of GSM1401614


title: BM-CD138+, diagnosis, rep1 [MM 89; re-analysis]

description: re-analysis of GSM1401623


title: BM-CD138+, diagnosis, rep1 [MM 99]

description: Gene expression data from BM-CD13+ cell fraction, obtained from newly diagnosed Multiple Myeloma patient


title: BM-CD138+, diagnosis, rep1 [MM 98; re-analysis]

description: re-analysis of GSM1401632


title: BM-CD138+, diagnosis, rep1 [MM 57; re-analysis]

description: re-analysis of GSM1401615


title: BM-CD138+, diagnosis, rep1 [MM 72; re-analysis]

description: re-analysis of GSM1401618


title: BM-CD138+, diagnosis, rep1 [MM 59; re-analysis]

description: re-analysis of GSM1401617


title: BM-CD138+, diagnosis, rep1 [MM 50; re-analysis]

description: re-analysis of GSM1401612


title: BM-CD138+, diagnosis, rep1 [MM 49; re-analysis]

description: re-analysis of GSM1401611


title: BM-CD138+, diagnosis, rep1 [MM 43; re-analysis]

description: re-analysis of GSM1401605


title: BM-CD138+, diagnosis, rep1 [MM 40; re-analysis]

description: re-analysis of GSM1401602


title: BM-CD138+, diagnosis, rep1 [MM 47; re-analysis]

description: re-analysis of GSM1401609


title: BM-CD138+, diagnosis, rep1 [MM 48; re-analysis]

description: re-analysis of GSM1401610


title: BM-CD138+, diagnosis, rep1 [MM 44; re-analysis]

description: re-analysis of GSM1401606


title: BM-CD138+, diagnosis, rep1 [MM 42; re-analysis]

description: re-analysis of GSM1401604


title: BM-CD138+, diagnosis, rep1 [MM 37; re-analysis]

description: re-analysis of GSM1401599


title: BM-CD138+, diagnosis, rep1 [MM 41; re-analysis]

description: re-analysis of GSM1401603


title: BM-CD138+, diagnosis, rep1 [MM 21; re-analysis]

description: re-analysis of GSM1401589


title: BM-CD138+, diagnosis, rep1 [MM 34; re-analysis]

description: re-analysis of GSM1401596


title: BM-CD138+, diagnosis, rep1 [MM 35; re-analysis]

description: re-analysis of GSM1401597


title: BM-CD138+, diagnosis, rep1 [MM 38; re-analysis]

description: re-analysis of GSM1401600


title: BM-CD138+, diagnosis, rep1 [MM 36; re-analysis]

description: re-analysis of GSM1401598


title: BM-CD138+, diagnosis, rep1 [MM 39; re-analysis]

description: re-analysis of GSM1401601


title: BM-CD138+, diagnosis, rep1 [MM 28; re-analysis]

description: re-analysis of GSM1401591


title: BM-CD138+, diagnosis, rep1 [MM 33; re-analysis]

description: re-analysis of GSM1401595


title: BM-CD138+, diagnosis, rep1 [MM 167; re-analysis]

description: re-analysis of GSM1401585


title: BM-CD138+, diagnosis, rep1 [MM 31; re-analysis]

description: re-analysis of GSM1401593


title: BM-CD138+, diagnosis, rep1 [MM 168; re-analysis]

description: re-analysis of GSM1401586


title: BM-CD138+, diagnosis, rep1 [MM 165; re-analysis]

description: re-analysis of GSM1401583


title: BM-CD138+, diagnosis, rep1 [MM 20; re-analysis]

description: re-analysis of GSM1401588


title: BM-CD138+, diagnosis, rep1 [MM 161; re-analysis]

description: re-analysis of GSM1401579


title: BM-CD138+, diagnosis, rep1 [MM 166; re-analysis]

description: re-analysis of GSM1401584


title: BM-CD138+, diagnosis, rep1 [MM 163; re-analysis]

description: re-analysis of GSM1401581


title: BM-CD138+, diagnosis, rep1 [MM 22; re-analysis]

description: re-analysis of GSM1401590


title: BM-CD138+, diagnosis, rep1 [MM 19; re-analysis]

description: re-analysis of GSM1401587


title: BM-CD138+, diagnosis, rep1 [MM 164; re-analysis]

description: re-analysis of GSM1401582


title: BM-CD138+, diagnosis, rep1 [MM 30; re-analysis]

description: re-analysis of GSM1401592


title: BM-CD138+, diagnosis, rep1 [MM 32; re-analysis]

description: re-analysis of GSM1401594


title: BM-CD138+, diagnosis, rep1 [MM 162; re-analysis]

description: re-analysis of GSM1401580


title: BM-CD138+, diagnosis, rep1 [MM 155; re-analysis]

description: re-analysis of GSM1401573


title: BM-CD138+, diagnosis, rep1 [MM 160; re-analysis]

description: re-analysis of GSM1401578


title: BM-CD138+, diagnosis, rep1 [MM 159; re-analysis]

description: re-analysis of GSM1401577


title: BM-CD138+, diagnosis, rep1 [MM 154; re-analysis]

description: re-analysis of GSM1401572


title: BM-CD138+, diagnosis, rep1 [MM 157; re-analysis]

description: re-analysis of GSM1401575


title: BM-CD138+, diagnosis, rep1 [MM 152; re-analysis]

description: re-analysis of GSM1401570


title: BM-CD138+, diagnosis, rep1 [MM 150; re-analysis]

description: re-analysis of GSM1401568


title: BM-CD138+, diagnosis, rep1 [MM 15; re-analysis]

description: re-analysis of GSM1401567


title: BM-CD138+, diagnosis, rep1 [MM 148; re-analysis]

description: re-analysis of GSM1401565


title: BM-CD138+, diagnosis, rep1 [MM 153; re-analysis]

description: re-analysis of GSM1401571


title: BM-CD138+, diagnosis, rep1 [MM 149; re-analysis]

description: re-analysis of GSM1401566


title: BM-CD138+, diagnosis, rep1 [MM 146; re-analysis]

description: re-analysis of GSM1401563


title: BM-CD138+, diagnosis, rep1 [MM 143; re-analysis]

description: re-analysis of GSM1401560


title: BM-CD138+, diagnosis, rep1 [MM 14; re-analysis]

description: re-analysis of GSM1401556


title: BM-CD138+, diagnosis, rep1 [MM 156; re-analysis]

description: re-analysis of GSM1401574


title: BM-CD138+, diagnosis, rep1 [MM 140; re-analysis]

description: re-analysis of GSM1401557


title: BM-CD138+, diagnosis, rep1 [MM 134; re-analysis]

description: re-analysis of GSM1401550


title: BM-CD138+, diagnosis, rep1 [MM 138; re-analysis]

description: re-analysis of GSM1401554


title: BM-CD138+, diagnosis, rep1 [MM 135; re-analysis]

description: re-analysis of GSM1401551


title: BM-CD138+, diagnosis, rep1 [MM 145; re-analysis]

description: re-analysis of GSM1401562


title: BM-CD138+, diagnosis, rep1 [MM 144; re-analysis]

description: re-analysis of GSM1401561


title: BM-CD138+, diagnosis, rep1 [MM 158; re-analysis]

description: re-analysis of GSM1401576


title: BM-CD138+, diagnosis, rep1 [MM 133; re-analysis]

description: re-analysis of GSM1401549


title: BM-CD138+, diagnosis, rep1 [MM 151; re-analysis]

description: re-analysis of GSM1401569


title: BM-CD138+, diagnosis, rep1 [MM 141; re-analysis]

description: re-analysis of GSM1401558


title: BM-CD138+, diagnosis, rep1 [MM 142; re-analysis]

description: re-analysis of GSM1401559


title: BM-CD138+, diagnosis, rep1 [MM 139; re-analysis]

description: re-analysis of GSM1401555


title: BM-CD138+, diagnosis, rep1 [MM 137; re-analysis]

description: re-analysis of GSM1401553


title: BM-CD138+, diagnosis, rep1 [MM 136; re-analysis]

description: re-analysis of GSM1401552


title: BM-CD138+, diagnosis, rep1 [MM 13; re-analysis]

description: re-analysis of GSM1401545


title: BM-CD138+, diagnosis, rep1 [MM 128; re-analysis]

description: re-analysis of GSM1401543


title: BM-CD138+, diagnosis, rep1 [MM 125; re-analysis]

description: re-analysis of GSM1401541


title: BM-CD138+, diagnosis, rep1 [MM 126; re-analysis]

description: re-analysis of GSM1401542


title: BM-CD138+, diagnosis, rep1 [MM 132; re-analysis]

description: re-analysis of GSM1401548


title: BM-CD138+, diagnosis, rep1 [MM 129; re-analysis]

description: re-analysis of GSM1401544


title: BM-CD138+, diagnosis, rep1 [MM 123; re-analysis]

description: re-analysis of GSM1401539


title: BM-CD138+, diagnosis, rep1 [MM 120; re-analysis]

description: re-analysis of GSM1401537


title: BM-CD138+, diagnosis, rep1 [MM 118; re-analysis]

description: re-analysis of GSM1401535


title: BM-CD138+, diagnosis, rep1 [MM 114; re-analysis]

description: re-analysis of GSM1401532


title: BM-CD138+, diagnosis, rep1 [MM 119; re-analysis]

description: re-analysis of GSM1401536


title: BM-CD138+, diagnosis, rep1 [MM 104; re-analysis]

description: re-analysis of GSM1401523


title: BM-CD138+, diagnosis, rep1 [MM 106; re-analysis]

description: re-analysis of GSM1401525


title: BM-CD138+, diagnosis, rep1 [MM 107; re-analysis]

description: re-analysis of GSM1401526


title: BM-CD138+, diagnosis, rep1 [MM 105; re-analysis]

description: re-analysis of GSM1401524


title: BM-CD138+, diagnosis, rep1 [MM 101; re-analysis]

description: re-analysis of GSM1401520


title: BM-CD138+, diagnosis, rep1 [MM 110; re-analysis]

description: re-analysis of GSM1401528


title: BM-CD138+, diagnosis, rep1 [MM 112; re-analysis]

description: re-analysis of GSM1401530


title: BM-CD138+, diagnosis, rep1 [MM 113; re-analysis]

description: re-analysis of GSM1401531


title: BM-CD138+, diagnosis, rep1 [MM 124; re-analysis]

description: re-analysis of GSM1401540


title: BM-CD138+, diagnosis, rep1 [MM 111; re-analysis]

description: re-analysis of GSM1401529


title: BM-CD138+, diagnosis, rep1 [MM 115; re-analysis]

description: re-analysis of GSM1401533


title: BM-CD138+, diagnosis, rep1 [MM 102; re-analysis]

description: re-analysis of GSM1401521


title: BM-CD138+, diagnosis, rep1 [MM 147; re-analysis]

description: re-analysis of GSM1401564


title: BM-CD138+, diagnosis, rep1 [MM 130; re-analysis]

description: re-analysis of GSM1401546


title: BM-CD138+, diagnosis, rep1 [MM 117; re-analysis]

description: re-analysis of GSM1401534


title: BM-CD138+, diagnosis, rep1 [MM 121; re-analysis]

description: re-analysis of GSM1401538


title: BM-CD138+, diagnosis, rep1 [MM 108; re-analysis]

description: re-analysis of GSM1401527


title: BM-CD138+, diagnosis, rep1 [MM 131; re-analysis]

description: re-analysis of GSM1401547


title: BM-CD138+, diagnosis, rep1 [MM 08; re-analysis]

description: re-analysis of GSM1401518


title: BM-CD138+, diagnosis, rep1 [MM 07; re-analysis]

description: re-analysis of GSM1401517


title: BM-CD138+, diagnosis, rep1 [MM 100; re-analysis]

description: re-analysis of GSM1401519


title: BM-CD138+, diagnosis, rep1 [MM 05; re-analysis]

description: re-analysis of GSM1401515


title: BM-CD138+, diagnosis, rep1 [MM 103; re-analysis]

description: re-analysis of GSM1401522


title: 180D-2, biological rep2

city: Beijing

first: Zhihua

last: Liu

address: No.17, Panjiayuannanli, Chaoyang District

department: Cancer Institute & Hospital

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Stronger motility than 180U subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
180D-21

hyb_protocol: This procedure was completed by LC Sciences. We received hyb QC report using bioB, bioC, bioD, and cre as controls.

scan_protocol: This procedure was completed by LC Sciences. We received QC report about scan images.

data_processing: Data was processed by professionals in LC Sciences using GCOS1.4 software (Affymetrix). RMA was used to calculate expressions of genes.

source_name: Human esophageal squamous cell carcinoma cell line KYSE180

label_protocol: This procedure was completed by LC Sciences. Notably, RNA for expression array and microRNA array was from the extracted samples.  We received label QC report using poly-A RNA Controls.

growth_protocol: Harvested 30U/D and 180U/D subpopulations were grown to about 80% confluence under standard cell culture condition and each subpopulation with the same passages (2 passages after the harvest) was used in the following RNA extraction.

extract_protocol: The frozen samples with dry ice were sent to LC Sciences (Texas, USA) and all of the following procedures were carried out by professionals in LC Sciences. We received RNA QC report analyzed by Agilent 2100 Bioanalyzer.

treatment_protocol: Approximately 80% confluent target cells maintained in 10-cm dishes were washed twice using pre-cooled PBS. Then 6 ml Trizol (Invitrogen) were added to lyse cells thoroughly. Finally, we transferred the lysed cells into 1.5 ml  RNase-free tubes and stored them in -80 degree fridge immediately.

value: esophageal squamous cell carcinoma cell line KYSE-180

tag: morphology

value: Epithelial

tag: primary tumor

value: well differentiated, a3 (Invasion depth)


title: BM-CD138+, diagnosis, rep1 [MM 06; re-analysis]

description: re-analysis of GSM1401516

tag: cell type


title: 180D-1, biological rep1

description:
Stronger motility than 180U subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
180D-31

tag: cell line


title: BM-CD138+, diagnosis, rep1 [MM 02; re-analysis]

description: re-analysis of GSM1401513


title: 180U-1, biological rep1

description:
Weaker motility than 180D subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
180U-11


title: 180U-2, biological rep2

description:
Weaker motility than 180D subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
180U-21


title: BM-CD138+, diagnosis, rep1 [MM 01]


title: 30U-2, biological rep2

description:
Weaker motility than 30D subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
30MU-4-2

source_name: Human esophageal squamous cell carcinoma cell line KYSE30

value: esophageal squamous cell carcinoma cell line KYSE-30


title: EF cells, plus doxycycline, biological rep1

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

description:
Sample name: EF_pos1
EF cells, treated with doxycycline

hyb_protocol: Following fragmentation, the cRNA were hybridized overnight hr at 45C.

scan_protocol: Microarrays were scanned according to manufacturer's instructions.

data_processing: GenePattern 3.8.0 was used to normalize the raw microarray data using the robust multichip average (RMA) algorithm.

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

growth_protocol: Cells were cultured in the presence or absence of doxycycline.

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

value: EF cells

value: treated with doxycycline


title: 30U-1, biological rep1

description:
Weaker motility than 30D subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
30MU-4-1


title: EF cells, no doxycycline, biological rep3

description:
Sample name: EF_Fib3
EF cells, never treated with doxycycline

value: never treated with doxycycline


title: 30D-2, biological rep2

description:
Stronger motility than 30U subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
30MD-4-2


title: EF cells, doxycycline removed, biological rep2

description:
Sample name: EF_neg2
EF cells, treated with doxycycline and then doxycycline removed


title: EF cells, plus doxycycline, biological rep2

description:
Sample name: EF_pos2
EF cells, treated with doxycycline


title: Multi-region sample HGG7-2

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: As directed by Affymetrix.

scan_protocol: As directed by Affymetrix.

data_processing: Cel files were imported to Partek Genomics Suite. Robust Multi-array average (RMA) was used as normalization method.

source_name: Primary human brain tumor sample

label_protocol: As directed by Affymetrix.

extract_protocol: Total RNA was extracted from frozen medulloblastoma tissue using the Trizol method (Invitrogen) as directed by the manufacturer.  RNA integrity was assessed using the Agilent 2100 Bioanalyzer prior to processing for the Gene Array.  Samples with RIN values equal to / greater 7 were included in the study.

value: high-grade glioma

tag: tumor

value: Glioblastoma multiforme

tag: patientid

value: Female


title: Multi-region sample HGG7-3

tag: tissue


title: Multi-region sample HGG7-5


title: Multi-region sample HGG7-6


title: EF cells, plus doxycycline, biological rep3

description:
Sample name: EF_pos3
EF cells, treated with doxycycline


title: Multi-region sample HGG7-4


title: Multi-region sample HGG7-1


title: 30D-1, biological rep1

description:
Stronger motility than 30U subpopulations. 30MU-4-1 and 30MD-4-1,30MU-4-2 and 30MD-4-2, 180U-11 and 180D-21, 180U-21 and 180D-31 were four pairs of subpopulations derived from simultaneously selected four independent parental populations, respectively.
30MD-4-1


title: EF cells, doxycycline removed, biological rep3

description:
Sample name: EF_neg3
EF cells, treated with doxycycline and then doxycycline removed


title: EF cells, no doxycycline, biological rep1

description:
Sample name: EF_Fib1
EF cells, never treated with doxycycline


title: EF cells, doxycycline removed, biological rep1

description:
Sample name: EF_neg1
EF cells, treated with doxycycline and then doxycycline removed


title: EF cells, no doxycycline, biological rep2

description:
Sample name: EF_Fib2
EF cells, never treated with doxycycline


title: Multi-region sample HGG6-6


title: Multi-region sample HGG6-4


title: Multi-region sample HGG6-7


title: Multi-region sample HGG6-1


title: Multi-region sample HGG1-8

value: Anaplastic astrocytoma

value: Male


title: Multi-region sample HGG1-6


title: Multi-region sample HGG6-3


title: Multi-region sample HGG1-7


title: Multi-region sample HGG1-4


title: Multi-region sample HGG1-2


title: Multi-region sample HGG1-3


title: c_P_40 (GEP)

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

description:
PCNSL
PNTR_037

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing:
The raw ‘.CEL’ files were converted into probeset-specific expression values using Affymetrix’ MAS5 summarization method as implemented in the BioConductor package ‘simpleaffy’ (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100.
The file lymphoma2009.nugen.rma.GSmed contains expression values for all probes of the U133plus2 chip across all samples hybridized with this chip. Furthermore, we generated a combined lymphoma.combined.nugen.rma.GS file, which contain gene-centered expression values for all genes assessed by both chips (U133A and U133plus2 chips). Since the expression profiles originated from two separate batches profiled at different times and on different chips (the first batch was profiled on U133A chip, and the 2nd batch was profiled on the U133plus2 chip), we further normalized the data carrying out a gene-specific normalization, whereby the mean and standard deviation of a gene in the 2nd batch were set to the mean and standard deviation of the corresponding gene in the 1st batch. In particular, for each profile j in batch 2, the expression of gene i was transformed as follows:  g'ij=gij-?i(2)si(2)* si(1)+?i(1), where ?i(b) and si(b) denote the mean and standard deviation of gene i in batch b=1,2.

source_name: PCNSL

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: 10-20 x 20 um sections from snap-frozen tumor specimens from newly diasnosted previously untreated samples were directly transferred to Trizol.

extract_protocol: For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols. RNA amplification was done with Nugen kit as described in detail in the associated manuscript.

value: primary PCNSL


title: c_TL_07 (GEP)

description:
TL
TL_07

source_name: TL

value: primary TL


title: Multi-region sample HGG6-2


title: c_P_34 (GEP)

description:
PCNSL
PNTR_019


title: c_P_52 (GEP)

description:
PCNSL
PNTR_026


title: c_TL_03 (GEP)

description:
TL
TL_03


title: c_TL_10 (GEP)

description:
TL
TL_10


title: c_TL_02 (GEP)

description:
TL
TL_02


title: c_TL_05 (GEP)

description:
TL
TL_05


title: c_TL_08 (GEP)

description:
TL
TL_08


title: c_P_6 (GEP)

description:
PCNSL
PNTR_032


title: c_P_4 (GEP)

description:
PCNSL
PNTR_029


title: c_P_7 (GEP)

description:
PCNSL
PNTR_034


title: c_P_5 (GEP)

description:
PCNSL
PNTR_031


title: c_P_2 (GEP)

description:
PCNSL
PNTR_018


title: Multi-region sample HGG1-1


title: c_P_12 (GEP)

description:
PCNSL
PCNSL_Bjoern_3


title: c_P_13 (GEP)

description:
PCNSL
PCNSL_Bjoern_5


title: c_P_11 (GEP)

description:
PCNSL
PCNSL_Bjoern_2


title: c_P_10 (GEP)

description:
PCNSL
PNTR_024


title: old_c494 (GEP)

description:
DLBCL
DLBCL_494_1

source_name: DLBCL

value: primary DLBCL


title: old_c492 (GEP)

description:
DLBCL
DLBCL_492


title: c_P_1 (GEP)

description:
PCNSL
PNTR_016


title: old_c467 (GEP)

description:
DLBCL
DLBCL_467


title: old_c495 (GEP)

description:
DLBCL
DLBCL_495_1


title: c_P_14 (GEP)

description:
PCNSL
PCNSL_Bjoern_6


title: c_P_20 (GEP)

description:
PCNSL
PCNSL_705_1


title: Silicon Starvation 18 hr- rep

city: La Jolla

first: Sarah

middle: R.

last: Smith

state: CA

address: 9500 Gilman Dr.

department: Scripps Institution of Oceanography

institute: University of California, San Diego

description: Tp_18hr_10-14-2009_(Tp_Affy1_tiling)_Rep2.lipids.rma-gene-core-Signal

hyb_protocol: Hybridization of labeled targets on the arrays was carried out using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: The arrays were scanned with the GeneChip® Scanner, to generate probe cell intensity data files.

data_processing:
Initial analysis of gene level expression was performed using Affymetrix Expression Console Software, version 1.1. The Robust Multichip Analysis (RMA) algorithm was applied to the probe cell intensity data files for all experimental conditions, using default parameters in the RMA-sketch workflow for core gene level analysis.
probe group file: Tp_Affy1_exon.pgf
meta-probeset file: Tp_Affy1_exon.mps
Tp_Affy_GeneLevel_ProbeID_map.txt

organism: Thalassiosira pseudonana

source_name: cells harvested at 18 hr of silicon starvation

label_protocol: For each hybridization, double stranded cDNA was synthesized from 7 ug of total RNA with no amplification using the GeneChip® WT Amplified Double-Stranded cDNA Synthesis Kit (Affymetrix). Cleanup of double-stranded cDNA was done with the GeneChip® Sample Cleanup Module (Affymetrix). Fragmentation and end-labeling was performed using the GeneChip® WT Double-stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Thalassiosira pseudonana (CCMP1335) cultures were grown to mid-exponential in nutrient replete medium, harvested, and re-suspended in silicon free medium. Samples were taken throughout a 24 hr time course (0, 4, 8, 12, 18, and 24 hr).

extract_protocol: Total RNA extracted with Trizol reagent (Sigma) from cells harvested at each time point.

treatment_protocol: Samples were treated with cycloheximide, pelleted, and stored at -80C prior to RNA isolation.

tag: strain

tag: time point

value: 18 hr of silicon starvation


title: Silicon Starvation 18 hr

description: Tp_18hr_10-14-2009_(Tp_Affy1_tiling).lipids.rma-gene-core-Signal


title: Silicon Starvation 4 hr- rep

description: Tp_4hr_10-14-2009_(Tp_Affy1_tiling)_Rep2.lipids.rma-gene-core-Signal

source_name: cells harvested at 4 hr of silicon starvation

value: 4 hr of silicon starvation


title: Silicon Starvation 24 hr

description: Tp_24hr_10-14-2009_(Tp_Affy1_tiling).lipids.rma-gene-core-Signal

source_name: cells harvested at 24 hr of silicon starvation

value: 24 hr of silicon starvation


title: Silicon Starvation 12 hr-rep

description: Tp_12hr_10-14-2009_(Tp_Affy1_tiling)_Rep2.lipids.rma-gene-core-Signal

source_name: cells harvested at 12 hr of silicon starvation

value: 12 hr of silicon starvation


title: Silicon Starvation 24 hr- rep

description: Tp_24hr_10-14-2009_(Tp_Affy1_tiling)_Rep2.lipids.rma-gene-core-Signal


title: ALL - CNS - Relapse -1

city: Rotterdam

first: Vincent

middle: HJ

last: van der Velden

address: Wytemaweg 80

department: Immunology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Ten micrograms of fragmented cRNA was  hybridized for 16 h to Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: After washing and staining, the arrays were scanned in a Hewlett-Packard/Affymetrix scanner at 570 nm.

data_processing: Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.

source_name: ALL - CNS - Relapse

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

growth_protocol: ALL cells from BM samples were sorted to >95% purity as described previously and subsequently used for RNA extraction. Given the relatively low cell numbers and generally high percentages of ALL cells in CSF, ALL cells in CSF were directly processed for RNA extraction

extract_protocol: RNA was extracted from the ALL cells using Qiagen RNeasy isolation kit according to the manufacturer’s instruction (Qiagen, Hilden, Germany).

value: m

tag: age at diagnosis

tag: wbc at diagnosis (10e9/l)

tag: side of relapse

value: CNS

value: relapse


title: ALL - CNS - Relapse -3

tag: gender

value: unknown


title: Silicon Starvation 8 hr-rep

description: Tp_8hr_10-14-2009_(Tp_Affy1_tiling)_Rep2.lipids.rma-gene-core-Signal

source_name: cells harvested at 8 hr of silicon starvation

value: 8 hr of silicon starvation


title: Silicon Starvation 12 hr

description: Tp_12hr_10-14-2009_(Tp_Affy1_tiling).lipids.rma-gene-core-Signal


title: ALL - CNS - Relapse -4


title: ALL - CNS - Relapse -2


title: ALL - CNS - Relapse -7

value: f


title: Silicon Starvation 8 hr

description: Tp_8hr_10-14-2009_(Tp_Affy1_tiling).lipids.rma-gene-core-Signal


title: Silicon Starvation 0 hr

description: Tp_0hr_10-14-2009_(Tp_Affy1_tiling).lipids.rma-gene-core-Signal

source_name: cells harvested at 0 hr of silicon starvation

value: 0 hr of silicon starvation


title: ALL - CNS - Relapse -5


title: old_c432 (GEP)

description:
DLBCL
DLBCL_432_1


title: Silicon Starvation 4 hr

description: Tp_4hr_10-14-2009_(Tp_Affy1_tiling).lipids.rma-gene-core-Signal


title: Silicon Starvation 0 hr- rep

description: Tp_0hr_10-14-2009_(Tp_Affy1_tiling)_Rep2.lipids.rma-gene-core-Signal


title: HME1

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

institute: University Lyon1

hyb_protocol: According to manufacturer's instructions (Affymetrix).

scan_protocol: The Arrays were scanned using the GeneChip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0.

data_processing: CHP files were processed using RMA analysis algorithm with Affymetrix Expression Console software 1.1.

source_name: HMEC hTERT immortalized cell line

growth_protocol: Primary human mammary epithelial cells (HMECs) immortalized by-hTert, called HME, were cultured in 1:1 Dulbecco's Modified Eagle's Medium (DMEM)/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex), 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (EGF) (PromoCell), 0.5 mg/ml hydrocortisone (Sigma) and 10 mg/ml insulin (Actrapid).

extract_protocol: Total RNAs were extracted with the Qiagen RNeasy minikit (Qiagen), then 100 ng of total RNAs were amplified using Kit GeneChip 3' IVT Express (Affymetrix).

treatment_protocol: HMEC hTERT immortalized cells were infected with retrovirus expressing H-RASV12 with or without a retrovirus expressing ZEB1.

value: immortalized human mammary epithelial cells

tag: state

value: immortalized


title: Thyrosphere thyroid cancer cell, biological rep1

city: St Louis

first: Reigh-Yi

last: Lin

state: MO

address: 1100 South Grand Blvd

department: Otolaryngology

institute: Saint Louis University

description:
THJ_11T_Thyrosphere1
Gene expression data from thyrosphere THJ-11T cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The preliminary data analysis was performed with R/Bioconductor using the gcRMA normalization method (which outputs log2-transformed expression values). Statistical analysis was performed with Partek Genomics Suite software.

source_name: THJ-11T, thyrosphere

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3_ivt_express_kit_manual, 2008, Affymetrix).

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated with the RNeasy kit.

treatment_protocol: To obtain thyrospheres, single cells were plated at 5,000 cells/well on ultra-low-attachment six-well plates for 7 days.

value: thyrosphere thyroid cancer cells


title: ALL - CNS - Relapse -6


title: HME1-ZEB1-RAS

source_name: HMEC hTERT immortalized cell line ectopically expressing HRasG12V and ZEB1

label_protocol: According to manufacturer's instructions (Affymetrix).

tag: retrovirus expression

value: HRasG12V and Zeb1

value: transformed


title: Thyrosphere thyroid cancer cell, biological rep2

description:
THJ_11T_Thyrosphere2
Gene expression data from thyrosphere THJ-11T cells.


title: HME1-RAS

source_name: HMEC hTERT immortalized cell line ectopically expressing HRasG12V

value: non-transformed


title: Monolayer thyroid cancer cell, biological rep1

description:
THJ_11T_Monolayer1
Gene expression data from parental monolayer THJ-11T cells.

source_name: THJ-11T, monolayer

value: monolayer thyroid cancer cells


title: Thyrosphere thyroid cancer cell, biological rep3


title: Brachytherapy subject 72

city: Tokyo

first: Afsaneh

last: Eslami

state: Tokyo To

address: 45-5-1, Yushima, Bunkyo Ku

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression data from tongue squamous cell carcinoma cells prior to brachytherapy

hyb_protocol: Fragmented aRNAs were validated in fragment size with BioAnalizer and applied to GeneChip Human Genome U133 plus 2.0 arrays (Affymetrix, Santa Clara, CA) and incubated at 45 C for 16 h. After the hybridization, microarray was washed and stained with streptavidin phycoerythrin (SAPE) conjugate using a fully automated system (GeneChip Fluidic Station 450; Affymetrix) according to the manufacturer's procedure.

scan_protocol: The hybridized probe arrays werescanned by GeneChip Scanner 3000 7G (Affymetrix).

data_processing: For microarray array analysis, raw expression data were processed with robust multi-array average (RMA) method using R statistical software version 2.12.1 (http://www.r-project.org/) and affy Bioconductor package (http://www.bioconductor.org/). Probe sets corresponding to known genes were selected based on the NetAffx annotation file version 32 (available at: http://www.affymetrix.com/analysis/index.affx).Then, probe sets marked as present by Expression Console Software version 1.1 (Affymetrix) in more than 50% of the patients were further selected. Differentially expressed genes were identified by using the Wilcoxon rank sum test using the wilcox_exact function provided by the coin package available in the Comprehensive R Archive Network (http://cran.r-project.org/).Probe sets that satisfied P < 0.01 and more than 2-fold change between endophytic and non-endophytic TSCCs were considered significant.To compare the results of qRT-PCR, the Wilcoxon rank sum test was applied to determine a difference between relative quantities of gene expression in endophytic and non-endophytic cancer tissues. In the IHC and migration assays, the Wilcoxon rank sum test was also used to determine differences between positive and negative ratio of stained cancer cells in each sample. The Kaplan-Meier method was applied to estimate the MFS curve andthe difference between the groups was calculated by thelog-rank test. A probability value < 0.05 was considered a statistically significant.

source_name: Tongue squamous cell carcinoma

label_protocol: Total RNAs were amplified and biotinylated with MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX). Biotinylated aRNAs were fragmented following MessageAmp II-Biotin Enhanced Kit protocol.

growth_protocol: Biopsy tissues were collected from patients with tongue squamous cell carcinoma prior to brachytherapy.

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer's procedure.

treatment_protocol: Using the cryostat, frozen OCT embedded tissues were cut into 9 m sections, placed on filmed glass slides, fixed with 70% ethanol and stained with Mayer's hematoxylin for 30 sec. Stained sections were water-washed and well dried for subsequent dissection process. Cancer cells were isolated from normal squamous cells by laser microdissection using Leica LMD6000.

tag: growth type

value: Exophytic type

tag: t stage

value: M

value: Tongue squamous cell carcinoma


title: Multi-region sample HGG6-5

source_name: Primary human brain tumor sample

value: high-grade glioma

value: Glioblastoma multiforme

tag: age

value: Female


title: Monolayer thyroid cancer cell, biological rep3

description:
THJ_11T_Monolayer3
Gene expression data from parental monolayer THJ-11T cells.


title: Brachytherapy subject 40

value: Superficial type


title: PWKd3_667 lung

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software10.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: lung

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

extract_protocol: RNA was prepared using Qiagen RNAeasy Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The CC founder (C57BL/6J, 129S1/SvlmJ, CAST/EiJ, PWK/PhJ) were intranasally infected with influenza A/HK/01/68 (H3N2) with 20μl virus solution (1x101 ffu) or mock infected (with PBS).

tag: infection

value: d3 pi

value: PWK/PhJ


title: Brachytherapy subject 74


title: Brachytherapy subject 39


title: Brachytherapy subject 45

value: F


title: PWKd3_660 lung


title: Brachytherapy subject 56


title: Brachytherapy subject 49

value: Invasive type


title: Brachytherapy subject 48


title: Monolayer thyroid cancer cell, biological rep2

description:
THJ_11T_Monolayer2
Gene expression data from parental monolayer THJ-11T cells.

tag: cell type


title: Brachytherapy subject 41


title: PWKd5_2 lung

value: d5 pi


title: Brachytherapy subject 60


title: PWKd5_3 lung


title: Brachytherapy subject 37


title: PWKd5_1 lung


title: Brachytherapy subject 83


title: Brachytherapy subject 36


title: PWKd3_1 lung


title: PWKmd3_544 lung

value: mock d3


title: PWKmd3_537 lung


title: Brachytherapy subject 32


title: PWKmd3_530 lung


title: Brachytherapy subject 31


title: Brachytherapy subject 30


title: Brachytherapy subject 22


title: Brachytherapy subject 20


title: CASTd5_7 lung

value: CAST/EiJ


title: CASTd5_4 lung


title: PWKmd3_2 lung


title: CASTd5_5 lung


title: Brachytherapy subject 15


title: PWKmd3_3 lung


title: Brachytherapy subject 25


title: Brachytherapy subject 33


title: Brachytherapy subject 24


title: Brachytherapy subject 14


title: Brachytherapy subject 17


title: CASTd3_6 lung


title: Brachytherapy subject 09


title: CASTd3_4 lung


title: Brachytherapy subject 10


title: CASTd3_2 lung


title: CASTd3_3 lung


title: CASTd3_5 lung


title: Brachytherapy subject 04


title: CASTmd3_3 lung


title: CASTmd3_2 lung


title: miR-224 cells 2

first: Yu

last: Wang

address: 11 Hospital Drive

department: Biochemistry

institute: National University of Singapore

description:
gene expression data from miR-224 cells
Sample#2.CEL

hyb_protocol: Labeling, hybridization and scanning were performed by Duke-NUS genome biology facilities

data_processing: Raw data were quantile normalized and extracted using Partek Genomic Suite using default settings for Affymetrix arrays and RMA analysis.

source_name: HCT116 cells transfected with miR-224 precursors

growth_protocol: HCT116 cells were grown in modified Mccoy's 5A media supplemented with 10% fetal calf serum at 37 C with 5% CO2

extract_protocol: Total RNA were extracted with mirVana microRNA isolation kit with recommended protocol

treatment_protocol: HCT116 cells were transfected with 50 nM of either miR-224 precursor molecules or control molecules and harvested at 24 hours post transfection

tag: cell line

value: HCT116 cancer cell line

tag: genotype/variation

value: mir-224 over-expression


title: X129d5_3 lung


title: miR-224 cells 3

description:
gene expression data from miR-224 cells
Sample#3.CEL

scan_protocol: Labeling, hybridization and scanning were performed by Duke-NUS genome biology facilities


title: Control cells 1

description:
gene expression data from control cells
control#1.CEL

source_name: HCT116 cells transfected with control oligos

label_protocol: Labeling, hybridization and scanning were performed by Duke-NUS genome biology facilities

value: control


title: Control cells 2

description:
gene expression data from control cells
control#2.CEL


title: X129d5_2 lung


title: Control cells 3

description:
gene expression data from control cells
control#3.CEL


title: X129d3_3 lung


title: miR-224 cells 1

description:
gene expression data from miR-224 cells
Sample#1.CEL


title: CASTmd3_1 lung


title: X129d3_1 lung


title: normal thyroid-905N

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description: Gene expression data from normal thyroid

hyb_protocol: Following fragmentation, 16 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 2.0 PLUS (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was acquired using GeneChip Command Console Software 1.1 (Affymetrix). The preprocessing was performed by Robust Multi-Array expression measure using sequence information (GCRMA, Bioconducor)

source_name: normal thyroid

label_protocol: Total RNA (2 ug) was used for synthesis of double stranded cDNA and aRNA labeling according to manufacturer's instructions (GeneChip 3' IVT Express Kit, Affymetrix).

extract_protocol: The material was provided by CTB as aliquots of total RNA from carefully selected PTC samples and respective normal thyroid tissue, after thorough histopathological review of specimens.

tag: type of thyroid tussue (ptc denotes papillary thyroid cancer)

value: normal thyroid

tag: batch


title: X129md3_3 lung

tag: strain


title: PTC-radiation exposed-886T

description: Gene expression data from PTC,radiation exposed

source_name: PTC,radiation exposed

value: PTC

tag: exposure to chernobyl radiation

value: yes

tag: region of residence

value: Chercassy

tag: age at ptc operation

tag: braf v600e mutation

value: not present

tag: ret/ptc rearrangements

tag: subtype of ptc (classical denotes classical variant of ptc; ptc-f denotes ptc with dominant pattern of follicular structures; ptc-s denotes ptc with dominant pattern of solid areas; ptc-fs denotes ptc with dominant pattern of folicular and solid areas)

value: PTC-S


title: normal thyroid-954N


title: PTC-radiation exposed-905T

value: Sumy

value: positive

value: PTC-F


title: normal thyroid-886N


title: X129md3_1 lung


title: PTC-radiation exposed-771T

value: Kiev


title: X129md3_2 lung


title: PTC-radiation exposed-758T

value: Zhytomyr

value: PTC-FS


title: normal thyroid-758N


title: ALL - CNS - Relapse -8

tag: gender

value: m

tag: age at diagnosis

tag: wbc at diagnosis (10e9/l)

tag: side of relapse

value: CNS

tag: time point

value: relapse


title: PTC-radiation exposed-756T

value: classical


title: B6d5_3 lung

tag: infection

value: d5 pi


title: PTC-radiation exposed-693T


title: B6d5_2 lung


title: normal thyroid-692N

value: normal thyroid


title: B6d5_1 lung


title: B6d3_3 lung

value: d3 pi


title: B6d3_324 lung


title: normal thyroid-691N


title: PTC-radiation exposed-679T

value: PTC

value: yes

value: Chernigov


title: PTC-radiation exposed-672T

value: not present


title: B6d3_336 lung


title: B6d3_330 lung


title: X129d5_1 lung


title: normal thyroid-672N


title: normal thyroid-601N


title: normal thyroid-671N


title: PWKd5_465 blood

source_name: Blood

value: PWK/PhJ


title: B6md3_3 lung

value: mock d3


title: B6d3_1 lung


title: B6md3_2 lung


title: PTC-radiation not exposed-607T

description: Gene expression data from PTC,radiation not exposed

source_name: PTC,radiation not exposed

value: no

value: PTC-F


title: B6md3_1 lung


title: X129d3_2 lung


title: normal thyroid-469N


title: PWKd5_1 blood


title: PTC-radiation exposed-597T

value: Rovno


title: normal thyroid-574N


title: PWKd5_3 blood


title: PWKd5_472 blood


title: normal thyroid-597N


title: PTC-radiation exposed-417T

value: Kiev


title: PWKd3_658 blood


title: PWKd3_665 blood


title: normal thyroid-412N


title: normal thyroid-368N


title: PWKd3_1 blood


title: PWKmd3_5 blood


title: normal thyroid-343N


title: normal thyroid-411N


title: PWKd3_5 blood


title: normal thyroid-374N


title: PWKd3_4 blood


title: CASTd5_7 blood

value: CAST/EiJ


title: PWKmd3_4 blood


title: PTC-radiation not exposed-312T

value: PTC-S


title: CASTd5_5 blood


title: normal thyroid-280N


title: PWKmd3_2 blood


title: normal thyroid-329N


title: CASTd3_393 blood


title: CASTd3_5 blood


title: normal thyroid-216N


title: CASTd3_6 blood


title: normal thyroid-192N


title: normal thyroid-208N


title: CASTd3_2 blood


title: PTC-radiation exposed-329T

value: Sumy

value: positive


title: normal thyroid-1486N


title: PTC-radiation not exposed-1426T


title: CASTmd3_3 blood


title: PTC-radiation not exposed-1502T

value: status unknown

value: PTC-FS


title: CASTd5_4 blood

value: d5 pi


title: normal thyroid-1426N

value: normal thyroid


title: CASTmd3_1042 blood


title: CASTd3_3 blood

value: d3 pi


title: CASTmd3_2 blood


title: normal thyroid-1502N


title: PTC-radiation exposed-216T

value: PTC

value: yes


title: CASTmd3_1 blood


title: 129d5_731 blood


title: normal thyroid-1367N


title: 129d5_7 blood


title: PTC-radiation not exposed-1367T

value: not present


title: PTC-radiation not exposed-1337T


title: 129d5_4 blood


title: 129d5_5 blood


title: 129d5_724 blood


title: CASTd3_4 blood


title: 129d3_2 blood


title: normal thyroid-1328N


title: normal thyroid-1337N


title: PTC-radiation not exposed-1328T


title: 129d3_1 blood


title: PTC-radiation not exposed-1253T


title: PTC-radiation not exposed-1319T

value: Zhytomyr


title: PTC-radiation exposed-173T


title: 129md3_5 blood

value: mock d3


title: 129md3_1035 blood


title: 129md3_773 blood


title: PTC-radiation not exposed-1486T

value: no

value: Chercassy

value: PTC-F


title: normal thyroid-1319N


title: normal thyroid-1247N


title: B6d5_1063 blood


title: PTC-radiation not exposed-1247T

value: classical


title: PTC-radiation not exposed-1243T

value: Chernigov

value: PTC-S


title: normal thyroid-1253N


title: 129d3_3 blood


title: B6d5_3 blood


title: 129md3_3 blood


title: B6d5_1056 blood


title: normal thyroid-1240N


title: PTC-radiation not exposed-1240T

value: positive


title: B6d5_1 blood


title: 129md3_4 blood


title: PWKd3_5 lung

value: PWK/PhJ


title: B6d3_651 blood


title: PTC-radiation not exposed-1224T

value: status unknown


title: PTC-radiation not exposed-1208T

value: Kiev


title: B6md3_343 blood


title: B6md3_570 blood


title: B6d3_2 blood


title: B6d3_644 blood


title: normal thyroid-1208N

value: normal thyroid


title: normal thyroid-1190N


title: PTC-radiation not exposed-1144T

value: Sumy


title: normal thyroid-1175N


title: PTC-radiation exposed-053T

value: PTC


title: PTC-radiation not exposed-1175T


title: B6md3_2 blood


title: B6md3_3 blood


title: Primary prostate p53-/- Rbf/f 2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

description: Gene expression of control p53-/- prostate cells in the presence of  Rb

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Whole Genome Microarray 4x44K v2 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Entities having Detected flag across all samples were extracted.

source_name: Prostate, lacZ

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions with some changes. 3rd Spike mix was made by diluted 2nd Spike-Mix 10 times, and 1.8 ul of 3rd Spike-Mix was added to samples. Cy3 labeled cRNA was synthesized at 40°C for 2 hours and purified by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Prostate cells were cultured in FBS lack Prostacult media supplemented with bFGF and bEGF

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (#74106, Qiagen) according to the manufacturer’s instruction. RNA was quantified, and quality was monitored by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Prostate cells were infected with adeno virus (lacZ) as a control or adeno virus (Cre) for deleting Rb overnight followed by changing of media. RNA was extracted after infection by 48 hours.

tag: tissue

value: prostate

tag: genotype

tag: rb status

value: Intact

tag: pten status


title: Primary prostate p53-/- Rb∆f/∆f 2

description: Gene expression of p53-/- prostate cells in the depletion of  Rb

source_name: Prostate, Cre

value: p53-/- Rb deltaf/deltaf

value: Deleted


title: Primary prostate p53-/- Rb∆f/∆f 3


title: normal thyroid-053N

tag: type of thyroid tussue (ptc denotes papillary thyroid cancer)

tag: batch


title: PTC-radiation not exposed-1190T

tag: exposure to chernobyl radiation

value: no

tag: region of residence

value: not present

value: PTC-FS


title: normal thyroid-gr_n_939


title: normal thyroid-1126N


title: Primary prostate p53-/- Rb∆f/∆f 1


title: normal thyroid-1144N


title: Primary prostate p53-/- Rbf/f 1


title: Primary prostate p53-/- Rbf/f 3


title: normal thyroid-1243N


title: normal thyroid-gr_n_710


title: Cerebellum_Control_42d_rep2

description: Gene expression 42 days post infection, uninfected control

hyb_protocol: Cy3- labeled cRNA was hybridized to Agilent´s mouse 4x44k GE microarrays  for 16 h at 68 ºC and scanned using the Agilent DNA Microarray Scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) according to manufacture´s recommendation

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_105_Dec08, GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Cerebellum, non-infected control

label_protocol: 100 ng of total RNA were applied for Cy3-labelling reaction using the MessageAmp II-Bacteria Kit according to supplier´s recommendation (Ambion). As a result of IVT (in vitro transcription) reaction using aminoallyl-dUTP antisense aRNA were generated and subsequently coupled with fluorescent dye Cy3.

extract_protocol: Total RNA was extracted with the RNeasy® Lipid Tissue Mini kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. On-column Dnase digestion was included in the protocol as described in the manual. RNA was eluted twice with 40 µl each time, resulting in a total volume of 80 µl RNA/sample. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: Cerebra and cerebella were stored in RNAlater (Qiagen, Hilden, Germany) upon extraction.

value: cerebellum

value: female

tag: age

value: 11 weeks

tag: strain

value: non-infected control


title: Cerebellum_Control_42_drep4


title: normal thyroid-gr_n_286


title: normal thyroid-gr_n_147


title: normal thyroid-gr_n_242


title: Cerebrum_Control_42d_rep2

source_name: Cerebrum, non-infected control

value: cerebrum

value: male


title: Cerebellum_Control_42d_rep3


title: Cerebellum_Control_42d_rep1


title: B6d3_1 blood

value: d3 pi


title: Cerebrum_Control_42d_rep4


title: normal thyroid-gr_n_243

value: normal thyroid


title: normal thyroid-gr_n_162


title: Cerebrum_Control_42d_rep1


title: normal thyroid-gr_n_144


title: normal thyroid-gr_n_1030


title: Cerebellum_T. cati_42d_rep3

description: Gene expression 42 days post infection. Infection with 2000 embryonated T. cati eggs.

source_name: Cerebellum, T. cati-infected

value: T. cati-infected


title: PTC-radiation not exposed-gr_939

value: PTC

value: Sumy

tag: age at ptc operation

tag: braf v600e mutation

value: positive

tag: ret/ptc rearrangements

tag: subtype of ptc (classical denotes classical variant of ptc; ptc-f denotes ptc with dominant pattern of follicular structures; ptc-s denotes ptc with dominant pattern of solid areas; ptc-fs denotes ptc with dominant pattern of folicular and solid areas)

value: PTC-F


title: PTC-radiation not exposed-gr_692

value: Zhytomyr

value: PTC-S


title: Cerebrum_Control_42d_rep3

tag: gender


title: PTC-radiation not exposed-gr_705

value: no

value: Kiev

value: status unknown

value: not present

value: classical


title: normal thyroid-gr_n_1050


title: normal thyroid-135N


title: PTC-radiation not exposed-gr_615

value: PTC-FS


title: PTC-radiation not exposed-gr_710

value: Chernigov


title: Cerebellum_T. cati_42d_rep1

value: cerebellum

value: female

value: 11 weeks


title: Cerebrum_T. cati_42d_rep1

source_name: Cerebrum, T. cati-infected

value: cerebrum

value: T. cati-infected


title: Cerebellum_T. cati_42d_rep2


title: Cerebellum_T. canis_42d_rep1

description: Gene expression 42 days post infection. Infection with 2000 embryonated T. canis eggs.

source_name: Cerebellum, T. canis-infected

value: T. canis-infected


title: PTC-radiation exposed-gr_671

value: PTC

value: yes


title: PTC-radiation not exposed-gr_691

value: Chercassy

value: PTC-F


title: Cerebrum_T. cati_42d_rep2


title: PTC-radiation exposed-gr_601

value: positive


title: Cerebellum_T. canis_42d_rep2


title: PTC-radiation exposed-gr_501


title: Cerebrum_T. canis_42d_rep2

source_name: Cerebrum, T. canis-infected


title: PTC-radiation not exposed-gr_574

value: no

value: Kiev

value: PTC-S


title: Cerebrum_T. cati_42d_rep3


title: Cerebrum_T. canis_42d_rep1


title: Hippocampus_Y+Itreatment_7day_animal4

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression after 2 hours of 7 day Y+I treated rat hippocampus

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Rat 8x60k designed (AMADID: 028279) 800ng 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 10.5.1.1)

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

organism: Rattus norvegicus

source_name: Hippocampus, Y+I treated for 7 day, animal 4

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 trancription 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

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit following the manufacturer recommendations.

value: Hippocampus

value: Sprague Dawley

value: Male

value: 3 month

tag: treatment


title: Cerebellum_T. canis_42d_rep3

value: cerebellum

value: female

tag: infection


title: PTC-radiation not exposed-gr_411

value: status unknown

value: not present


title: PTC-radiation exposed-gr_469

value: Rovno


title: PTC-radiation exposed-gr_343

value: PTC

value: PTC-FS


title: PTC-radiation exposed-gr_280

value: yes

value: Chernigov


title: PTC-radiation not exposed-gr_496

value: Chercassy

value: PTC-F


title: PTC-radiation exposed-gr_456

value: positive


title: Cerebrum_T. canis_42d_rep3

tag: tissue

value: cerebrum

value: 11 weeks

value: T. canis-infected


title: PTC-radiation exposed-gr_286

value: Zhytomyr


title: Hippocampus_Y+Itreatment_7day_animal3

source_name: Hippocampus, Y+I treated for 7 day, animal 3

value: Hippocampus

value: Sprague Dawley

value: Male

value: 3 month

value: 2 hours of 7 day Y+I treated rat hippocampus


title: PTC-radiation not exposed-gr_368

value: no

value: Sumy

value: not present


title: PTC-radiation exposed-gr_515

value: PTC

value: yes


title: Lung_OVAsens_OVAchal_DEXtreat_rep4

city: New Lambton Heights

first: Maximilian

last: Plank

state: Australia

address: Lot 1 Kookaburra Circuit

country: Australia

institute: University of Newcastle

hyb_protocol: MiRNA microarrays were performed according to manufacturer’s protocol using the miRNA Complete Labeling and Hyb Kit and Mouse miRNA Microarray Release 12.0 slides (Agilent Technologies, Technology number 21828, version 2010.11.04).

scan_protocol: Samples were scanned with a High-Resolution C Scanner (Agilent Technologies, USA).

data_processing: Data was processed using the Feature Extraction software version 10.7.3.1 and data analysis was performed using Genespring GX version 11.5.1 (Agilent Technologies, USA).

source_name: Lung, OVA sensitsation, OVA challenge, DEX treatment, replicate 4

extract_protocol: Total RNA was extracted from lung samples using phenol-chloroform separation and isopropanol precipitation.

treatment_protocol: Mice were systemically sensitised via i.p. injection of 50 μg chicken egg OVA complexed with 1 mg Alhydrogel in PBS (day 0). Non-sensitized control mice were injected with 1 mg Alhydrogel in PBS. On days 12, 13, 14 and 15, all mice were challenged (i.n.) with 10 μg of OVA in PBS or PBS for non-challenged control mice. Endpoints were performed 24 hours after the last OVA challenge. Dexamethasone (DEX) treatments (3 mg/kg body weight, i.p.) were performed on day 11 and every second day thereafter 1 hour before challenges.

value: Lung

tag: sensitisation

value: OVA

tag: challenge

value: DEX


title: Hippocampus_Vehicletreatment_7day_animal3

description: Gene expression after 2 hours of 7 day vehicle treated rat hippocampus

source_name: Hippocampus, vehicle treated for 7 day, animal 3


title: Hippocampus_Y+Itreatment_7day_animal2

source_name: Hippocampus, Y+I treated for 7 day, animal 2


title: PTC-radiation exposed-gr_243

value: Kiev

value: PTC-F


title: normal thyroid-1224N

source_name: normal thyroid

value: normal thyroid


title: PTC-radiation exposed-gr_208

source_name: PTC,radiation exposed

value: Chernigov

value: PTC-FS


title: Lung_OVAsens_OVAchal_DEXtreat_rep3

source_name: Lung, OVA sensitsation, OVA challenge, DEX treatment, replicate 3

label_protocol: MiRNA microarrays were performed according to manufacturer’s protocol using the miRNA Complete Labeling and Hyb Kit and Mouse miRNA Microarray Release 12.0 slides (Agilent Technologies, Technology number 21828, version 2010.11.04).


title: Hippocampus_Vehicletreatment_7day_animal2

source_name: Hippocampus, vehicle treated for 7 day, animal 2

value: Hippocampus

value: Sprague Dawley

value: 2 hours of 7 day vehicle treated rat hippocampus


title: Lung_OVAsens_OVAchal_DEXtreat_rep2

source_name: Lung, OVA sensitsation, OVA challenge, DEX treatment, replicate 2


title: PTC-radiation exposed-gr_192


title: Hippocampus_Vehicletreatment_7day_animal4

source_name: Hippocampus, vehicle treated for 7 day, animal 4

value: Male

value: 3 month


title: TRPV3_Wildtype_293T_24h

city: Seattle

first: Kai

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: Probes were then loaded on the array hybridization chambers then hybridized at 65°C for 17 h.

scan_protocol: The slides were washed and scanned (Agilent, Santa Clara, CA) with Agilent DNA microarray scanner.

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

label_protocol: Fluorescent-labeled (Cy3) probes were prepared with the single color labeling kit from Agilent (Santa Clara, CA).

extract_protocol: Total RNA was isolated with miRNeasy kit (Qiagen, Germantown, MD) according to manufacturer's instructions.

tag: cell line

tag: transfected trpv3 variant

value: wildtype TRPV3

tag: time


title: PTC-radiation exposed-gr_242

tag: type of thyroid tussue (ptc denotes papillary thyroid cancer)

tag: exposure to chernobyl radiation

value: not present

value: status unknown

value: classical

tag: batch


title: TRPV3_692_Gly_293T_24h

value: 692 Gly TRPV3


title: PTC-radiation exposed-gr_165

value: PTC

value: yes

tag: region of residence


title: TRPV3_573_Ser_293T_24h

value: 573 Ser TRPV3


title: Control_293T_24h

value: Control (none)


title: Hippocampus_Y+Itreatment_7day_animal1

source_name: Hippocampus, Y+I treated for 7 day, animal 1

tag: strain

tag: age

value: 2 hours of 7 day Y+I treated rat hippocampus


title: TRPV3_573_Ser_293T_16hr


title: Control_293T_16hr


title: Hippocampus_Vehicletreatment_7day_animal1

source_name: Hippocampus, vehicle treated for 7 day, animal 1


title: TRPV3_573_Cys_293T_16hr

value: 573 Cys TRPV3


title: TRPV3_692_Gly_293T_16hr


title: PTC-radiation not exposed-gr_162

source_name: PTC,radiation not exposed

value: no

value: Zhytomyr

tag: age at ptc operation

tag: braf v600e mutation

value: positive

tag: ret/ptc rearrangements


title: TRPV3_580_Pro_293T_16hr

value: 580 Pro TRPV3


title: PTC-radiation exposed-gr_145

tag: subtype of ptc (classical denotes classical variant of ptc; ptc-f denotes ptc with dominant pattern of follicular structures; ptc-s denotes ptc with dominant pattern of solid areas; ptc-fs denotes ptc with dominant pattern of folicular and solid areas)

value: PTC-F


title: Lung_OVAsens_OVAchal_DEXtreat_rep1

source_name: Lung, OVA sensitsation, OVA challenge, DEX treatment, replicate 1

value: Lung

value: OVA

tag: treatment

value: DEX


title: PTC-radiation exposed-gr_147

value: not present


title: TRPV3_Wildtype_293T_16hr

value: wildtype TRPV3


title: Lung_OVAsens_OVAchal_rep5

source_name: Lung, OVA sensitsation, OVA challenge, replicate 5

tag: tissue

value: PBS


title: TRPV3_580_Pro_293T_24h


title: TRPV3_573_Cys_293T_24h


title: Lung_OVAsens_OVAchal_rep4

source_name: Lung, OVA sensitsation, OVA challenge, replicate 4

tag: sensitisation


title: Lung_OVAsens_OVAchal_rep6

source_name: Lung, OVA sensitsation, OVA challenge, replicate 6

tag: challenge


title: Lung_OVAsens_OVAchal_rep3

source_name: Lung, OVA sensitsation, OVA challenge, replicate 3


title: HEK293T_Wildtype

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

source_name: Wildtype

tag: cell line

value: Wildtype


title: Lung_OVAsens_OVAchal_rep2

source_name: Lung, OVA sensitsation, OVA challenge, replicate 2


title: Lung_OVAsens_OVAchal_rep1

source_name: Lung, OVA sensitsation, OVA challenge, replicate 1


title: PTC-radiation exposed-gr_135

value: PTC

value: yes

value: PTC-S


title: PTC-radiation exposed-gr_144

value: Chernigov


title: HEK293T_R348X

value: mutation R348X


title: HaCaT_shRNA_control

value: HaCaT

value: shRNA control


title: PTC-radiation not exposed-gr_1091

value: no

value: Kiev

value: positive

value: classical


title: HEK293T_Control

source_name: Control

value: Control


title: HGF4

city: Tokushima

first: Yosuke

last: Shikama

address: 2-50-1 Kuramoto-cho

department: Tokushima University Hospital

institute: Clinical Research Center for Diabetes

description: US82800151_253949426377_S01_GE1_107_Sep09_2_2

hyb_protocol: 0.6 mg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human 8x60k ver. 2.0 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan resolution 3 mm).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: HGF were prepared from explants of normal gingival tissues, and the explants were cut into pieces and cultured in DMEM supplemented with 10% fetal bovine serum. After three to four subcultures by trypsinization, homogeneous, slim, spindle-shaped cells grown in characteristic swirls were obtained.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. RNA quality was determined using an agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: HGF were treated with either 1% bovine serum albumin (without stimulation) or 100 mM palmitate. The cultures were incubated for 36 hours at 37C in a humidified incubator with 5% CO2.

tag: subject gender

value: male

value: normal gingival tissue

tag: cell type

value: human gingival fibroblasts (HGF)

tag: stimulated with

value: 100 mM palmitate


title: HaCaT_R348X

tag: time


title: HGF3

description: US82800151_253949426377_S01_GE1_107_Sep09_2_1


title: HaCaT_R142C

value: mutation R142C


title: PTC-radiation exposed-gr_103

source_name: PTC,radiation exposed

tag: type of thyroid tussue (ptc denotes papillary thyroid cancer)

value: PTC

tag: exposure to chernobyl radiation

value: Zhytomyr

value: not present

value: PTC-FS

tag: batch


title: HaCaT_shRNA_combined

value: shRNA combined


title: HaCaT_Control

value: HaCaT


title: Lung_PBSsens_OVAchal_rep3

source_name: Lung, PBS sensitsation, OVA challenge, replicate 3

value: Lung

value: PBS

value: OVA


title: PTC-radiation not exposed-gr_1050

value: no

tag: region of residence


title: Lung_PBSsens_OVAchal_rep2

source_name: Lung, PBS sensitsation, OVA challenge, replicate 2