title: Barcoded PCA pool-yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 3

status: Public on Apr 30 2017

type: genomic

city: Palo Alto

first: Ulrich

last: Schlecht

address: 3165 Porter Drive

department: Biochemistry

country: USA

institute: Stanford University

description:
BPII-RBD2-MTX-ATC.3
Barcoded PCA pool-10 generations yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 3.

hyb_protocol: PCR reactions of up- and down-tags were mixed in equal volumes (30 ul each) and hybridized overnight to custom-built TAG4 microarrays (Affymetrix).

scan_protocol: After hybridization, arrays were stained and scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).

data_processing: All cells carry two tags that hybridize to the GenFlex tag 16k array, an uptag and a downtag. From each array, we extracted the fluorescence intensity values for every uptag and downtag associated with the 1383 strains in the bar-coded PCA pool. These raw fluorescence values were quantile-normalized and then log2-transformed using the normalize.quantiles function of the preprocessCore package in R. Quantile normalization was performed separately for uptags and downtags. Fourteen experimental conditions were measured in duplicate, and the control condition (DMSO) was measured with 6 replicates. The distance between the means (fold-change or FC) of the control condition and each experimental condition was calculated separately for uptags and downtags. A moderated t-statistic was then calculated using the R package LIMMA, and the derived p-values were further converted to q-values using Benjamini & Hochberg False Discovery Rate (FDR) correction using the p.adjust function in R. A separate q-value was calculated for uptags and downtags. PCA strains with a significant increase in their tag abundance in response to an experimental condition were identified using (q-value < 0.05 for both uptag and downtag) and FC > 0.25 (for both uptag and downtag) as cutoffs. PCA strains with a significant decrease in tag abundance were identified using (q-value < 0.05 for both uptag and downtag) and FC < -0.25 (for both uptag and downtag) as cutoffs.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: barcoded PCA pool-10 generations yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 3

label_protocol: The strain-specific barcodes contained in the DNA were amplified by PCR using a set of biotinylated primers.

growth_protocol: Growth in minimal media (yeast nitrogen base and ammonium sulfate) supplemented with 2% of either glucose or 2% ethanol at 30 °C with vigorous shaking. Measurements of optical density at 595 nm (OD595) were used to monitor growth every 15 min. Samples were harvested after precisely 3 pool generations. CRISPRi samples were harvested after 10 generations.

extract_protocol: Genomic DNA was extracted from cell pellets using the YeaStar Genomic DNA kit from Zymo Research (D2002).

treatment_protocol: FK506, CuSO4, doxorubicin, 1181-0519, atorvastatin, hydrogen peroxide, low concentration of ammonium sulfate, NaCl, Sorbitol, Menadione, High Temperature, complete synthetic amino acid mix, methionine were incorporated into growth media in the treatment samples.

tag: pool

value: barcoded protein-complementation assay strains

tag: strain/background

tag: growth stage

value: 10 generations

tag: agent


title: Barcoded PCA pool-yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 2

description:
BPII-RBD2-MTX.2
Barcoded PCA pool-10 generations yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 2.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 1

description:
BPII-RBD2-MTX-ATC.1
Barcoded PCA pool-10 generations yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 1.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 2

description:
BPII-RBD2-MTX-ATC.2
Barcoded PCA pool-10 generations yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 2.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and methotrexate and ATC with gRNA directed against RBD2-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 1

description:
BPII-RBD2-MTX.1
Barcoded PCA pool-10 generations yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 1.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 3

description:
BPII-RBD2-ATC.3
Barcoded PCA pool-10 generations yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 3.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 3


title: Barcoded PCA pool-yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 3

description:
BPII-RBD2-MTX.3
Barcoded PCA pool-10 generations yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 3.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and methotrexate with gRNA directed against RBD2-biological rep 3


title: Barcoded PCA pool-yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 2

description:
BPII-RBD2-ATC.2
Barcoded PCA pool-10 generations yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 2.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with gRNA directed against RBD2-biological rep 1

description:
BPII-RBD2.1
Barcoded PCA pool-10 generations yeast nitrogen base with gRNA directed against RBD2-biological rep 1.

source_name: barcoded PCA pool-10 generations yeast nitrogen base with gRNA directed against RBD2-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with complete synthetic media-biological rep 2

description:
CSM.2
Barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media-biological rep 2

value: 3 generations


title: Barcoded PCA pool-yeast nitrogen base with complete synthetic media-biological rep 1

description:
CSM.1
Barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 1

description:
BPII-RBD2-ATC.1
Barcoded PCA pool-10 generations yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 1.

source_name: barcoded PCA pool-10 generations yeast nitrogen base and ATC with gRNA directed against RBD2-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with ethanol-biological rep 2

description:
EtOH.2
Barcoded PCA pool-3 generations yeast nitrogen base with ethanol-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with ethanol-biological rep 2

value: yeast nitrogen base with ethanol


title: Barcoded PCA pool-yeast nitrogen base with ethanol-biological rep 1

description:
EtOH.1
Barcoded PCA pool-3 generations yeast nitrogen base with ethanol-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with ethanol-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with heat-shock-biological rep 2

description:
High-Temp.2
Barcoded PCA pool-3 generations yeast nitrogen base with heat-shock-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with heat-shock-biological rep 2

value: yeast nitrogen base with heat


title: Barcoded PCA pool-yeast nitrogen base with gRNA directed against RBD2-biological rep 2

description:
BPII-RBD2.2
Barcoded PCA pool-10 generations yeast nitrogen base with gRNA directed against RBD2-biological rep 2.

source_name: barcoded PCA pool-10 generations yeast nitrogen base with gRNA directed against RBD2-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with gRNA directed against RBD2-biological rep 3

description:
BPII-RBD2.3
Barcoded PCA pool-10 generations yeast nitrogen base with gRNA directed against RBD2-biological rep 3.

source_name: barcoded PCA pool-10 generations yeast nitrogen base with gRNA directed against RBD2-biological rep 3


title: Barcoded PCA pool-yeast nitrogen base with menadione-biological rep 1

description:
Menadione.1
Barcoded PCA pool-3 generations yeast nitrogen base with menadione-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with menadione-biological rep 1

value: yeast nitrogen base with menadione


title: Barcoded PCA pool-yeast nitrogen base with menadione-biological rep 2

description:
Menadione.2
Barcoded PCA pool-3 generations yeast nitrogen base with menadione-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with menadione-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with methionine-biological rep 1

description:
Methionine.1
Barcoded PCA pool-3 generations yeast nitrogen base with methionine-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with methionine-biological rep 1

value: yeast nitrogen base with methionine


title: Barcoded PCA pool-yeast nitrogen base with heat-shock-biological rep 1

description:
High-Temp.1
Barcoded PCA pool-3 generations yeast nitrogen base with heat-shock-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with heat-shock-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with sorbitol-biological rep 2

description:
Sorbitol.2
Barcoded PCA pool-3 generations yeast nitrogen base with sorbitol-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with sorbitol-biological rep 2

value: yeast nitrogen base with sorbitol


title: Barcoded PCA pool-yeast nitrogen base with sorbitol-biological rep 1

description:
Sorbitol.1
Barcoded PCA pool-3 generations yeast nitrogen base with sorbitol-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with sorbitol-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with low nitrogen-biological rep 2

description:
AS.2
Barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen-biological rep 2

value: yeast nitrogen base with low nitrogen


title: Barcoded PCA pool-yeast nitrogen base with NaCl-biological rep 1

description:
NaCl.1
Barcoded PCA pool-3 generations yeast nitrogen base with NaCl-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with NaCl-biological rep 1

value: yeast nitrogen base with NaCl


title: Barcoded PCA pool-yeast nitrogen base with low nitrogen-biological rep 1

description:
AS.1
Barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with NaCl-biological rep 2

description:
NaCl.2
Barcoded PCA pool-3 generations yeast nitrogen base with NaCl-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with NaCl-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with H2O2-biological rep 2

description:
H2O2.2
Barcoded PCA pool-3 generations yeast nitrogen base with H2O2-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with H2O2-biological rep 2

value: yeast nitrogen base with H2O2


title: Barcoded PCA pool-yeast nitrogen base with doxorubicin-biological rep 1

description:
Doxorubicin.1
Barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin-biological rep 1

value: yeast nitrogen base with doxorubicin


title: Barcoded PCA pool-yeast nitrogen base with CuSO4-biological rep 2

description:
CuSO4.2
Barcoded PCA pool-3 generations yeast nitrogen base with CuSO4-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with CuSO4-biological rep 2

value: yeast nitrogen base with CuSO4


title: Barcoded PCA pool-yeast nitrogen base with CuSO4506-biological rep 1

description:
CuSO4.1
Barcoded PCA pool-3 generations yeast nitrogen base with CuSO4506-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with CuSO4506-biological rep 1

value: yeast nitrogen base with CuSO4506


title: Barcoded PCA pool-yeast nitrogen base with 1181-0519-biological rep 2

description:
X1181-0519.2
Barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519-biological rep 2

value: yeast nitrogen base with 1181


title: Barcoded PCA pool-yeast nitrogen base with 1181-0519-biological rep 1

description:
X1181-0519.1
Barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with doxorubicin-biological rep 2

description:
Doxorubicin.2
Barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with atorvastatin-biological rep 1

description:
Atorvastatin.1
Barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin-biological rep 1

value: yeast nitrogen base with atorvastatin


title: Barcoded PCA pool-yeast nitrogen base with H2O2-biological rep 1

description:
H2O2.1
Barcoded PCA pool-3 generations yeast nitrogen base with H2O2-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with H2O2-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with atorvastatin-biological rep 2

description:
Atorvastatin.2
Barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with DMSO-biological rep 4

description:
DMSO.4
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 4.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 4

value: yeast nitrogen base with DMSO


title: Barcoded PCA pool-yeast nitrogen base with DMSO-biological rep 3

description:
DMSO.3
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 3.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 3

value: barcoded protein-complementation assay strains


title: Barcoded PCA pool-yeast nitrogen base with DMSO-biological rep 5

description:
DMSO.5
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 5.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 5


title: Barcoded PCA pool-yeast nitrogen base with methionine and methotrexate-biological rep 2

description:
Methionine.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with methionine and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with methionine and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with DMSO-biological rep 1

description:
DMSO.1
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with DMSO-biological rep 2

description:
DMSO.2
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with DMSO-biological rep 6

description:
DMSO.6
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 6.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO-biological rep 6


title: Barcoded PCA pool-yeast nitrogen base with FK506-biological rep 2

description:
FK506.2
Barcoded PCA pool-3 generations yeast nitrogen base with FK506-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with FK506-biological rep 2

value: yeast nitrogen base with FK506


title: Barcoded PCA pool-yeast nitrogen base with FK506-biological rep 1

description:
FK506.1
Barcoded PCA pool-3 generations yeast nitrogen base with FK506-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with FK506-biological rep 1

value: 3 generations


title: Barcoded PCA pool-yeast nitrogen base with methionine and methotrexate-biological rep 1

description:
Methionine.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with methionine and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with methionine and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with complete synthetic media and methotrexate-biological rep 2

description:
CSM.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate-biological rep 1

description:
EtOH.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with ethanol and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with ethanol and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate-biological rep 2

description:
EtOH.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with ethanol and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with ethanol and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with heat-shock and methotrexate-biological rep 2

description:
High-Temp.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with heat-shock and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with heat-shock and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with menadione and methotrexate-biological rep 2

description:
Menadione.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with menadione and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with menadione and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with menadione and methotrexate-biological rep 1

description:
Menadione.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with menadione and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with menadione and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with sorbitol and methotrexate-biological rep 2

description:
Sorbitol.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with sorbitol and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with sorbitol and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with sorbitol and methotrexate-biological rep 1

description:
Sorbitol.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with sorbitol and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with sorbitol and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with NaCl and methotrexate-biological rep 2

description:
NaCl.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with NaCl and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with NaCl and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with heat-shock and methotrexate-biological rep 1

description:
High-Temp.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with heat-shock and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with heat-shock and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with atorvastatin and methotrexate-biological rep 1

description:
Atorvastatin.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with NaCl and methotrexate-biological rep 1

description:
NaCl.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with NaCl and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with NaCl and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with doxorubicin and methotrexate-biological rep 2

description:
Doxorubicin.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with H2O2 and methotrexate-biological rep 2

description:
H2O2.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with H2O2 and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with H2O2 and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with 1181-0519 and methotrexate-biological rep 1

description:
X1181-0519.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519 and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519 and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with H2O2 and methotrexate-biological rep 1

description:
H2O2.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with H2O2 and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with H2O2 and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with 1181-0519 and methotrexate-biological rep 2

description:
X1181-0519.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519 and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with 1181-0519 and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with low nitrogen and methotrexate-biological rep 2

description:
AS.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with complete synthetic media and methotrexate-biological rep 1

description:
CSM.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with complete synthetic media and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with CuSO4 and methotrexate-biological rep 2

description:
CuSO4.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with CuSO4 and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with CuSO4 and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with DMSO and methotrexate-biological rep 5

description:
DMSO.MTX.5
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 5.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 5


title: Barcoded PCA pool-yeast nitrogen base with low nitrogen and methotrexate-biological rep 1

description:
AS.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with low nitrogen and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with CuSO4506 and methotrexate-biological rep 1

description:
CuSO4.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with CuSO4506 and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with CuSO4506 and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with doxorubicin and methotrexate-biological rep 1

description:
Doxorubicin.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with doxorubicin and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with DMSO and methotrexate-biological rep 6

description:
DMSO.MTX.6
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 6.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 6


title: Barcoded PCA pool-yeast nitrogen base with FK506 and methotrexate-biological rep 1

description:
FK506.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with FK506 and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with FK506 and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with FK506 and methotrexate-biological rep 2

description:
FK506.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with FK506 and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with FK506 and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with atorvastatin and methotrexate-biological rep 2

description:
Atorvastatin.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with atorvastatin and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with methionine-biological rep 2

description:
Methionine.2
Barcoded PCA pool-3 generations yeast nitrogen base with methionine-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with methionine-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with DMSO and methotrexate-biological rep 4

description:
DMSO.MTX.4
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 4.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 4


title: Barcoded PCA pool-yeast nitrogen base with DMSO and methotrexate-biological rep 3

description:
DMSO.MTX.3
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 3.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 3


title: Barcoded PCA pool-yeast nitrogen base with DMSO and methotrexate-biological rep 2

description:
DMSO.MTX.2
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 2.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 2


title: Barcoded PCA pool-yeast nitrogen base with DMSO and methotrexate-biological rep 1

description:
DMSO.MTX.1
Barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 1.

source_name: barcoded PCA pool-3 generations yeast nitrogen base with DMSO and methotrexate-biological rep 1


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 12h timepoint-biological rep 1

type: RNA

description:
Ethanol.12h.1
mRNA
Streptavidin-phycoerythrin conjugate

hyb_protocol: 220 µl hybridization cocktail containing heat-fragmented and biotin-labeled cRNA at a concentration of 0.05 µg/µl were injected into GeneChips and incubated at 45°C on a rotator in a Hybridization Oven 640 (Affymetrix) overnight at 60 rpm. The arrays were washed and stained with a streptavidin-phycoerythrin conjugate (SAPE; Molecular Probes).

data_processing: CEL files containing the raw data were computed from DAT array image files using the statistical algorithm implemented in MAS 5.0 (Affymetrix). Raw data were preprocessed (background adjustment, normalization, and summarization of probe sets) by using the Robust Multiarray Analysis (RMA) package from BioConductor.

label: Biotin

molecule: total RNA

source_name: barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate, 12h timepoint

label_protocol: cDNA was synthesized in 10 μl reactions containing 1 μg/μl total RNA, 12.5 ng/μl Oligo(dT)12-18 primer (Invitrogen, catalog no. 18418-012), 15 units/μl SuperScript II (Invitrogen, catalog no. 18064-014), 1 x First Strand Buffer, 10 mM DTT, and 10 mM dNTPs (Invitrogen, catalog no. 18427013). After the RNA and primers were denatured for 10 min at 70°C, the remaining reagents were added, and the reaction was incubated at 42°C for 60 min. To remove the RNA template, 2 units of RNase H were then added and the mix was incubated at 37°C for 20 min and then at 95°C for 5 min. Quality of total RNA and cRNA was monitored using RNA Nano 6000 chips processed using the 2100 BioAnalyzer (Agilent).

growth_protocol: Growth in minimal media (yeast nitrogen base and ammonium sulfate) supplemented with 2% dextrose. Then shifted to minimal media (yeast nitrogen base and ammonium sulfate) supplemented with 2% ethanol and methotrexate at 30 °C with vigorous shaking. Samples were harvested precisely 0h, 30min, 1h, 4h and 12 hours after shift.

extract_protocol: Total RNA was extracted from cell pellets using RiboPure RNA Purification Kit for yeast (Thermo Fisher Scientific).

value: 12h after transfer to ethanol


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 4h timepoint-biological rep 2

description:
Ethanol.4h.2
mRNA
Streptavidin-phycoerythrin conjugate

source_name: barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate, 4h timepoint

value: 4h after transfer to ethanol


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 30min timepoint-biological rep 2

description:
Ethanol.30min.2
mRNA
Streptavidin-phycoerythrin conjugate

source_name: barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate, 30min timepoint

value: 30min after transfer to ethanol


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 12h timepoint-biological rep 2

description:
Ethanol.12h.2
mRNA
Streptavidin-phycoerythrin conjugate


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 1h timepoint-biological rep 2

description:
Ethanol.1h.2
mRNA
Streptavidin-phycoerythrin conjugate

source_name: barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate, 1h timepoint

value: 1h after transfer to ethanol


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 0h timepoint-biological rep 2

description:
Ethanol.0h.2
mRNA
Streptavidin-phycoerythrin conjugate

source_name: barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate, 0h timepoint

value: 0h after transfer to ethanol


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 1h timepoint-biological rep 1

description:
Ethanol.1h.1
mRNA
Streptavidin-phycoerythrin conjugate


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 0h timepoint-biological rep 1

description:
Ethanol.0h.1
mRNA
Streptavidin-phycoerythrin conjugate


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 30min timepoint-biological rep 1

description:
Ethanol.30min.1
mRNA
Streptavidin-phycoerythrin conjugate


title: Barcoded PCA pool-yeast nitrogen base with ethanol and methotrexate 4h timepoint-biological rep 1

description:
Ethanol.4h.1
mRNA
Streptavidin-phycoerythrin conjugate


title: G91_MES_siRNA_PRCs

city: Boston

first: Arun

middle: Kumar

last: Rooj

state: Massachusetts

address: 4 Blackfan Circle

department: Neurosurgery

institute: Brigham and Women's Hospital

description: Gene expression of patient derived Proneural GSC146 after knoickdown of miR-128, grown in vitro in serum free condition.

hyb_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: .Raw signal intensities were normalized in quantile method by GeneSpring GX software (v12.1), and low intensity genes were filtered (Genes that at least 3 out of 22 samples have flags in Detected were chosen for further analysis).

organism: Homo sapiens

source_name: Brain tumor

growth_protocol: GSCs were established by dissociation of human patient samples, and the GSCs were cultured as neurospheres in stem cell-enriching conditions using neurobasal medium supplemented with 1% Glutamine, 2% B27 and 20 ng/mL EGF and FGF–2. The unique identity of cultured patient-derived cells was confirmed by short tandem repeat analysis.

extract_protocol: Total RNA was extracted using the manufacturer’s protocol from TRIzol

treatment_protocol: GSC were engineered to stably overexpressing miR-128 or anti-miR-128. In Knockdown experiments G33 and G44 GSCs were treated with either siRNA NC or siRNA against BMI1 and SUZ12.

tag: tissue

value: GBM

value: GBM Stem Cells


title: PH_RNA_7_pharmacyclics_20140611

city: Sunnyvale

first: Hsu-Ping

last: Kuo

state: CA

address: 995 E Arques Ave

institute: Pharmacyclics

description: gene expression data from TMD8 cells

hyb_protocol: The fragmented single-stranded cDNA was combined with hybridization controls from Affymetrix and hybridized in the HTA 2.0 array overnight for 16-18 hours in the Affymetrix Genechip Hybridization Oven 645

scan_protocol: Arrays were stained and washed in the Affymetrix GeneChip Fluidics Station 450. Mircoarrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CHP files were generated using Affymetrix Power Tools (APT) and analyzed with Transcriptome Analysis Console from Affymetrix.

source_name: ibrutinib-resistant TMD8 cells

label_protocol: single-stranded cDNA was fragmented and labeled using the GeneChip WT Terminal Labeling kit from Affymetrix (900671)

growth_protocol: TMD8 cells were cultured in RPMI 1640 medium with 10% FBS, 1mM sodium pyruvate, and 1% Pen/Strep.

extract_protocol: RNA was isolated using the Qiagen RNeasy mini Kit (cat 74104). Column based.

treatment_protocol: Ibrutinib-resistant TMD8 cells were generated by in vitro culture of the parental cells for prolonger periods of time with progressively increasing concentrations of ibrutinib.

tag: sample group

value: ibrutinib-resistant TMD8 cells


title: LNCaP [3]

city: Hirosaki

first: Tohru

last: Yoneyama

address: 5 Zaifu-cho

department: Advanced Transplant & regenerative medicine

country: Japan

institute: Hirosaki University

description: Gene expression data from laminin binding O-lycan moderate expressing andorogen-independent prostate cancer cell line

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX version 12.6 software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: High LB O-glycan cell

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

growth_protocol: Prostate cancer cells were grown in RPMI1640 medium containing 100 U/mL of penicillin and 100 μg/mL of streptomycin with 10% FBS.

extract_protocol: ISOGEN II Reagent (Nippon gene) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: sample [1 and 2] isolated from PC3 cells using anti-laminin binding glycan antibody (IIH6C4). Sample[4] was isolated from LNCaP cell by culturing RPMI1640 containinig charcole stripped FBS.

tag: cell line

value: LN-CaP

tag: origin

value: Lymphnode metastasis site from Prostate cancer

tag: cell motility and invasiveness

value: Low cell motility and invasion capacity

tag: androgen indepedency

value: androgen-dependent


title: G157_PN_siRNA_NC

description: Gene expression of patient derived Proneural G44 transfected with siRNA against BMI1 and SUZ12, grown in vitro in serum free condition.

scan_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.


title: PH_RNA_5_pharmacyclics_20140611

description: gene expression data from TMD8 cells

source_name: parental TMD8 cells

value: parental TMD8 cells


title: G157_PN_siRNA_PRCs

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.


title: PH_RNA_6_pharmacyclics_20140611

description: gene expression data from TMD8 cells


title: PC3-L [2]

description: Gene expression data from laminin binding O-lycan high expressing andorogen-independent prostate cancer cell line

source_name: Low LB O-glycan cell

value: Bone metastasis site from Prostate cancer

value: High cell motility and invasion capacity

value: androgen-independent


title: G146_PN_siRNA_PRCs


title: 157_PN_miR128

description: Gene expression of patient derived Proneural GSC146 grown in vitro in serum free condition.


title: G146_PN_siRNA_NC


title: Cre+ KTC

city: Tokyo

first: Hayato

last: Nakagawa

address: 7-3-1 Hongo Bunkyo-ku

institute: The University of Tokyo

hyb_protocol: cRNA was hybridized to a 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

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

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

organism: Mus musculus

source_name: Cre+ KTC organoid

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

growth_protocol: Isolated mouse EHBD tissue was cut into small pieces and incubated in dissociation buffer [RPMI with 4 % fetal calf serum, 1 mg/mL collagenase D (Roche), 0.5 mg/mL dispase (Gibco), and 40 μg/mL DNase (Roche)] at 37 °C for 30 min. Incubated EHBD was mixed with Matrigel and seeded onto plates overlaid with culture medium [Ad-DMEM/F12 (Invitrogen) supplemented with B27 and N2, 1 mM N-acetylcysteine, 10 mM nicotinamide (Wako), 50 ng/mL EGF, 1 μg/mL Rspo1, 100 ng/mL Noggin, 100 ng/mL FGF10 (Peprotech), and 10 % Wnt3a-conditioned medium (ATCC)]. Passaging was performed at 1:4–1:8 split ratios once per week. For passaging, organoids were incubated on ice in Cell Recovery Solution (BD) for 30 min, passed twice through 29-guage needle, and re-embedded in Matrigel. The ROCK inhibitor Y-27632 (10 µM; Wako) was added to the initial culture and after organoid passaging.

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

treatment_protocol: Organoids isolated from KTC mice were infected with Cre-expressing or control lentivirus, and transduced cells were selected using puromycin. Two weeks later, RNA was extracted.

value: Biliary organoids

tag: strain

tag: lentivirus

value: expressing Cre-recombinase


title: Cre- KTC

source_name: Cre- KTC organoid

value: control


title: G91_MES_siRNA_NC


title: G88_MES_siRNA_PRCs

description: Gene expression of patient derived Proneural GSC44 after knoickdown of miR-128, grown in vitro in serum free condition.


title: PC3-H [1]

description: Gene expression data from laminin binding O-lycan low expressing andorogen-independent prostate cancer cell line


title: LNCaP-AI [4]

description: Gene expression data from laminin binding O-lycan low expressing andorogen-independent prostate cancer cell line grown in human perineural cell conditional medium.

value: androgen independent LNCaP cell.


title: G88_MES_siRNA_NC

description: Gene expression of patient derived Proneural GSC44 grown in vitro in serum free condition.


title: 146_PN_miR128


title: PH_RNA_8_pharmacyclics_20140611

description: gene expression data from TMD8 cells


title: G107_MES_NC

description: Gene expression of patient derived Mesenchymal G107 grown in vitro in serum free condition.

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

source_name: patient derived Mesenchymal G107

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

value: Glioblastoma (GBM)

tag: cell type

value: GBM Stem Cells (GSCs)

tag: cell subtype

value: Mesenchymal

tag: genotype/variation


title: 91_MES_miR128

description: Gene expression of patient derived Mesenchymal GSC91 after overexpression of miR-128, grown in vitro in serum free condition.

source_name: patient derived Mesenchymal GSC91

value: stably overexpressing miR-128


title: 88_MES_miR128

description: Gene expression of patient derived Mesenchymal GSC88 after overexpression of miR-128, grown in vitro in serum free condition.

source_name: patient derived Mesenchymal GSC88


title: G44_PN_NC

source_name: patient derived Proneural GSC44

value: Proneural


title: 157_PN_amiR128

description: Gene expression of patient derived Proneural GSC157 after knoickdown of miR-128, grown in vitro in serum free condition.

source_name: patient derived Proneural GSC157

value: stably overexpressing anti-miR-12


title: G61557_MES_NC

description: Gene expression of patient derived Mesenchymal G61557 grown in vitro in serum free condition.

source_name: patient derived Mesenchymal G61557


title: 91_MES_NC

description: Gene expression of patient derived Mesenchymal G91 grown in vitro in serum free condition.

source_name: patient derived Mesenchymal G91


title: G44_PN_siRNA_NC

description: Gene expression of patient derived Proneural G44 transfected with siRNA negative control, grown in vitro in serum free condition.

source_name: patient derived Proneural G44

value: transfected with siRNA NC


title: G44_PN_siRNA_PRCs

value: transfected with siRNA against BMI1 and SUZ12


title: BT188_PN_NC

description: Gene expression of patient derived Proneural BT188 grown in vitro in serum free condition.

source_name: patient derived Proneural BT188


title: 35_MES_NC

description: Gene expression of patient derived Mesenchymal G35 grown in vitro in serum free condition.

source_name: patient derived Mesenchymal G35


title: G157_PN_NC

description: Gene expression of patient derived Proneural GSC157 grown in vitro in serum free condition.


title: 44_PN_miR128

source_name: Brain tumor

value: GBM

value: GBM Stem Cells


title: 35_MES_miR128

description: Gene expression of patient derived Mesenchymal GSC35 after overexpression of miR-128, grown in vitro in serum free condition.

source_name: patient derived Mesenchymal GSC35


title: G88_MES_NC

description: Gene expression of patient derived Mesenchymal G88 grown in vitro in serum free condition.

source_name: patient derived Mesenchymal G88


title: G33_MES_siRNA_NC

description: Gene expression of patient derived Mesenchymal G33 transfected with siRNA negative control, grown in vitro in serum free condition.

source_name: patient derived Mesenchymal G33


title: 157_PN_NC


title: 88_MES_NC


title: 44_PN_amiR128

description: Gene expression of patient derived Proneural GSC44 after knoickdown of miR-128, grown in vitro in serum free condition.


title: 146_PN_amiR128

description: Gene expression of patient derived Proneural GSC146 after knoickdown of miR-128, grown in vitro in serum free condition.

source_name: patient derived Proneural GSC146


title: FFPE embedded lymph node at baseline [CE_SNSA_madbID120023_re-analysis]

description: gene expression data from DLBCL patient tumor

hyb_protocol: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing: data were analyzed using ArrayStudio by OmicSoft

source_name: FFPE embedded lymph node at baseline

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

tag: subject status

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: CE

tag: response

value: PD

tag: class

value: NR

tag: subtype

value: ABC


title: 146_PN_NC

description: Gene expression of patient derived Proneural GSC146 grown in vitro in serum free condition.

value: control


title: 44_PN_NC

description: Gene expression of patient derived Proneural GSC44 grown in vitro in serum free condition.


title: FFPE embedded lymph node at baseline [CG_SNSA_madbID120527_re-analysis]

value: CG


title: FFPE embedded lymph node at baseline [CF_SNSA_madbID120024_re-analysis]

value: CF


title: FFPE embedded lymph node at baseline [CC_SNSA_madbID120526_re-analysis]

value: CC


title: FFPE embedded lymph node at baseline [CA_SNSA_madbID120525_re-analysis]

value: CA


title: FFPE embedded lymph node at baseline [BU_SNSA_madbID120019_re-analysis]

value: BU


title: FFPE embedded lymph node at baseline [BJ_SNSA_madbID120519_re-analysis]

value: BJ


title: FFPE embedded lymph node at baseline [BL_SNSA_madbID120520_re-analysis]

value: BL


title: FFPE embedded lymph node at baseline [BT_SNSA_madbID120018_re-analysis]

value: BT


title: FFPE embedded lymph node at baseline [BD_SNSA_madbID120007_re-analysis]

value: BD


title: FFPE embedded lymph node at baseline [AT_SNSA_madbID120513_re-analysis]

value: AT


title: FFPE embedded lymph node at baseline [AP_SNSA_madbID120002_re-analysis]

value: AP


title: FFPE embedded lymph node at baseline [AZ_SNSA_madbID120516_re-analysis]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AZ


title: Bone Marrow-diagnosis 12

city: Beijing

first: Shi

last: Long

state: Peking

address: Road One

country: China

institute: NDUT

description: Human

hyb_protocol: Infinium HD methylation assay kit

scan_protocol: Illumina hybridization oven

data_processing:
Genome Studio version 2010.3 methylation module (Illumina)
Quality control inclusion valuation depended on hybridization detection P < 0.05.

label: Cy5 and Cy3

source_name: Bone Marrow-diagnosis

label_protocol: EZ DNA methylation gold kit

growth_protocol: Freezer

extract_protocol: Wizard genomic DNA purification kit

tag: diagnosis

value: Healthy donor

tag: aml subtype


title: FFPE embedded lymph node at baseline [AE_SNSA_madbID119991_re-analysis]

value: AE

value: PD

value: NR


title: fbn5_Leaf_rep4

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: fbn5-1 plant_3weeks_0.5x MS media 1% sucrose supplemented

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 20 hr at 48C on Affymetrix® Arabidopsis Gene 1.1 ST Array Strip,. GeneChips were washed and stained in the GeneAtlas® System Fluidics station.

scan_protocol: GeneArrays were scanned using the GeneAtlas® System Imaging station

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabdiopsis grown for 3 weeks at 25 C, 16/8 hours light/dark condition, 60% humidity, grown on the 0.5x MS media supplemented with 1% sucrose

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

treatment_protocol: No treatment

tag: ecotype

value: T-DNA insertion mutant


title: FFPE embedded lymph node at baseline [BZ_SNSA_madbID120524_re-analysis]

value: BZ

value: SD

value: ABC


title: fbn5_Leaf_rep3


title: Bone Marrow-diagnosis 11

description: Human


title: fbn5_Leaf_rep2


title: Bone Marrow-diagnosis 1

description: Human

value: t(8;21)-positive AML


title: G33_MES_siRNA_PRCs

description: Gene expression of patient derived Mesenchymal G33 transfected with siRNA against BMI1 and SUZ12, grown in vitro in serum free condition.

tag: tissue

value: Glioblastoma (GBM)

value: GBM Stem Cells (GSCs)

value: Mesenchymal


title: FFPE embedded lymph node at baseline [AN_SNSA_madbID120001_re-analysis]

value: AN


title: FFPE embedded lymph node at baseline [BY_SNSA_madbID120805_re-analysis]

value: BY


title: FFPE embedded lymph node at baseline [CH_SNSA_madbID120528_re-analysis]

value: CH

value: PR

value: RR


title: Bone Marrow-diagnosis 6

description: Human

value: t(8;21)-negative AML

value: NRAS mutation


title: WT_Leaf_rep4

description: WT plant_ 3 weeks_0.5x MS media 1% sucrose supplemented

value: Control plant


title: Bone Marrow-diagnosis 5

description: Human


title: Bone Marrow-diagnosis 7

description: Human

value: MLL/MLL


title: WT_Leaf_rep3


title: FFPE embedded lymph node at baseline [CD_SNSA_madbID120022_re-analysis]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: CD


title: WT_Leaf_rep2


title: fbn5_Leaf_rep1

value: T-DNA insertion mutant


title: Homo_HCC_R24

city: Guangzhou

first: Yunfei

last: Yuan

state: Guangdong

address: Dongfeng Road East No.651

institute: Sun Yat-sen University Cancer Center

description: SAMPLE 61

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

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

data_processing:
Data was processed using GenomeStudio V2011.1, normalized using the Beta Mixture Quantile dilation (BMIQ) method, and imputated with the K-nearest neighbor method.
Unmethylated and methylated signal intensities in series supplementary file

label: Cy3 and Cy5

source_name: genomic DNA from frozen hepatocellular carcinoma sample R24

label_protocol: Standard Illumina Protocol for Infinium 450k Chip

extract_protocol: genomic DNA was extracted and purified from hepatocellular carcinoma samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: Bone Marrow-diagnosis 8

description: Human

value: TLS/ERG


title: Homo_HCC_R28

description: SAMPLE 65

source_name: genomic DNA from frozen hepatocellular carcinoma sample R28


title: Bone Marrow-diagnosis 2

description: Human

value: t(8;21)-positive AML


title: Homo_HCC_R27

description: SAMPLE 64

source_name: genomic DNA from frozen hepatocellular carcinoma sample R27


title: Homo_HCC_R25

description: SAMPLE 62

source_name: genomic DNA from frozen hepatocellular carcinoma sample R25


title: WT_Leaf_rep1


title: FFPE embedded lymph node at baseline [AI_SNSA_madbID120802_re-analysis]

value: AI

value: ABC


title: Homo_HCC_R26

description: SAMPLE 63

source_name: genomic DNA from frozen hepatocellular carcinoma sample R26


title: Homo_HCC_R23

description: SAMPLE 60

source_name: genomic DNA from frozen hepatocellular carcinoma sample R23


title: 2212

city: Genova

first: Sara

last: Stigliani

address: largo R Benzi 10

country: Italy

institute: IRCCS AOU San Martino-IST

description: miRNA profiling

hyb_protocol: After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on Human microRNA Microarray G4471A-029297 (Agilent Technologies) containing probes for 866 human microRNAs.

scan_protocol: After washing, slides were scanned by Agilent G2565CA scanner and images were processed by Feature Extraction software using Agilent HD_miRNA protocol miRNA_1100_Jul11 (Agilent Technologies).

data_processing: Tab-delimited text file were acquired and analyzed in R v3.1.3 software  environment (www.r-project.org) using the limma package v (Smith 2005) of Bioconductor   (www.bioconductor.org). Background was subtracted   from signal for each detected spot (we used the value gBGSubSignal). Control type spots were removed. Undetected spots (i.e., those spots having a signal minus the background stricly smaller than zero) were removed. Probes with less than 5 of detected spots across all arrays in one of the two groups (ALK+ and  ALK-) were removed from the analysis. Background corrected intensities of the remining spots after filtering (n=7200) were then log2-transformed and normalized for between-array comparison using quantile normalization (Bolstad et al.2003).

source_name: neuroblastoma samples

label_protocol: miRNA were labelled according Microarray System protocol v.2.4 (Agilent Technologies). Briefly Labeling Spike-In were added to 100 ng of total RNA, then dephosphorylated and labelled using miRNA Complete Labeling and Hyb Kit; after labeling samples were purified using Micro Bio-Spin 6 (Bio-Rad, Hercules, CA, USA).

extract_protocol: total RNA containing miRNA were extracted using miRNeasy kit (Qiagen), then quantification and quality control were performed on Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using Agilent RNA 6000 Nano Kit  and Agilent Small RNA kit.

tag: Stage

tag: age at diagnosis (months)

tag: alk expression

value: high


title: Homo_HCC_R29

description: SAMPLE 66

source_name: genomic DNA from frozen hepatocellular carcinoma sample R29


title: FFPE embedded lymph node at baseline [BR_SNSA_madbID120016_re-analysis]

value: BR


title: FFPE embedded lymph node at baseline [AG_SNSA_madbID119993_re-analysis]

value: AG

value: PR


title: FFPE embedded lymph node at baseline [AF_SNSA_madbID119992_re-analysis]

value: AF

value: RR


title: 2368

description: miRNA profiling


title: Bone Marrow-diagnosis 10

description: Human

value: t(8;21)-negative AML

value: NRAS mutation


title: 2271

description: miRNA profiling


title: Bone Marrow-diagnosis 3

description: Human


title: Bone Marrow-diagnosis 4

description: Human


title: 2200

description: miRNA profiling


title: FFPE embedded lymph node at baseline [BO_SNSA_madbID120015_re-analysis]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: BO

value: CR


title: Homo_HCC_R21

description: SAMPLE 58

source_name: genomic DNA from frozen hepatocellular carcinoma sample R21

value: recurrent early stage HCC


title: Bone Marrow-diagnosis 9

description: Human


title: 2854

description: miRNA profiling


title: 2240

description: miRNA profiling


title: Homo_HCC_R20

description: SAMPLE 57

source_name: genomic DNA from frozen hepatocellular carcinoma sample R20

value: early-stage hepatocellular carcinoma


title: Homo_HCC_R17

description: SAMPLE 54

source_name: genomic DNA from frozen hepatocellular carcinoma sample R17


title: FFPE embedded lymph node at baseline [BG_SNSA_madbID120010_re-analysis]

value: BG


title: FFPE embedded lymph node at baseline [BQ_SNSA_madbID120522_re-analysis]

value: BQ


title: Homo_HCC_R22

description: SAMPLE 59

source_name: genomic DNA from frozen hepatocellular carcinoma sample R22


title: Homo_HCC_R19

description: SAMPLE 56

source_name: genomic DNA from frozen hepatocellular carcinoma sample R19


title: FFPE embedded lymph node at baseline [BK_SNSA_madbID120012_re-analysis]

value: BK


title: Homo_HCC_R18

description: SAMPLE 55

source_name: genomic DNA from frozen hepatocellular carcinoma sample R18


title: Homo_HCC_R16

description: SAMPLE 53

source_name: genomic DNA from frozen hepatocellular carcinoma sample R16


title: 2243

description: miRNA profiling

value: low


title: 2674

description: miRNA profiling


title: 2653

description: miRNA profiling

value: high


title: 2230

description: miRNA profiling


title: FFPE embedded lymph node at baseline [CG_SNSA_madbID120527]

source_name: FFPE embedded lymph node at baseline

value: CG

value: PD

value: NR

value: ABC


title: FFPE embedded lymph node at baseline [AU_SNSA_madbID120514_re-analysis]

value: AU

value: RR


title: FFPE embedded lymph node at baseline [CH_SNSA_madbID120528]

value: CH

value: PR


title: 2503

description: miRNA profiling


title: 2221

description: miRNA profiling


title: Homo_HCC_R14

description: SAMPLE 51

source_name: genomic DNA from frozen hepatocellular carcinoma sample R14


title: Homo_HCC_R15

description: SAMPLE 52

source_name: genomic DNA from frozen hepatocellular carcinoma sample R15


title: FFPE embedded lymph node at baseline [CF_SNSA_madbID120024]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: CF


title: Homo_HCC_R11

description: SAMPLE 48

source_name: genomic DNA from frozen hepatocellular carcinoma sample R11

value: recurrent early stage HCC


title: Homo_HCC_R12

description: SAMPLE 49

source_name: genomic DNA from frozen hepatocellular carcinoma sample R12

value: early-stage hepatocellular carcinoma


title: Homo_HCC_R10

description: SAMPLE 47

source_name: genomic DNA from frozen hepatocellular carcinoma sample R10


title: Homo_HCC_R8

description: SAMPLE 45

source_name: genomic DNA from frozen hepatocellular carcinoma sample R8


title: 2968

description: miRNA profiling


title: FFPE embedded lymph node at baseline [CD_SNSA_madbID120022]

value: CD


title: Homo_HCC_R9

description: SAMPLE 46

source_name: genomic DNA from frozen hepatocellular carcinoma sample R9


title: 2616

description: miRNA profiling

source_name: neuroblastoma samples


title: 2265

description: miRNA profiling


title: Homo_HCC_R7

description: SAMPLE 44

source_name: genomic DNA from frozen hepatocellular carcinoma sample R7


title: 2624

description: miRNA profiling


title: 2841

description: miRNA profiling


title: 2916

description: miRNA profiling


title: 2716

description: miRNA profiling


title: FFPE embedded lymph node at baseline [CE_SNSA_madbID120023]

value: CE


title: FFPE embedded lymph node at baseline [CB_SNSA_madbID120806]

value: CB

value: GCB


title: FFPE embedded lymph node at baseline [BY_SNSA_madbID120805]

value: BY

value: SD


title: FFPE embedded lymph node at baseline [CC_SNSA_madbID120526]

value: CC

value: PD


title: 2996

description: miRNA profiling

value: low


title: Homo_HCC_R13

description: SAMPLE 50

source_name: genomic DNA from frozen hepatocellular carcinoma sample R13


title: Homo_HCC_R6

description: SAMPLE 43

source_name: genomic DNA from frozen hepatocellular carcinoma sample R6


title: FFPE embedded lymph node at baseline [CA_SNSA_madbID120525]

value: CA

value: NR

value: ABC


title: FFPE embedded lymph node at baseline [BX_SNSA_madbID120523]

value: BX


title: FFPE embedded lymph node at baseline [BZ_SNSA_madbID120524]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: BZ


title: FFPE embedded lymph node at baseline [BW_SNSA_madbID120021]

value: BW


title: LAN1

description: miRNA profiling

scan_protocol: After washing, slides were scanned by Agilent G2565CA scanner and images were processed by Feature Extraction software using Agilent HD_miRNA protocol miRNA_107_Sep09 (Agilent Technologies).

data_processing: Tab-delimited text file were acquired and analyzed in R v3.1.3 software  environment (www.r-project.org) using the limma package v (Smith 2005) of Bioconductor   (www.bioconductor.org). Background was subtracted   from signal for each detected spot (we used the value gBGSubSignal). Control type spots were removed. Undetected spots (i.e., those spots having a signal minus the background stricly smaller than zero) were removed. Probes with less than 5 of detected spots across all arrays in one of the two groups (ALK+ and  ALK-) were removed from the analysis. Background corrected intensities of the remining spots after filtering (n=2491) were then log2-transformed and normalized for between-array comparison using quantile normalization (Bolstad et al.2003).

source_name: NB cell line

growth_protocol: Neuroblastoma cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS),1% penicillin/streptomycin, 1% glutamine at 37°C, 5% CO2.

treatment_protocol: no treatment

tag: cell line

value: neuroblastoma cell line  LAN1

value: ALK+

tag: mycn status

value: amplified


title: FFPE embedded lymph node at baseline [BV_SNSA_madbID120020]

value: BV

value: UNC


title: GIMEN

description: miRNA profiling

value: neuroblastoma cell line  GIMEN

value: ALK -

value: single copy


title: LA1-5s

description: miRNA profiling

value: neuroblastoma cell line  LA1-5s


title: GILIN

description: miRNA profiling

value: neuroblastoma cell line  GILIN


title: FFPE embedded lymph node at baseline [BU_SNSA_madbID120019]

value: BU

value: PD


title: GICAN

description: miRNA profiling

value: neuroblastoma cell line  GICAN


title: FFPE embedded lymph node at baseline [BR_SNSA_madbID120016]

value: BR

value: PR

value: RR

value: ABC


title: FFPE embedded lymph node at baseline [BS_SNSA_madbID120017]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: BS

value: NR


title: FFPE embedded lymph node at baseline [BT_SNSA_madbID120018]

value: BT


title: FFPE embedded lymph node at baseline [BP_SNSA_madbID120521]

value: BP

value: UNC


title: FFPE embedded lymph node at baseline [BQ_SNSA_madbID120522]

value: BQ

value: CR


title: FFPE embedded lymph node at baseline [BO_SNSA_madbID120015]

value: BO


title: Homo_HCC_R5

description: SAMPLE 42

source_name: genomic DNA from frozen hepatocellular carcinoma sample R5

value: recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: IMR5

description: miRNA profiling

value: neuroblastoma cell line  IMR5

value: ALK+

value: amplified


title: Homo_HCC_R4

description: SAMPLE 41

source_name: genomic DNA from frozen hepatocellular carcinoma sample R4


title: SKNBE2C

description: miRNA profiling

value: neuroblastoma cell line  SKNBE2C

value: ALK -


title: Homo_HCC_NR35

description: SAMPLE 35

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR35

value: non-recurrent early stage HCC


title: IMR32

description: miRNA profiling

value: neuroblastoma cell line  IMR32


title: Homo_HCC_NR37

description: SAMPLE 37

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR37


title: Homo_HCC_NR36

description: SAMPLE 36

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR36


title: Homo_HCC_NR34

description: SAMPLE 34

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR34


title: FFPE embedded lymph node at baseline [BN_SNSA_madbID120014]

source_name: FFPE embedded lymph node at baseline

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: BN

value: PD

value: GCB


title: ACN

description: miRNA profiling

value: neuroblastoma cell line  ACN

value: single copy


title: SKNSH

description: miRNA profiling

value: neuroblastoma cell line  SKNSH


title: FFPE embedded lymph node at baseline [BM_SNSA_madbID120013]

value: BM

value: NR

value: UNC


title: Homo_HCC_R1

description: SAMPLE 38

source_name: genomic DNA from frozen hepatocellular carcinoma sample R1

value: recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: FFPE embedded lymph node at baseline [BL_SNSA_madbID120520]

value: BL

value: ABC


title: KELLY

description: miRNA profiling

value: neuroblastoma cell line  KELLY

value: ALK+

value: amplified


title: Homo_HCC_R2

description: SAMPLE 39

source_name: genomic DNA from frozen hepatocellular carcinoma sample R2


title: FFPE embedded lymph node at baseline [BJ_SNSA_madbID120519]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: BJ


title: Homo_HCC_NR31

description: SAMPLE 31

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR31

value: non-recurrent early stage HCC


title: Homo_HCC_NR29

description: SAMPLE 29

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR29


title: UKF-NB3

description: miRNA profiling

value: neuroblastoma cell line  UKF-NB3


title: FFPE embedded lymph node at baseline [BH_SNSA_madbID120011]

value: BH

value: PD


title: Homo_HCC_NR26

description: SAMPLE 26

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR26


title: Homo_HCC_NR30

description: SAMPLE 30

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR30


title: Homo_HCC_NR28

description: SAMPLE 28

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR28


title: LAN5

description: miRNA profiling

value: neuroblastoma cell line  LAN5


title: Homo_HCC_R3

description: SAMPLE 40

source_name: genomic DNA from frozen hepatocellular carcinoma sample R3


title: SKNAS

description: miRNA profiling

value: neuroblastoma cell line  SKNAS

value: ALK -

value: single copy


title: Homo_HCC_NR27

description: SAMPLE 27

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR27


title: Homo_HCC_NR32

description: SAMPLE 32

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR32


title: FFPE embedded lymph node at baseline [BG_SNSA_madbID120010]

value: BG

value: CR

value: RR


title: Homo_HCC_NR33

description: SAMPLE 33

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR33

value: early-stage hepatocellular carcinoma


title: FFPE embedded lymph node at baseline [BF_SNSA_madbID120009]

value: BF

value: NR

value: GCB


title: Homo_HCC_NR25

description: SAMPLE 25

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR25


title: SHSY-5Y

description: miRNA profiling

source_name: NB cell line

value: neuroblastoma cell line  SHSY-5Y

value: ALK+


title: FFPE embedded lymph node at baseline [BA_SNSA_madbID120517]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: BA


title: FFPE embedded lymph node at baseline [BD_SNSA_madbID120007]

value: BD

value: ABC


title: FFPE embedded lymph node at baseline [BE_SNSA_madbID120008]

value: BE

value: PD

value: UNC


title: Homo_HCC_NR21

description: SAMPLE 21

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR21

value: non-recurrent early stage HCC


title: Homo_HCC_NR22

description: SAMPLE 22

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR22


title: FFPE embedded lymph node at baseline [BB_SNSA_madbID120006]

value: BB


title: FFPE embedded lymph node at baseline [BK_SNSA_madbID120012]

value: BK

value: CR


title: FFPE embedded lymph node at baseline [BI_SNSA_madbID120518]

value: BI


title: FFPE embedded lymph node at baseline [BC_SNSA_madbID120804]

value: BC


title: Homo_HCC_NR20

description: SAMPLE 20

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR20

value: early-stage hepatocellular carcinoma


title: TumorTissue507

city: Vilnius

first: Kristina

last: Daniunaite

address: Sauletekio Ave. 7

department: Institute of Biosciences

country: Lithuania

institute: Vilnius University

description:
T507
DNA methylation in primary prostate tumor from patient 507

hyb_protocol: Labeled samples were hybridized onto two-color Human DNA Methylation 1×244 K Microarrays, design ID 023795 (Agilent Technologies), for 40 hours at 67°C in a rotating hybridization oven, following manufacturer's protocol (Agilent technologies).

scan_protocol: Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).

data_processing: Scanned images were analyzed with Feature Extraction software v10.7.3.1 (Agilent Technologies) using default parameters (protocol ChIP_107_Sep09, 023795_D_F_20111018). Background subtracted and spatially detrended signals were obtained.

source_name: Prostate tumor tissue_5mC immunoprecipitated

label_protocol: Sample labeling was performed following the Agilent Microarray Analysis of Methylated DNA Immunoprecipitation v2.1 protocol (Agilent Technologies). Five μg of purified genomic DNA were sonicated with Bioruptor (Diagenode) to fragments of 150-900 bp in size. One fifth of sheared DNA was immunoprecipitated using 50 μL of Dynabeads Pan Mouse IgG (Thermo Fisher Scientific) and 5 μg of 5mC monoclonal antibody (Diagenode). DNA was then purified with phenol/chloroform using MaXtract High Density gel-filled tubes (Qiagen) and labeled using SureTag DNA Labeling Kit (Agilent Technologies). Cy5- and Cy3-labeled immunoprecipitated and reference samples were combined in a single mixture.

growth_protocol: not applicable

extract_protocol: Genomic DNA was isolated from 10-30 mg of tissue, snap-frozen in liquid nitrogen and mechanically homogenized into power using cryoPREP™ CP02 Impactor with tissueTUBE TT1 (Covaris). Samples were treated with proteinase K (Thermo Fisher Scientific) for up to 18 hours and DNA was extracted following standard phenol-chloroform purification and ethanol precipitation. Extracted DNA was quantified using NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific) and quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tissue samples were obtained from radical prostatectomy material of prostate cancer patients. None of the patients had preoperatively received radiotherapy, chemotherapy, or hormone therapy. Tissues were sampled and tumor cellularity was evaluated by expert pathologist.

value: prostate cancer patient

tag: subject id

value: patient 507

tag: age at surgery (yrs)

tag: biochemical disease recurrence

value: yes

tag: pathological tumor stage

tag: gleason score

value: Prostate tumor tissue obtained from radical prostatectomy material; 70% of cancer cells

tag: immunopreciated with

value: anti-5-methylcytosine antibody [33D3] (Diagenode)

source_name: Prostate tumor tissue_untreated reference DNA

tag: age at surgery

tag: immunoprecipitated with


title: Homo_HCC_NR24

description: SAMPLE 24

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR24


title: FFPE embedded lymph node at baseline [AZ_SNSA_madbID120516]

source_name: FFPE embedded lymph node at baseline

tag: subject status

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AZ

tag: response

tag: class

value: NR

tag: subtype


title: Homo_HCC_NR18

description: SAMPLE 18

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR18

tag: disease state

tag: tissue


title: Homo_HCC_NR19

description: SAMPLE 19

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR19


title: NoncancerousTissue507

description:
N507
DNA methylation in noncancerous prostate tissue from patient 507

value: not applicable

value: Noncancerous tissue obtained from radical prostatectomy material; 0% of cancer cells

source_name: Noncancerous tissue_untreated reference DNA

value: Dynabeads Pan Mouse IgG (Thermo Fisher Scientific)


title: FFPE embedded lymph node at baseline [AY_SNSA_madbID120803]

value: AY

value: PD

value: GCB


title: FFPE embedded lymph node at baseline [AW_SNSA_madbID120004]

value: AW

value: PR

value: RR


title: TumorTissue606

description:
T606
DNA methylation in primary prostate tumor from patient 606

value: prostate cancer patient

value: patient 606

value: Prostate tumor tissue obtained from radical prostatectomy material; 95% of cancer cells


title: TumorTissue349

description:
T349
DNA methylation in primary prostate tumor from patient 349

value: patient 349

value: yes

value: Prostate tumor tissue obtained from radical prostatectomy material; 100% of cancer cells


title: Homo_HCC_NR17

description: SAMPLE 17

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR17

value: non-recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: NoncancerousTissue349

description:
N349
DNA methylation in noncancerous prostate tissue from patient 349

value: not applicable

value: anti-5-methylcytosine antibody [33D3] (Diagenode)


title: FFPE embedded lymph node at baseline [AV_SNSA_madbID120003]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AV

value: SD

value: NR

value: UNC


title: Homo_HCC_NR14

description: SAMPLE 14

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR14


title: Homo_HCC_NR16

description: SAMPLE 16

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR16


title: Homo_HCC_NR23

description: SAMPLE 23

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR23


title: Homo_HCC_NR13

description: SAMPLE 13

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR13


title: TumorTissue124

description:
T124
DNA methylation in primary prostate tumor from patient 124

value: patient 124

value: no

value: Prostate tumor tissue obtained from radical prostatectomy material; 50% of cancer cells

value: Dynabeads Pan Mouse IgG (Thermo Fisher Scientific)


title: FFPE embedded lymph node at baseline [AU_SNSA_madbID120514]

value: AU

value: CR

value: RR

value: ABC


title: NoncancerousTissue606

description:
N606
DNA methylation in noncancerous prostate tissue from patient 606

value: prostate cancer patient

value: patient 606

value: yes

value: Noncancerous tissue obtained from radical prostatectomy material; 0% of cancer cells


title: TumorTissue120

description:
T120
DNA methylation in primary prostate tumor from patient 120

value: patient 120

value: Prostate tumor tissue obtained from radical prostatectomy material; 98% of cancer cells

value: anti-5-methylcytosine antibody [33D3] (Diagenode)


title: Homo_HCC_NR11

description: SAMPLE 11

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR11

value: non-recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: NoncancerousTissue120

description:
N120
DNA methylation in noncancerous prostate tissue from patient 120

value: not applicable


title: NoncancerousTissue124

description:
N124
DNA methylation in noncancerous prostate tissue from patient 124

value: patient 124

value: no


title: Homo_HCC_NR15

description: SAMPLE 15

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR15


title: Homo_HCC_NR12

description: SAMPLE 12

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR12


title: FFPE embedded lymph node at baseline [AX_SNSA_madbID120005]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AX

value: PD

value: NR

value: UNC


title: FFPE embedded lymph node at baseline [AT_SNSA_madbID120513]

value: AT

value: ABC


title: FFPE embedded lymph node at baseline [AS_SNSA_madbID120512]

value: AS

value: PR

value: RR


title: NoncancerousTissue114

description:
N114
DNA methylation in noncancerous prostate tissue from patient 114

value: prostate cancer patient

value: patient 114

value: Noncancerous tissue obtained from radical prostatectomy material; 0% of cancer cells

value: Dynabeads Pan Mouse IgG (Thermo Fisher Scientific)


title: FFPE embedded lymph node at baseline [AP_SNSA_madbID120002]

description: gene expression data from DLBCL patient tumor

value: AP


title: Homo_HCC_NR9

description: SAMPLE 9

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR9

value: non-recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: FFPE embedded lymph node at baseline [AQ_SNSA_madbID120510]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AQ

value: SD

value: GCB


title: Homo_HCC_NR10

description: SAMPLE 10

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR10


title: FFPE embedded lymph node at baseline [AR_SNSA_madbID120511]

value: AR

value: PD

value: NR


title: TumorTissue116

description:
T116
DNA methylation in primary prostate tumor from patient 116

source_name: Prostate tumor tissue_5mC immunoprecipitated

value: patient 116

value: no

value: Prostate tumor tissue obtained from radical prostatectomy material; 98% of cancer cells

value: anti-5-methylcytosine antibody [33D3] (Diagenode)


title: Homo_HCC_NR7

description: SAMPLE 7

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR7


title: FFPE embedded lymph node at baseline [AN_SNSA_madbID120001]

value: AN

value: ABC


title: FFPE embedded lymph node at baseline [AM_SNSA_A_madbID119999]

value: AM

value: UNC


title: Homo_HCC_NR8

description: SAMPLE 8

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR8

value: non-recurrent early stage HCC


title: siSRC-1_E, biological rep 2

city: Pittsburgh

first: Rebecca

middle: Jean

last: Watters

state: PA

address: 204 Craft Avenue

institute: University of Pittsburgh

description: Gene expression data from U2OS-ER-alpha cell lines, 17-B-estradiol treatment, siRNA targeting NCOA1

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Human 1.0 ST Genome 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:
Affymetrix CEL files of the microarray experiments were processed using the “affy” package and differential expression was assessed using the “limma” package of the Bioconductor Suite (http://www.bioconductor.org/).
The threshold for detecting differential expression was set at p-value < 0.01 and q-value < 0.05.

source_name: U2OS-ER-alpha cell line

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

growth_protocol: U2OS-ER-alpha cell lines were grown and maintained in phenol red free IMEM with 5% charcoal stripped serum.

extract_protocol: RNA was isolated using Qiagen RNeasy kit

treatment_protocol: Cells were treated with siRNA that was either targeting SRC-1 or a non-targeting control.  Both of these groups were then treated with either ethanol vehicle control or 17-B-estradiol for 3 hours.

value: bone

tag: sirna

value: siRNA targeting NCOA1

tag: treatment


title: NoncancerousTissue116

description:
N116
DNA methylation in noncancerous prostate tissue from patient 116

value: prostate cancer patient

value: not applicable

value: Noncancerous tissue obtained from radical prostatectomy material; 0% of cancer cells

value: Dynabeads Pan Mouse IgG (Thermo Fisher Scientific)


title: Clinical grade-III

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: pooled samples

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60°C and hybridized on to a Agilent's Human Gene Expression  8x60k Array (AMADID: 039494). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .Gene based analysis was performed.

source_name: Corneal epithelium

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized 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 using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Corneal epithelium were collected after the surgical procedures of photorefractive keratectomy (PRK) and topography guided photorefractive keratectomy (T-PRK)

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit with Dnase Treatment.

treatment_protocol: Corneal epithelium were stored in -80’C deep freezer for downstream process

value: Corneal epithelium

value: keratoconus

tag: age


title: Homo_HCC_NR6

description: SAMPLE 6

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR6

value: early-stage hepatocellular carcinoma


title: Clinical grade-IV

description: pooled samples


title: FFPE embedded lymph node at baseline [AL_SNSA_A_madbID119997]

source_name: FFPE embedded lymph node at baseline

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AL

value: PD

value: NR


title: siSRC-1_E, biological rep 1

tag: cell line


title: NoncancerousTissue092

description:
N092
DNA methylation in noncancerous prostate tissue from patient 092

tag: subject id

value: patient 092

tag: age at surgery (yrs)

value: no

value: anti-5-methylcytosine antibody [33D3] (Diagenode)

source_name: Noncancerous tissue_untreated reference DNA


title: NoncancerousTissue103

description:
N103
DNA methylation in noncancerous prostate tissue from patient 103

value: patient 103

tag: biochemical disease recurrence

tag: pathological tumor stage


title: TumorTissue114

description:
T114
DNA methylation in primary prostate tumor from patient 114

value: patient 114

tag: gleason score

value: Prostate tumor tissue obtained from radical prostatectomy material; 50% of cancer cells

tag: immunopreciated with

source_name: Prostate tumor tissue_untreated reference DNA


title: FFPE embedded lymph node at baseline [AK_SNSA_madbID119996]

value: AK

value: GCB


title: TumorTissue092

description:
T092
DNA methylation in primary prostate tumor from patient 092

value: prostate cancer patient

value: Prostate tumor tissue obtained from radical prostatectomy material; 95% of cancer cells

tag: age at surgery

tag: immunoprecipitated with


title: FFPE embedded lymph node at baseline [AO_SNSA_madbID120064]

tag: subject status

value: AO

tag: response


title: FFPE embedded lymph node at baseline [AJ_SNSA_madbID119995]

value: AJ

tag: class

tag: subtype


title: Clinical grade-II

description: pooled samples

tag: tissue

value: Corneal epithelium

tag: disease state

value: keratoconus


title: Homo_HCC_NR4

description: SAMPLE 4

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR4

value: non-recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: Homo_HCC_NR3

description: SAMPLE 3

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR3


title: siSRC-1_V, biological rep 2

description: Gene expression data from U2OS-ER-alpha cell lines, EtOH treatment control, siRNA targeting NCOA1

value: bone

tag: sirna

value: siRNA targeting NCOA1

tag: treatment

value: Ethanol


title: Homo_HCC_NR5

description: SAMPLE 5

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR5


title: siSRC-1_V, biological rep 3

tag: cell line


title: Clinical grade-I

description: pooled samples

tag: age


title: TumorTissue103

description:
T103
DNA methylation in primary prostate tumor from patient 103

tag: subject id

tag: age at surgery (yrs)

value: no

value: anti-5-methylcytosine antibody [33D3] (Diagenode)

value: Dynabeads Pan Mouse IgG (Thermo Fisher Scientific)


title: siSRC-1_E, biological rep 3


title: FFPE embedded lymph node at baseline [AI_SNSA_madbID120802]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AI

value: PR

value: RR

value: ABC


title: Controls

description: pooled samples

value: control


title: FFPE embedded lymph node at baseline [AH_SNSA_madbID119994]

value: AH

value: SD

value: NR

value: GCB


title: Homo_HCC_NR2

description: SAMPLE 2

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR2

value: non-recurrent early stage HCC

value: early-stage hepatocellular carcinoma


title: siSRC-1_V, biological rep 1

value: bone

value: siRNA targeting NCOA1


title: Imature seeds Replicate 2

city: Hangzhou

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

institute: Zhejiang Academy of Agricultural Sciences

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

organism: Vigna unguiculata

source_name: Imature seeds

label_protocol: cDNA were labeled with the fluorescent dye Cy5- or Cy3-dCTP by using cRNA amplification and labeling kit (CapitalBio, Beijing, China)

growth_protocol: Plants were growing under field conditions

extract_protocol: Total RNA was extracted using the Plant RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: No special treatments

value: Imature seeds

tag: Stage

value: Seeds at 1 week after pollination


title: NT_E, biological rep 3

description: Gene expression data from U2OS-ER-alpha cell lines, 17-B-estradiol treatment, non targeting siRNA

value: non-targeting control siRNA


title: Imature seeds Replicate 3


title: Homo_HCC_NR1

description: SAMPLE 1

source_name: genomic DNA from frozen hepatocellular carcinoma sample NR1


title: Imature seeds Replicate 1


title: NT_E, biological rep 2


title: NT_E, biological rep 1


title: FFPE embedded lymph node at baseline [AG_SNSA_madbID119993]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AG


title: Pooled clinical grade

description: pooled samples

value: Corneal epithelium

value: keratoconus


title: FFPE embedded lymph node at baseline [AE_SNSA_madbID119991]

value: AE

value: PD

value: ABC


title: NT_V, biological rep 2

description: Gene expression data from U2OS-ER-alpha cell lines, EtOH treatment control, non targeting siRNA

value: Ethanol


title: FFPE embedded lymph node at baseline [AF_SNSA_madbID119992]

value: AF

value: PR

value: RR


title: NT_V, biological rep 3


title: Short-pod pool Replicate 3

source_name: immature pods pooled

value: developing pods

value: 3 to 5 days after pollination


title: mutant_grown_in_pyruvate_rep2

description: Gene expression in pyruvate grown culture

hyb_protocol: The labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed R palustris Gene Expression  8x15k Array (AMADID: 075878). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using Percentile shift normalization method .Gene based analysis was performed.

organism: Rhodopseudomonas palustris

source_name: bacterial pellet_mid log phase culture

growth_protocol: The growth analysis of mutant and wild type strain of TIE-1 was carried out in YP media with carbon source (succinate and pyruvate at 10mM concentration). Exponential growth phase cells normalised to 0.5 OD660nm were inoculated (2% inoculum) in triplicate into the appropriate medium. The growth was monitored over time by increase in absorbance at 660nm.

treatment_protocol: Wild type and mutant cells were harvested from the mid-log phase for microarray experiment. Cells (10ml each) were harvested by centrifugation (40C, 2000g for 10min) and washed twice with PBS buffer. The cell pellet was snap freeze immediately in liquid nitrogen and stored in -800C till further process. The experiment was carried out in triplicate, each with three biological replicates. Three biological replicates from individual experiment was pooled together to minimize biological variation.

tag: strain

tag: genotype/variation

value: mutant

tag: culture

value: pyruvate


title: FFPE embedded lymph node at baseline [AB_SNSA_madbID119987]

value: AB

value: SD

value: NR

value: GCB


title: Whole flowers  Replicate 2

source_name: Whole flowers

value: flower

value: Flower opening


title: FFPE embedded lymph node at baseline [AD_SNSA_madbID119989]

value: Diffuse large B-cell lymphoma (DLBCL) patient

value: AD


title: Whole flowers  Replicate 3


title: Whole flowers  Replicate 1


title: Short-pod pool Replicate 1


title: FFPE embedded lymph node at baseline [AA_SNSA_madbID119985]

value: AA

value: PD

value: UNC


title: FCRL4 positive cells 3

city: Montpellier

first: Jerome

last: Moreaux

address: 80 Av. Augustin Fliche

department: Biological Hematology

country: France

institute: CHRU Montpellier

description: RNA expression data from purified FCRL4 positive cells

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were normalized in R software using MAS5 algorithm (scaling factor 100)

source_name: FCRL4 positive cells 3

label_protocol: Standard Affymetrix procedures

growth_protocol: Cultures were performed in Iscove’s modified Dubelcco medium (IMDM, Invitrogen) and 10% FCS (Invitrogen). Purified MBCs were cultured for four days with IL-2 (20 U/ml), IL-10 (50 ng/ml) and IL-15 (10 ng/ml) in 6 well culture plates (1.5 x 105/ml in 5 ml/well). Ten µg/ml of phosphorothioate CpG ODN 2006 (ODN) (Sigma), histidine-tagged recombinant human sCD40L (50 ng/ml) and anti-poly-histidine mAb (5 µg/ml) (R&D Systems) were added at culture start.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Kit.

value: FCRL4 positive cells


title: mutant_grown_in_pyruvate_rep1


title: Wild type_grown_in_pyruvate_rep1

value: wild type


title: Short-pod pool Replicate 2

value: developing pods


title: FFPE embedded lymph node at baseline [AC_SNSA_madbID119988]

value: AC


title: mutant_grown_in_succinate_rep2

description: Gene expression in succinate grown culture

value: mutant

value: succinate


title: Wild type_grown_in_pyruvate_rep2

value: pyruvate


title: FCRL4 positive cells 1

source_name: FCRL4 positive cells 1


title: Long-pod pool Replicate 2

value: 3 to 5 days after pollination


title: FCRL4 positive cells 2

source_name: FCRL4 positive cells 2


title: Wild type_grown_in_succinate_rep2


title: Long-pod pool Replicate 1


title: mutant_grown_in_succinate_rep1


title: Long-pod pool Replicate 3


title: Wild type_grown_in_succinate_rep1


title: FCRL4 negative cells 1

description: RNA expression data from purified FCRL4 negative cells

source_name: FCRL4 negative cells 1

value: FCRL4 negative cells


title: FCRL4 negative cells 2

source_name: FCRL4 negative cells 2


title: FCRL4 negative cells 3

source_name: FCRL4 negative cells 3


title: axe1-5, 15days_drought-treated plants, biological rep3

status: Public on Apr 29 2017

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

description:
axe1-5_drought_15d-3
Gene expression data from 15d drought-treated axe1-5 plants

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer' s instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-015059 Arabidopsis Ver.3 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and 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 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring (Agilent). Percentile normalization (75 percentile) was performed for each chip.

source_name: Drought-treated Arabidopsis axe1-5 plants, 15 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in soil for 3 weeks under 16-h-light/8-h-dark.

extract_protocol: The total RNA was extracted from the above-ground plants before or after drought treatment using Plant RNA Purification Reagent (Invitrogen) according to manufacturer's instruction.

treatment_protocol: The plants were treated with or without 6, 9, 12, 15 days of drought treatment by withholding water supply.

tag: ecotype

value: Columbia

tag: line

tag: genotype

value: aerial parts

value: drought

tag: treatment duration

value: 15 days


title: axe1-5, 12days_drought-treated plants, biological rep3

description:
axe1-5_drought_12d-3
Gene expression data from 12d drought-treated axe1-5 plants

source_name: Drought-treated Arabidopsis axe1-5 plants, 12 days

value: 12 days


title: axe1-5, 12days_drought-treated plants, biological rep1

description:
axe1-5_drought_12d-1
Gene expression data from 12d drought-treated axe1-5 plants


title: axe1-5, 9days_drought-treated plants, biological rep2

description:
axe1-5_drought_9d-2
Gene expression data from 9d drought-treated axe1-5 plants

source_name: Drought-treated Arabidopsis axe1-5 plants, 9 days

value: 9 days