title: Molt cells control (exon), replicate 3

description: Molt-4 cells control

label_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)


title: Molt cells control (exon), replicate 2

status: Public on Dec 31 2014

type: RNA

city: Esch-sur-Alzette

first: Ines

last: Thiele

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

description: Molt-4 cells control

hyb_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)

data_processing:
We generated DABG calls using ROOT (version 22) and XPS package for R (version 11.1). Calls for data mapping were assigned based on p<0.05 as cutoff probability distinguishing presence versus absence of genes. All 18 data sets were summarized for this analysis, using RMA.    Analysis for differential gene expression and alternative splicing were performed using AltAnalyse software (v2.02beta) using default options from raw data (CEL) files and Homo sapiens Ensemble release 65 database, probe set filtering was kept as DABG p-value < 0.05 and non-log expression < 70 for constitutive probe sets to determine gene expression levels. AltAnalyse relies on RMA for normalization.  For the comparison, CCRF-CEM was the experimental and Molt-4 the baseline group, and only CEL files of CCRF-CEM cells control replicate 1-3, and Mot-4 cells control replicate 1-3 were introduced into the analysis. The set of differentially expressed genes among cell lines was identified based on a p<0.05 FDR cutoff. Alternative splicing analysis was performed on core probe sets with a minimum alternative exon score of 2 and a maximum absolute gene expression change of 3.
AltAnalyze & XPS: HuEx-1_0-st-v2.r2.pgf
Bioconductor XPS package was used to generate Detection above background (DABG) calls after RMA normalisation for the entire data set of 18 CEL files (MixRMAMetacore and MixDABGMetacore_pval). Additionally, higher-level analysis of Differential gene expression (DATASET-CompareCelllines(geneLevel)) and Alternative splicing (Hs_Exon_C_vs_M.p5_average-splicing-index-exon-inclusion-GENE-results) were carried out for a subset of 6 CEL files (A834_01-A834_03 and A834_10-A834_12) using Altanalyse software after pre-processing of the  Affymetrix CEL files by AltAnalyze (using APT and RMA). Expression values for the RMA normalization for the subset of 6 CEL files (exp.CompareCellines(probesetLevel)).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Molt-4 cells

extract_protocol: Molt-4 and CCRF-CEM growing in RPMI advanced, 2 mM glutamax were resuspended in medium containing DMSO (0.67%) or 0.5 mM AICAR or 0.1 mM A-769662 at a cell concentration of 5 x 105 cells/ml. 2 ml cell suspensions were seeded in 12 well plates in triplicates. After 48 hrs of growth the cells were collected by centrifugation at 201 x g for 5 min. Cell pellets were snap frozen in liquid N2 and kept frozen until RNA extraction and analysis by Aros (Aarhus, Denmark).

tag: cell line

value: Molt-4 cells

tag: treatment

value: control


title: sample469

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

source_name: RNA from blood

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..

treatment_protocol: stored at -20 degree

tag: disease

value: others


title: sample468

value: ductal adenocarcinoma


title: sample471


title: CCRF-CEM cells control (exon), replicate 3

description: CCRF-CEM cells control

scan_protocol: standard Affymetrix protocol by Aros (Aarhus, Denmark)

source_name: CCRF-CEM cells

value: CCRF-CEM cells


title: D2 E15 rep2

city: Vancouver

first: Thomas

last: Ha

state: British Columbia

address: 950 West 28th Avenue

department: CMMT

country: Canada

institute: University of British Columbia

description:
E15  1735640108_D
biological replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

organism: Mus musculus

source_name: DBA/2J mouse whole cerebellum

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

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

tag: strain

tag: age

tag: tissue

value: whole cerebellum


title: Mouse_51_cyclophosphamide_ZT20_T1

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: Quality Control: Approved

hyb_protocol: RNA was hybridized on Affymetrix HT Mouse Genome 430 PM Array plates (Affymetrix Inc., Santa Clara, CA, USA) at the Microarray Department of the University of Amsterdam, the Netherlands.

scan_protocol: The array images were acquired using a GeneChip HT Array Plate Scanner (Affymetrix)

data_processing: The array images analyzed with Affymetrix HT software suite including expression console software (Affymetrix).

label_protocol: biotins labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3” IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Three-week-old male C57BL/6 mice were purchased from Charles River Laboratories International, Inc., France. Animals were synchronized to a 12-hr light: 12-hr dark cycle for 5 weeks. Food and water were provided ad libitum.

extract_protocol: RNA was extracted from liver stored in RNAlater using the miRNeasy Mini Kit (Qiagen Benelux, Venlo, The Netherlands ).

treatment_protocol: At 8 weeks of age mice received a single i.p. injection of either 300 mg/kg bodyweight Cyclophosphamide (CP, CAS 6055-19-2, Sigma-Aldrich) or the vehicle (PBS) at two different Zeitgeber times, ZT8 and ZT20 (ZT0 = lights on). Animals (n=4 per time point) were sacrificed by cervical dislocation at 0.5, 1, 2 and 4 hours after CP injection (T0.5, T1, T2 and T4), and at 0 and 4 hours after vehicle injection (C0 and C4).

tag: Sex

value: Male

value: cyclophosphamide

tag: regime

tag: time


title: D2 E14 rep3

description:
E14  1855545041_A
biological replicate 3


title: D2 E15 rep1

description:
E15  1716756033_D
biological replicate 1


title: Mouse_53_cyclophosphamide_ZT20_T1

description: Quality Control: Approved


title: D2 E14 rep1

description:
E14  1714451045_A
biological replicate 1


title: D2 E14 rep2

description:
E14  1735640022_C
biological replicate 2


title: Mouse_52_cyclophosphamide_ZT20_T1

description: Quality Control: Approved


title: CCRF-CEM cells control (exon), replicate 1

description: CCRF-CEM cells control


title: D2 E12 rep3

description:
E12  4370199020_D
biological replicate 3


title: sample465

value: Wilms Tumor


title: D2 E13 rep3

description:
E13  1855545041_E
biological replicate 3


title: sample464


title: sample466


title: sample467

value: pancreatitis


title: D2 E12 rep1

description:
E12  1735640053_A
biological replicate 1


title: Mouse_47_cyclophosphamide_ZT20_T0.5

description: Quality Control: Approved


title: D2 E13 rep2

description:
E13  1863191016_A
biological replicate 2


title: B6 P9 rep3

description:
P9  4370199023_B.AVG_Signal
biological replicate 3

source_name: C57BL/6J mouse whole cerebellum


title: Mouse_50_cyclophosphamide_ZT20_T1

description: Quality Control: Approved


title: Mouse_46_cyclophosphamide_ZT20_T0.5

description: Quality Control: Approved


title: sample463


title: B6 P6 rep3

description:
P6  4370199020_B.AVG_Signal
biological replicate 3


title: D2 E12 rep2

description:
E12  1863191016_F
biological replicate 2


title: D2 E18 rep1

description:
E18  1716756025_B
biological replicate 1


title: Mouse_44_cyclophosphamide_ZT20_T0.5

description: Quality Control: Approved


title: B6 P9 rep1

description:
P9  1855545004_F.AVG_Signal
biological replicate 1


title: Mouse_45_cyclophosphamide_ZT20_T0.5

description: Quality Control: Approved


title: D2 E13 rep1

description:
E13  1714451043_C
biological replicate 1


title: B6 P9 rep2

description:
P9  1863191016_D.AVG_Signal
biological replicate 2


title: sample461


title: sample462


title: Mouse_41_controle_ZT20_T0

description: Quality Control: Approved

value: controle


title: B6 P6 rep2

description:
P6  1855545004_E.AVG_Signal
biological replicate 2


title: B6 P3 rep3

description:
P3  1855545041_B.AVG_Signal
biological replicate 3


title: B6 P3 rep1

description:
P3  1735640153_A.AVG_Signal
biological replicate 1


title: Mouse_40_controle_ZT20_T0

description: Quality Control: Approved


title: sample460


title: sample459


title: B6 P3 rep2

description:
P3  1735640153_C.AVG_Signal
biological replicate 2


title: B6 P0 rep2

description:
P0  1855545004_B.AVG_Signal
biological replicate 2


title: B6 P6 rep1

description:
P6  1855545004_D.AVG_Signal
biological replicate 1


title: B6 P0 rep3

description:
P0  1863191035_F.AVG_Signal
biological replicate 3


title: B6 P0 rep1

description:
P0  1855545004_A.AVG_Signal
biological replicate 1


title: Mouse_35_controle_ZT8_T4

description: Quality Control: Approved


title: B6 E19 rep3

description:
E19  1725572018_D.AVG_Signal
biological replicate 3


title: Mouse_38_controle_ZT20_T0

description: Quality Control: Approved


title: Mouse_39_controle_ZT20_T0

description: Quality Control: Approved


title: B6 E19 rep2

description:
E19  1725572018_C.AVG_Signal
biological replicate 2


title: B6 E19 rep1

description:
E19  1714451043_E.AVG_Signal
biological replicate 1


title: sample457


title: sample458


title: sample456


title: sample470


title: sample455


title: sample454


title: sample453


title: B6 E18 rep3

description:
E18  1716756033_C.AVG_Signal
biological replicate 3


title: Mouse_34_controle_ZT8_T4

description: Quality Control: Approved


title: B6 E16 rep3

description:
E16  1735640151_B.AVG_Signal
biological replicate 3


title: sample452


title: Mouse_33_controle_ZT8_T4

description: Quality Control: Approved


title: B6 E18 rep2

description:
E18  1716756025_E.AVG_Signal
biological replicate 2


title: B6 E15 rep3

description:
E15  1716756033_A.AVG_Signal
biological replicate 3


title: B6 E17 rep2

description:
E17  1716756033_B.AVG_Signal
biological replicate 2


title: B6 E18 rep1

description:
E18  1716756025_A.AVG_Signal
biological replicate 1


title: B6 E15 rep2

description:
E15  1716756025_D.AVG_Signal
biological replicate 2


title: B6 E17 rep1

description:
E17  1714451075_C.AVG_Signal
biological replicate 1


title: B6 E17 rep3

description:
E17  1735640022_D.AVG_Signal
biological replicate 3


title: B6 E16 rep2

description:
E16  1716756059_A.AVG_Signal
biological replicate 2


title: B6 E16 rep1

description:
E16  1714451075_B.AVG_Signal
biological replicate 1


title: Mouse_32_controle_ZT8_T4

description: Quality Control: Approved


title: Mouse_26_cyclophosphamide_ZT8_T4

description: Quality Control: Approved


title: sample451


title: B6 E14 rep1

description:
E14  1716756025_C.AVG_Signal
biological replicate 1


title: Mouse_28_cyclophosphamide_ZT8_T4

description: Quality Control: Approved


title: B6 E15 rep1

description:
E15  1714451045_D.AVG_Signal
biological replicate 1


title: B6 E14 rep2

description:
E14  1855545041_C.AVG_Signal
biological replicate 2


title: Mouse_27_cyclophosphamide_ZT8_T4

description: Quality Control: Approved


title: sample450

value: non-ischaemic systolic heart failure


title: sample447


title: B6 E13 rep3

description:
E13  1863191016_C.AVG_Signal
biological replicate 3


title: sample449


title: Mouse_23_cyclophosphamide_ZT8_T2

description: Quality Control: Approved


title: sample448

value: normal


title: B6 E13 rep1

description:
E13  1855545041_D.AVG_Signal
biological replicate 1


title: sample446


title: B6 E13 rep2

description:
E13  1863191035_B.AVG_Signal
biological replicate 2


title: sample445


title: Mouse_22_cyclophosphamide_ZT8_T2

description: Quality Control: Approved


title: Mouse_21_cyclophosphamide_ZT8_T2

description: Quality Control: Approved


title: Normal_3

city: hangzhou

first: zhenzhong

last: yang

address: Yuhangtang 866

country: China

institute: zhejiang univ.

description: C57BL/6J mice

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 640 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings. Global scaling normalization was performed with Median Scaling Normalization in ArrayTrack 3.5.0 using a target median value of 1000.

source_name: liver

label_protocol: Total RNA were amplified, labeled, and purified using GeneChip® 3’IVT Express Kit (Affymetrix) according to the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The mice were maintained in air-conditioned rooms (temperature, 22 ± 2°C) with a 12-h light-dark cycle.

extract_protocol: Total RNA was extracted using mirVanaTM RNA Isolation Kit and purified using RNeasy Mini kit (QIAGEN), following manufacturers’ protocols.

treatment_protocol: The tissue samples were stored at -80℃ refrigerator.

tag: gender

value: male

value: liver


title: B6 E12 rep3

description:
E12  4370199020_E.AVG_Signal
biological replicate 3


title: B6 E12 rep1

description:
E12  1735640053_C.AVG_Signal
biological replicate 1


title: Normal_4

description: C57BL/6J mice


title: Normal_1

description: C57BL/6J mice


title: Mouse_16_cyclophosphamide_ZT8_T1

description: Quality Control: Approved


title: sample444


title: Normal_5

description: C57BL/6J mice


title: Mouse_20_cyclophosphamide_ZT8_T2

description: Quality Control: Approved


title: Mouse_17_cyclophosphamide_ZT8_T1

description: Quality Control: Approved


title: Normal_2

description: C57BL/6J mice


title: sample443


title: B6 E12 rep2

description:
E12  1735640151_F.AVG_Signal
biological replicate 2


title: sample442


title: Mouse_14_cyclophosphamide_ZT8_T1

description: Quality Control: Approved


title: sample440


title: sample441


title: XKA_4

description: KKAy mice

value: KKAy


title: XKA_3

description: KKAy mice


title: Mouse_15_cyclophosphamide_ZT8_T1

description: Quality Control: Approved


title: Mouse_11_cyclophosphamide_ZT8_T0.5

description: Quality Control: Approved


title: XKA_1

description: KKAy mice


title: XKA_2

description: KKAy mice


title: Model_3

description: KKAy mice


title: XKA_5

description: KKAy mice


title: Model_2

description: KKAy mice


title: sample439


title: Model_4

description: KKAy mice


title: Model_1

description: KKAy mice


title: sample437


title: Model_5

description: KKAy mice


title: sample438


title: sample435


title: sample436


title: sample434

value: chronic obstructive pulmonary disease (COPD)


title: sample433


title: sample432


title: Mouse_9_cyclophosphamide_ZT8_T0.5

description: Quality Control: Approved


title: Mouse_4_controle_ZT8_T0

description: Quality Control: Approved


title: Mouse_10_cyclophosphamide_ZT8_T0.5

description: Quality Control: Approved


title: Mouse_5_controle_ZT8_T0

description: Quality Control: Approved


title: Mouse_2_controle_ZT8_T0

description: Quality Control: Approved


title: Mouse_3_controle_ZT8_T0

description: Quality Control: Approved


title: Raji cells treated with Dasa vs. control 8

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: dye swap

hyb_protocol: The hybridization was performed with AMADID Release GE 8x60K microarrays (Agilent, USA) using Gene Expression Hybridization Kit (Agilent, USA) according to the manufacturer`s protocol.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: Raji control cells

label_protocol: The Quick Amp Labeling Kit (Agilent, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA) for oligo microarrays used in gene expression profiling and other downstream analyses.

growth_protocol: Cells were cultured in optimal conditions: a medium (RPMI-1640) enriched with 10% heat-inactivated fetal bovine serum (FBS) supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin and 250 ng/mL amphotericin B (reagents obtained from Sigma Aldrich, USA), in an atmosphere of 5% CO2 and 95% humidified air at 37°C, and routinely subcultured every second day.

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol.

treatment_protocol: Cells treated with 100 nM dasatinib or 10 µM PP2 for 24 hrs and vehicle-treated cells as a control were used for this study.

value: Raji

source_name: Raji cells treated with Dasa

value: Dasa


title: Raji cells treated with Dasa vs. control 7

description: dye swap

value: control


title: Raji cells treated with PP2 vs. control 6

description: dye swap

source_name: Raji cells treated with PP2


title: sample428


title: sample430

value: others


title: sample427


title: Mouse_8_cyclophosphamide_ZT8_T0.5

description: Quality Control: Approved


title: sample429

value: ductal adenocarcinoma


title: sample431


title: sample426


title: Mouse_29_cyclophosphamide_ZT8_T4

description: Quality Control: Approved


title: sample424


title: Raji cells treated with PP2 vs. control 5

description: dye swap


title: normal CB-adult_4

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

description: Gene expression data from non-neoplastic adult mouse cerebellum.

hyb_protocol: According to manufacturer's instructions.

data_processing: Affymetrix CEL files were processed using Affymetrix Expression Console (v1.3.1) and normalized signal intensities were generated using the RMA algorithm.

source_name: Non-neoplastic mouse cerebellar tissue

extract_protocol: Total RNA was extracted from mouse cerebellar tumours and non-neoplastic mouse cerebellum using the Qiagen AllPrep DNA/RNA Mini Kit according to manufacturer's instructions.

value: cerebellum


title: sample425


title: sample422


title: Raji cells treated with PP2 vs. control 2

description: Biological replicate 2 of 4


title: normal CB-adult_2

scan_protocol: According to manufacturer's instructions.


title: Raji cells treated with Dasa vs. control 4

description: Biological replicate 2 of 4


title: Raji cells treated with Dasa vs. control 3

description: Biological replicate 1 of 4


title: normal CB-adult_1

label_protocol: According to manufacturer's instructions.


title: GNPs_3

description: Gene expression data from non-neoplastic mouse cerebellar granule neuron progenitor cells isolated between P4-P7.

source_name: Non-neoplastic mouse cerebellar cells


title: normal CB-adult_3


title: Raji cells treated with PP2 vs. control 1

description: Biological replicate 1 of 4


title: MERP_4

description: Gene expression data from mouse cerebellar tumour generated by postnatal disruption of Ptch1 in Math1-expressing cells.

source_name: Mouse cerebellar tumour

value: cerebellar tumour


title: MERP_5


title: GNPs_1


title: MERP_3


title: GNPs_2


title: sample423


title: sample419

value: prostate cancer


title: sample418


title: Ptc+/-_4

description: Gene expression data from mouse cerebellar tumour generated by germline disruption of Ptch1.


title: MERP_1


title: Ptc+/-_3


title: sample420


title: CPT_CLB-Ma

type: genomic

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: CLB-Ma

scan_protocol: GeneChip Scanner acc to Affymetrix user manual `Cytoscan assay´

data_processing:
GeneChip Console (Affymetrix)
CYCHP files are provided:
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.2.0
program-name = apt-copynumber-cyto
program-version = 1.14.3-rc5

label: Neuroblastoma cell line, MYCN amplified

molecule: genomic DNA

source_name: CLB-Ma neuroblastoma cell line, Camptothecin 5 nM, 3 weeks

growth_protocol: RPMI1640 GlutaMAX medium (Gibco, Life Technologies) supplemented with 1x Penicilin/Streptomycin, Na-Pyruvate, HEPES and 10% FCS (all PAA Laboratories GmbH, Austria) in a CO2 incubator at 37°C

extract_protocol: high salt method DNA extraction

treatment_protocol: Camptothecin 5 nM, 3 weeks

value: CLB-Ma

tag: cell type

value: Neuroblastoma


title: GTML_3

description: Gene expression data from sporadic mouse cerebellar tumour generated by overexpression of the Mycn oncogene.


title: CPT_STA-NB10

hyb_protocol: acc to Affymetrix user manual `Cytoscan assay´

source_name: STA-NB-10 primary neuroblastoma cell line, Camptothecin 3 nM, 3 weeks

treatment_protocol: Camptothecin 3 nM, 3 weeks


title: GTML_2


title: Crispr-Ptc-EP_1

description: Gene expression data from mouse cerebellar tumour generated using CRISPR/Cas9 technology to disrupt Ptch1 in the embryonic cerebellum by in utero electroporation.


title: CTRL_STA-NB10

source_name: STA-NB-10 primary neuroblastoma cell line, untreated

label_protocol: acc to Affymetrix user manual `Cytoscan assay´

treatment_protocol: CTRL


title: GTML_4


title: Ptc+/-_1


title: Crispr-Ptc-TF

description: Gene expression data from mouse cerebellar tumour generated using CRISPR/Cas9 technology to disrupt Ptch1 in the neonatal cerebellum by in vivo transfection.


title: Ptc+/-_2


title: MERP_2


title: sample417


title: sample421


title: Crispr-Ptc-EP_2


title: CTRL_CLB-Ma

description: CLB-Ma

source_name: CLB-Ma neuroblastoma cell line, untreated


title: GTML_1


title: sample416


title: iKras1-on-2

city: Houston

first: Avnish

last: Kapoor

state: Texas

address: 1901 East Rd

country: USA

institute: MD Anderson Cancer Center

description:
iKras-1-2
parental culture of iKras1

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was RMA processed using  Affy R package, The raw intensity values are background corrected, log2 transformed and then quantile normalized.

label: Biotin

source_name: parental culture of iKras1, on dox

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

growth_protocol: Cells were grown in Tet-Free FBS (Clontech) at 37C, 5% CO2

extract_protocol: Trizol extraction of total RNA followed by RNeasy column cleanup was performed according to the manufacturer's instructions.

treatment_protocol: Cells were grown in Tet-Free FBS (Clontech) in the presence or absence of doxycycline

tag: strain background

value: FVB/B6 mix

tag: genotype/variation

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

value: parental control cell line

value: On Dox


title: sample413


title: iKras2-on-2

description:
iKras-2-2
parental culture of iKras2

source_name: parental culture of iKras2, on dox


title: sample412

source_name: RNA from blood


title: sample414


title: iKras1-on-1

description:
iKras-1-1
parental culture of iKras1


title: sample410


title: sample411


title: Relapse tumor E-15-off-Rep1

description:
E-15-1
Culture of relapse tumor E-15

source_name: Culture of relapse tumor E-15 off dox

value: primary relapsed pancreatic tumor cell line

value: Off Dox


title: Relapse tumor E-16-off-Rep2

description:
E-16-2
Culture of relapse tumor E-16

source_name: Culture of relapse tumor E-16 off dox


title: Relapse tumor E-13-off-Rep1

description:
E-13-1
Culture of relapse tumor E-13

source_name: Culture of relapse tumor E-13 off dox


title: iKras2-on-1

description:
iKras-2-1
parental culture of iKras2


title: Relapse tumor E-13-off-Rep2

description:
E-13-2
Culture of relapse tumor E-13


title: Relapse tumor E-15-off-Rep2

description:
E-15-2
Culture of relapse tumor E-15


title: Relapse tumor E-16-off-Rep1

description:
E-16-1
Culture of relapse tumor E-16


title: Relapse tumor E-14-off-Rep2

description:
E-14-2
Culture of relapse tumor E-14

source_name: Culture of relapse tumor E-14 off dox


title: sample409


title: sample407

value: Wilms Tumor


title: sample408

value: benign prostate hyperplasia


title: Relapse tumor E-11-off-Rep1

description:
E-11-1
Culture of relapse tumor E-11

source_name: Culture of relapse tumor E-11 off dox


title: Relapse tumor E-12-off-Rep1

description:
E-12-1
Culture of relapse tumor E-12

source_name: Culture of relapse tumor E-12 off dox


title: sample406


title: sample405


title: sample404

value: normal


title: Relapse tumor E-12-off-Rep2

description:
E-12-2
Culture of relapse tumor E-12


title: CSCC-13

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

description: CSCC

hyb_protocol: Each dye-labeled DNA was purified and mixed with hybridization reagents, applied on the array and incubated for 24 hours at 65ºC in a hybridization oven (Agilent). After hybridization, slides were washed sequentially.

scan_protocol: The arrays were scanned using Agilent microarray scanner.

data_processing: Raw data were generated from scanned images of Agilent array data using Agilent Feature Extraction Software 10.7.3.1.

label_protocol: 1 µg of genomic DNA were labeled with fluorescent dye at 37°C for 2 hours. BioPrime aCGH labeling system (Invitrogen) was used for labeling step.

extract_protocol: genomic DNA extracted using DNeasy Blood & Tissue Kit (Qiagen) following manufacturer's instructions.

value: Cervix

value: Female

tag: tag


title: CSCC-12

description: CSCC


title: CSCC-6

description: CSCC


title: sample415

value: lung cancer


title: Relapse tumor E-11-off-Rep2

description:
E-11-2
Culture of relapse tumor E-11


title: Relapse tumor E-10-off-Rep2

description:
E-10-2
Culture of relapse tumor E-10

source_name: Culture of relapse tumor E-10 off dox


title: CSCC-18

description: CSCC


title: Relapse tumor E-10-off-Rep1

description:
E-10-1
Culture of relapse tumor E-10


title: K9-162 P5

city: Paris

first: Anne

last: Janin

address: 1 Av C Vellefaux

country: France

institute: University Paris 7, INSERM, APHP

description: K9-162 P5

hyb_protocol: The digested DNAs were labeled with random primers using Agilent Genomic DNA Labeling Kit Plus for 2 hours at 37°C, according to the manufacturer’s instructions

scan_protocol: Agilent DNA Microarray Scanner G2565BA

data_processing: Log ratios were determined with Agilent Feature Extraction software (v 9.1.3.1)

source_name: Kidney tumor

extract_protocol: Genomic DNA was isolated from human renal cancer and from spheres using DNeasy MiniKit (Qiagen, France) according to the manufacturer’s protocol

tag: Stage

value: Xenografted tumor at P5

source_name: Universal Reference HAPMAP (Promega, USA, Madison)

tag: reference

value: Human Universal Reference


title: Relapse tumor E-9-off-Rep2

description:
E-9-2
Culture of relapse tumor E-9

source_name: Culture of relapse tumor E-9 off dox


title: Relapse tumor E-14-off-Rep1

description:
E-14-1
Culture of relapse tumor E-14


title: sample403

value: ovarian cancer


title: K9-162 P0

description: K9-162 P0

label_protocol: The digested DNAs were labeled with random primers using Agilent Genomic DNA Labeling Kit Plus for 2 hours at 37°C, according to the manufacturer’s instructions

value: Initial tumor at P0


title: CIN-9

description: CIS


title: MIC-1

description: MIC


title: sample402


title: sample401


title: Relapse tumor E-9-off-Rep1

description:
E-9-1
Culture of relapse tumor E-9


title: PT7

first: Peter. F.

last: Ambros

department: Tumor Biology

institute: Children's Cancer Research Institute

scan_protocol: by GeneChip Scanner according to the Affymetrix user manual `Cytoscan HD assay´

data_processing:
CYCHP files are provided:
ChAS software (Affymetrix)
affymetrix-algorithm-name = CYTO2
affymetrix-algorithm-version = 1.15.1
program-name = apt-copynumber-cyto.exe
program-version = 1.15.1

tag: individual

value: Patient 7

tag: disease state

value: Neuroblastoma

value: Tumor

value: male

tag: patient age

value: ˃ 18 months

value: M

tag: time of sampling

value: diagnosis


title: Relapse tumor E-8-off-Rep2

description:
E-8-2
Culture of relapse tumor E-8

source_name: Culture of relapse tumor E-8 off dox

value: FVB/B6 mix

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

tag: cell line

value: primary relapsed pancreatic tumor cell line

tag: treatment

value: Off Dox


title: PT9

hyb_protocol: according to the Affymetrix user manual `Cytoscan HD assay´

value: Patient 9

value: DTCs from BM

value: female

value: relapse


title: CIN-6

description: CINIII

tag: tissue

value: Cervix

value: Female


title: K8-614 P0

description: K8-614 P0

value: Initial tumor at P0

value: Human Universal Reference


title: sample400

tag: disease

value: normal


title: CIN-5

description: CIS


title: Relapse tumor E-8-off-Rep1

description:
E-8-1
Culture of relapse tumor E-8


title: sample399


title: PT6

label_protocol: according to the Affymetrix user manual `Cytoscan HD assay´

value: Patient 6

value: Neuroblastoma

value: male


title: Relapse tumor E-7-off-Rep2

description:
E-7-2
Culture of relapse tumor E-7

source_name: Culture of relapse tumor E-7 off dox


title: sample398

value: ovarian cancer


title: Relapse tumor E-7-off-Rep1

description:
E-7-1
Culture of relapse tumor E-7

value: FVB/B6 mix


title: K8-614 P5

description: K8-614 P5

value: Xenografted tumor at P5


title: sample397


title: PT4

value: Patient 4

value: M

value: diagnosis


title: PT2

value: Patient 2

value: DTCs from BM

value: ˃ 18 months


title: Relapse tumor E-6-off-Rep2

description:
E-6-2
Culture of relapse tumor E-6

source_name: Culture of relapse tumor E-6 off dox

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

value: primary relapsed pancreatic tumor cell line

value: Off Dox


title: sample395

value: chronic obstructive pulmonary disease (COPD)


title: Relapse tumor E-6-off-Rep1

description:
E-6-1
Culture of relapse tumor E-6


title: PT8

value: Patient 8

value: relapse


title: sample393


title: sample396

value: lung cancer


title: sample392

value: normal


title: sample394


title: PT3

value: Patient 3

value: Neuroblastoma

value: female


title: sample391


title: PT1

value: Patient 1

value: male


title: sample390


title: Sucrose_treatment_replication_2

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

hyb_protocol: Standard Agilent  hybridization protocols

scan_protocol: Agilent G2565CA Microarray Scanner

data_processing: log2 values of gMedianSignal were normalized using quantile normalization method

source_name: Sucrose treatment

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Media: MEM and 20% Fetal Bovine Serum

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with 50 mM sucrose for 7 days

value: sucrose

value: MNT-1 Melanoma Cancer Cell Line


title: Spleen_80COdiet_24HPI_pIC_fish9

city: St. John's

first: Marije

last: Booman

state: NL

address: 1 Marine Lab Road

department: Ocean Sciences

institute: Memorial University of Newfoundland

hyb_protocol: Arrays were prehybridized at 42°C in Nexterion Oligo Prehyb Buffer (Schott Nexterion) for at least 2 hours. Arrays were washed at room temperature for with 0.1% SDS for 5 minutes, followed by 3 5-minute washes with water. Slides were dried by spinning them for 5 minutes at 200x g and kept at 42°C. LifterSlips were prepared by washing them sequentially with water, water, 70% ethanol and 100% ethanol and drying them using compressed air. For each array two labeled cDNAs were combined (one sample, one reference) and 2 μl of LNA blocker (Genisphere) and 40 μl of prewarmed 2x formamide-based hybridization buffer (Genisphere) was added. These samples were incubated at 80°C for 10 minutes and then kept at 42°C. Pre-warmed arrays were put in Corning hybridization chambers, LifterSlips were applied and the samples were loaded under the LifterSlips. Hybridizations were performed overnight for ~16 hours in a water bath at 42°C. After hybridization, arrays were washed at room temperature for 15 minutes with 2xSSC/0.2% SDS which was pre-warmed at 42°C. Next slides were washed  at room temperature for 15 minutes with 2xSSC, followed by 2 15-minute washes with 0.2xSSC. Slides were dried by spinning them for 5 minutes at 200x g.

scan_protocol: Arrays were scanned at a resolution of 5 μm using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer).

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 3 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene. Logratios of duplicate spots were averaged.

label: AlexaFluor 647

organism: Gadus morhua

source_name: Speen tissue, 80% camelina oil diet, pIC injected, 24 hours post-injection, individual fish

label_protocol: 5 μg of DNAse-treated column-purified total RNA was labeled using the SuperScript Direct cDNA Labeling kit (Invitrogen) according to the manufacturer's protocol. Test samples were labeled with AlexaFluor 647, the common reference was labeled with AlexaFluor 555.

growth_protocol: Juvenile cod (average weight 19.4 grams) were kept in 620L tanks. Fish were kept in flow-through seawater at a temperature of 10°C, oxygen saturation > 90% and a photoperiod of 12 hours light / 12 hours dark. Fish were fed with one of three practical diets (three tanks per diet): a control diet using herring oil as a lipid source (FO diet), and two experimental diets using vegetable oil from Camelina sativa to replace 40% or 80% of herring oil (40CO and 80CO diets). Fish were fed 1 % of body weight of feed per tank twice daily in order to ensure equal consumption of feed among treatments.

extract_protocol: Spleens were disrupted and homogenized in TRIzol (Invitrogen) using the TissueLyzer II system with 5 mm stainless steel beads (Qiagen) and total RNA was extracted from the TRIzol homogenate according to the manufacturers’ instructions. Total RNA was treated with DNAse I (Qiagen) to remove genomic DNA, and then purified using the RNeasy 96 kit (Qiagen) according to the manufacturer’s instructions for RNA cleanup using centrifugation.

treatment_protocol: For injections, fish were lightly anesthetized in an aqueous solution of tricaine methane sulfonate (TMS, 100 mg/L) and received an intraperitoneal injection of either a 0.5 mg/ml solution of pIC in ice-cold, 0.2 μm-filtered phosphate-buffered saline (PBS), at a dose of 2 μg per gram body weight (3 tanks per diet), or PBS alone at the same volume of 4 μl per gram body weight (3 tanks per diet). At sampling time,fish were euthanized with a lethal dose of TMS (400 mg/L), and spleens were collected, flash-frozen in liquid nitrogen and stored at -80°C until further processing.

value: Spleen

tag: life stage

value: Juvenile

source_name: pool of RNAs from spleen tissues, all three time points (0h, 6HPI, 24HPI), both treatments (PBS and pIC), all three diets (FO, 40CO, 80CO).


title: Relapse tumor E-4-off-Rep2

description:
E-4-2
Culture of relapse tumor E-4

source_name: Culture of relapse tumor E-4 off dox

value: FVB/B6 mix

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+


title: Relapse tumor E-3-off-Rep2

description:
E-3-2
Culture of relapse tumor E-3

source_name: Culture of relapse tumor E-3 off dox

value: primary relapsed pancreatic tumor cell line

value: Off Dox


title: PT5

value: Patient 5

value: Tumor

value: M

value: diagnosis


title: Relapse tumor E-5-off-Rep1

description:
E-5-1
Culture of relapse tumor E-5

source_name: Culture of relapse tumor E-5 off dox


title: Sucrose_treatment_replication_1


title: Relapse tumor E-3-off-Rep1

description:
E-3-1
Culture of relapse tumor E-3


title: BH3

city: Beijing

first: Yu

last: Xia

state: Beijing

address: Tsinghua University, Haidian District

department: Environmental school

institute: Tsinghua Univeristy

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System BH, replicate 3.

hyb_protocol: All labeled DNA was resuspended in 10 μl hybridization solution as previously described (Wu et al. 2006) and was hybridized with GeoChip 4.2 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA) at 42℃ with 40% formamide for 16h.

scan_protocol: Microarrays were scanned by a ScanArray 5000 Microarray Analysis System (PerkinElmer, Wellesley, MA, USA) at 100% laser power.

data_processing: Signal intensities of the spots were measured with ImaGene 6.0 (Biodiscovery Inc., El Segundo, CA, USA). Low-quality spots with a signal to noise ratio (SNR) of less than 2.0 or with signal intensity less than 1000 were removed before further data analysis. The genes detected in only one out of three samples from the same system were removed. Then the intensities of replicates were transformed to the natural logarithmic form and divided by mean signal intensity.

organism: activated sludge metagenome

source_name: Microbes in activated sludge of full-scale wastewater treatment plant BH

label_protocol: As previously described (Lu et al. 2012), 1000 ng of each DNA sample was labeled with the fluorescent dye Cy5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried.

growth_protocol: On August 13, 2011, mixed-liquor suspended sludge samples were taken from the aerobic zones of the three full-scale wastewater treatment systems. At each site, three 50 ml samples were collected.

extract_protocol: Microbial genomic DNA was extracted from the pellets of activated sludge samples through joint use of freezing and sodium dodecyl sulfate (SDS) for cell lysis (Zhou et al. 1996). The extracted products were then purified employing the Wizard® SV Genomic DNA Purification Kit (Promega, Madison WI). DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

treatment_protocol: Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for analysis.

tag: source

value: activated sludge

tag: location

value: wastewater treatment system

tag: system

value: BH


title: sample389

source_name: RNA from blood

value: lung cancer


title: Control_replication_2

source_name: NC

value: control


title: Spleen_80COdiet_24HPI_pIC_fish8


title: Relapse tumor E-5-off-Rep2

description:
E-5-2
Culture of relapse tumor E-5

tag: strain background

tag: cell type


title: Control_replication_1


title: sample388

value: prostate cancer


title: Relapse tumor E-4-off-Rep1

description:
E-4-1
Culture of relapse tumor E-4

tag: genotype/variation


title: sample387


title: Relapse tumor E-2-off-Rep2

description:
E-2-2
Culture of relapse tumor E-2

source_name: Culture of relapse tumor E-2 off dox


title: Spleen_80COdiet_24HPI_pIC_fish7


title: sample386


title: Spleen_80COdiet_24HPI_pIC_fish6


title: Spleen_80COdiet_24HPI_pIC_fish5


title: BH2

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System BH, replicate 2.


title: sample385

value: normal


title: BH1

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System BH, replicate 1.


title: Relapse tumor E-1-off-Rep2

description:
E-1-2
Culture of relapse tumor E-1

source_name: Culture of relapse tumor E-1 off dox


title: Spleen_80COdiet_24HPI_pIC_fish2

value: Spleen


title: Relapse tumor E-2-off-Rep1

description:
E-2-1
Culture of relapse tumor E-2


title: Spleen_80COdiet_24HPI_pIC_fish3

value: Juvenile


title: Relapse tumor E-1-off-Rep1

description:
E-1-1
Culture of relapse tumor E-1

value: FVB/B6 mix


title: sample383


title: Spleen_80COdiet_24HPI_pIC_fish1


title: Xenografted carcinoma

hyb_protocol: Samples were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 24 hours.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner

data_processing: Log2 ratios were determined with Agilent Feature Extraction software (v 9.1.3.1) and the global quality of the individual microarrays used in the experiment was validated against the quality metrics (QCmetrics) of this software. Results were analyzed with Agilent’s Genomic Workbench Standard Edition 5.0.14

source_name: Xenografted Carcinoma

label_protocol: CGH labeling and hybridization were performed using high-density 244K arrays from Agilent Technologies, as recommended by the manufacturer. Genomic DNA (1µg) was double-digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled with random primers using Agilent Genomic DNA Labeling Kit Plus for 2 hours at 37°C, according to the manufacturer’s instructions.

extract_protocol: Genomic DNA was isolated using DNeasy MiniKit (Qiagen, France) according to the manufacturer’s protocol.

value: Human renal cell carcinoma xenografted into nude mice

value: Human Universal Reference HAPMAP (Promega, USA, Madison)


title: Spleen_80COdiet_24HPI_pIC_fish4


title: LFB2

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System LFB, replicate 2.

source_name: Microbes in activated sludge of full-scale wastewater treatment plant LFB

value: LFB


title: 3T3-L1 adipocytes_Berberine_6h_rep3

city: shanghai

first: Ying

last: Yang

address: 197 Ruijin Road II, Shanghai 200025, China

institute: Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine

description:
Gene expression data from 3T3-L1 adipocytes
s6h_3

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

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US)

source_name: 3T3-L1 adipocytes were treated with berberine for 6h

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

growth_protocol: 3T3-L1 cell line was obtained from the America Cell Type Culture Collection (ATCC, 58786883) and cultured in Dulbecco’s Modified Eagle’s Medium (GIBCO, 11965) containing 10% fetal bovine serum (PAA, A15-151). Adipocyte differentiation was induced by 48h treatment with 5μg/ml insulin (Eli Lilly S.A.S., HI0240), 1μM dexamethasone (Sigma, D-4902), and 0.5mM 3-Isobutyl-1-methylxanthine (IBMX, Sigma, I5879). After 2 days, media were replaced with a maintenance medium (DMEM containing 10% fetal bovine serum and 5μg/ml insulin). Fresh maintenance medium was replaced every two days thereafter.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: 3T3-L1 cells were used between days 8 and 10 post-differentiation. Cells were maintained in DMEM supplemented with 0.2% bovine serum albumin (Genebase, 0332) for 12h prior to treatments, and then treated with berberine for 3h, 6h, or 12h.

value: 3T3-L1 cells

tag: Stage

value: days 8 and 10 post-differentiation

tag: agent

value: Berberine

tag: time


title: 3T3-L1 adipocytes_Berberine_6h_rep2

description:
Gene expression data from 3T3-L1 adipocytes
s6h_2


title: LFB1

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System LFB, replicate 1.


title: Plasma_healthy control_rep010

first: Lijuan

last: Guo

address: 2 Yinghua Dongjie, Hepingli Beijing

institute: intensive care unit

hyb_protocol: Hybridization was performed with the miRCURY™ LNA Array (v.14.0) under 56℃ on a rotator at 2 RPM overnight.

scan_protocol: Scanning was performed on the Axon GenePix 4000B microarray scanner and GenePix v6.0 was used to read the raw intensity.

data_processing: The intensity of green signal of all four replicated spots of each probe on the same slide were collected and calculated. After background subtraction, median normalization method was used to obtain “Normalized Data”. Normalized Data=(Foreground-Background)/Median, and the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

source_name: Plasma of healthy control

label_protocol: Ten μL total RNA of each sample was labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit according to the standard protocol.

extract_protocol: Total RNA were harvested from 200μL plasma using TRIzol and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions and dissolved in 20μL DEPC water. Quality control were performed on the Nanodrop instrument.

treatment_protocol: Whole blood (2 mL) was drawn into Vacutainer (anti-coagulated with EDTA), and plasma isolation was done within 2 hours by centrifugation at 1000 g for 10 minutes. The plasma were stored under -80℃ before RNA extraction.

tag: sample type

value: plasma

tag: disease state

value: healthy control

tag: gender

value: M

tag: age

tag: mpap(mmhg)

tag: pvr (dyn s cm-5)

tag: who functional class


title: sample382

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. R Version 3.0.2

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

tag: disease

value: ovarian cancer


title: LFA3

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System LFA, replicate 3.

source_name: Microbes in activated sludge of full-scale wastewater treatment plant LFA

tag: source

value: activated sludge

value: wastewater treatment system

value: LFA


title: 3T3-L1 adipocytes_Berberine_6h_rep1

description:
Gene expression data from 3T3-L1 adipocytes
s6h_1

tag: cell line


title: sample380


title: Spleen_80COdiet_24HPI_PBS_fish9

source_name: Speen tissue, 80% camelina oil diet, PBS injected, 24 hours post-injection, individual fish

tag: tissue

tag: life stage


title: LFB3

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System LFB, replicate 3.

tag: location

tag: system


title: LFA2

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System LFA, replicate 2.


title: sample381


title: Spleen_80COdiet_24HPI_PBS_fish8


title: Spleen_80COdiet_24HPI_PBS_fish7


title: sample379


title: Plasma_healthy control_rep008

value: F


title: Plasma_healthy control_rep007


title: sample378


title: 3T3-L1 adipocytes_Berberine_3h_rep2

description:
Gene expression data from 3T3-L1 adipocytes
s3h_2

source_name: 3T3-L1 adipocytes were treated with berberine for 3h

tag: Stage


title: Plasma_healthy control_rep006


title: 3T3-L1 adipocytes_Berberine_3h_rep1

description:
Gene expression data from 3T3-L1 adipocytes
s3h_1

tag: agent


title: Plasma_healthy control_rep009


title: sample377


title: Spleen_80COdiet_24HPI_PBS_fish6

value: Spleen


title: LFA1

description:
Microbes in activated sludge.
GeoChip data for activated sludge sample collected at System LFA, replicate 1.


title: Plasma_healthy control_rep005


title: 3T3-L1 adipocytes_Berberine_3h_rep3

description:
Gene expression data from 3T3-L1 adipocytes
s3h_3

tag: time


title: Spleen_80COdiet_24HPI_PBS_fish3

value: Juvenile


title: sample384

value: normal


title: Spleen_80COdiet_24HPI_PBS_fish4


title: Spleen_80COdiet_24HPI_PBS_fish5


title: 3T3-L1 adipocytes_Berberine_12h_rep3

description:
Gene expression data from 3T3-L1 adipocytes
s12h_3

source_name: 3T3-L1 adipocytes were treated with berberine for 12h


title: 3T3-L1 adipocytes_Berberine_12h_rep2

description:
Gene expression data from 3T3-L1 adipocytes
s12h_2


title: Stem Cell

scan_protocol: were scanned with an Agilent DNA Microarray Scanner (G2565BA)

source_name: Stem Cell

extract_protocol: Genomic DNA was isolated from human renal cancer and from spheres using DNeasy MiniKit (Qiagen, France) according to the manufacturer’s protocol.

value: tumor stem cell obtained from human renal tumor xenografted into nude mice

source_name: Universal Reference HAPMAP (Promega, USA, Madison)

tag: reference


title: sample375

extract_protocol: Blood of controls and patients was extracted in PAXgene Blood RNA tubes (BD, Franklin Lakes, New Jersey USA). The content of blood sampling tubes of each patient and healthy donor was used for RNAe extraction. The total RNA including the miRNA was isolated using the miRNeasy kit (Qiagen GmbH, Hilden) according to manufacturers instructions..


title: 3T3-L1 adipocytes_Berberine_12h_rep1

description:
Gene expression data from 3T3-L1 adipocytes
s12h_1


title: Plasma_healthy control_rep004

tag: sample type

tag: disease state


title: Plasma_healthy control_rep003

tag: gender

tag: age


title: Spleen_80COdiet_24HPI_PBS_fish1

source_name: pool of RNAs from spleen tissues, all three time points (0h, 6HPI, 24HPI), both treatments (PBS and pIC), all three diets (FO, 40CO, 80CO).


title: sample376


title: Plasma_healthy control_rep001

tag: mpap(mmhg)

tag: pvr (dyn s cm-5)


title: sample374

tag: disease


title: Spleen_80COdiet_24HPI_PBS_fish2


title: Plasma_CTEPH patient_rep010

source_name: Plasma of CTEPH patient

value: chronic thromboembolic pulmonary hypertension

tag: who functional class


title: sample372

value: chronic obstructive pulmonary disease (COPD)


title: Plasma_CTEPH patient_rep009


title: Spleen_40COdiet_24HPI_pIC_fish9

source_name: Speen tissue, 40% camelina oil diet, pIC injected, 24 hours post-injection, individual fish


title: 3T3-L1 adipocytes_DMSO_rep3

description:
Gene expression data from 3T3-L1 adipocytes
Con_3

source_name: 3T3-L1 adipocytes were treated with DMSO as control

tag: cell line

value: 3T3-L1 cells

value: DMSO

value: control


title: 3T3-L1 adipocytes_DMSO_rep2

description:
Gene expression data from 3T3-L1 adipocytes
Con_2

value: days 8 and 10 post-differentiation


title: sample373

source_name: RNA from blood


title: Spleen_40COdiet_24HPI_pIC_fish7

tag: tissue


title: Spleen_40COdiet_24HPI_pIC_fish8

tag: life stage


title: sample371


title: Plasma_CTEPH patient_rep008

value: plasma


title: sample370


title: Spleen_40COdiet_24HPI_pIC_fish6


title: Spleen_40COdiet_24HPI_pIC_fish5


title: MD_Pr.14_mouse_SS_31102012_(Mouse430_2)

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description: Gene expression data from murine cells

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

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

data_processing: The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed

source_name: 32D cells

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

growth_protocol: 32D cells were stably transduced with the respective FLT3-ITD retroviral constructs. Infected cells (5x106) were starved for 3h followed by 1h TKI-treatment.

extract_protocol: RNA was isolated from 32D cells transduced with the respective FLT3-ITD constructs using TRIzol (Life Technologies).

tag: transduction

value: FLT3 ITD598


title: MD_Pr.13_mouse_SS_31102012_(Mouse430_2)

description: Gene expression data from murine cells

treatment_protocol: 32D cells were stably transduced with the respective FLT3-ITD retroviral constructs. Infected cells (5x106) were starved for 3h followed by 1h TKI-treatment.

value: FLT3 ITD78


title: Spleen_40COdiet_24HPI_pIC_fish4


title: Plasma_CTEPH patient_rep007


title: sample368

first: Andreas

last: Keller

institute: Saarland University


title: Plasma_healthy control_rep002

value: healthy control

value: M


title: MD_Pr.11_mouse_SS_31102012_(Mouse430_2)

description: Gene expression data from murine cells

value: FLT3 ITD613


title: MD_Pr.10_mouse_SS_21112012_(Mouse430_2)

description: Gene expression data from murine cells

value: FLT3 ITD602


title: sample367


title: 3T3-L1 adipocytes_DMSO_rep1

description:
Gene expression data from 3T3-L1 adipocytes
Con_1


title: Plasma_CTEPH patient_rep006

value: F


title: sample369


title: MD_Pr.12_mouse_SS_31102012_(Mouse430_2)

description: Gene expression data from murine cells

value: FLT3 ITD611


title: sample366

value: normal


title: Plasma_CTEPH patient_rep004


title: Spleen_40COdiet_24HPI_pIC_fish3

value: Spleen

value: Juvenile


title: Plasma_CTEPH patient_rep003

value: chronic thromboembolic pulmonary hypertension


title: sample365


title: sample364

value: others


title: Plasma_CTEPH patient_rep002


title: Spleen_40COdiet_24HPI_pIC_fish2


title: sample363

value: ductal adenocarcinoma


title: Plasma_CTEPH patient_rep005


title: Spleen_40COdiet_24HPI_PBS_fish8

source_name: Speen tissue, 40% camelina oil diet, PBS injected, 24 hours post-injection, individual fish


title: Spleen_40COdiet_24HPI_pIC_fish1


title: Plasma_CTEPH patient_rep001


title: sample361

value: pancreatitis


title: Balb/c_rad_rep2

city: Stanford

first: Matthew

middle: D

last: Li

address: 265 Campus Dr.

institute: Stanford University

description: 10 Gy irradiated

hyb_protocol: Standard Affymetrix procedures at the Stanford Protein and Nucleic Acid (PAN) core facility

data_processing: The data were pre-processed with GC-RMA and quantile normalization in R/Bioconductor. Additional analyses were completed in R/Bioconductor.

source_name: Hippocampi microglia

label_protocol: RNA was quantified using an Agilent 2100 Bioanalyzer and all samples used for arrays had an RNA Integrity Number (RIN) > 7.4. These samples were subjected to reverse transcription, 2 consecutive rounds of linear amplification, and production and fragmentation of biotinylated cRNA (Affymetrix, Santa Clara, CA).

growth_protocol: Mice used for this study were 6.5 week-old female C57BL/6 and Balb/c mice from Jackson Laboratory.

extract_protocol: RNA from 5,000–10,000 CD11b+ FACS-sorted cells per animal was extracted using Trizol (Life Technologies), then purified and concentrated using the RNeasy MinElute Cleanup Kit (Qiagen), as per the manufacturer’s protocol.

treatment_protocol: Mice were anesthetized with i.p. ketamine/xylazine and placed in a custom irradiation jig exposing a 1 cm circular region centered over the forebrain, shielding the eyes and nose and cerebellar formation. A single dose of 10 Gy X-ray irradiation was delivered with a Kimtron Polaris SC-500 with the following settings: 225 Kv, 13.3 mA, 0.5 mm Cu filter and measured half-value layer of 1.46 mm Cu. Dose calibration was performed using intracranially implanted thermoluminescent dosimeters (TLDs provided and read by Stanford University Department of Radiation Oncology).

tag: strain

value: Balb/c

value: CD11b+ hippocampal microglia

value: 10.5 weeks


title: Spleen_40COdiet_24HPI_PBS_fish9


title: sample362

address: Building 60


title: Balb/c_rad_rep1

description: 10 Gy irradiated

scan_protocol: Standard Affymetrix procedures at the Stanford Protein and Nucleic Acid (PAN) core facility


title: Balb/c_rad_rep3

description: 10 Gy irradiated


title: Balb/c_sham_rep3

description: sham irradiated


title: Spleen_40COdiet_24HPI_PBS_fish7


title: Balb/c_sham_rep2

description: sham irradiated


title: sample360


title: Spleen_40COdiet_24HPI_PBS_fish6


title: C57BL/6_rad_rep3

description: 10 Gy irradiated


title: Spleen_40COdiet_24HPI_PBS_fish4


title: Spleen_40COdiet_24HPI_PBS_fish3


title: Balb/c_sham_rep1

description: sham irradiated


title: Spleen_40COdiet_24HPI_PBS_fish5


title: C57BL/6_rad_rep1

description: 10 Gy irradiated


title: C57BL/6_sham_rep3

description: sham irradiated


title: sample359


title: sample358


title: C57BL/6_sham_rep2

description: sham irradiated


title: sample357

value: ovarian cancer


title: sample356


title: sample355


title: sample354


title: sample353

value: long-lived individuals


title: Spleen_40COdiet_24HPI_PBS_fish2


title: sample352


title: Spleen_FOdiet_24HPI_pIC_fish6

source_name: Speen tissue, fish oil diet, pIC injected, 24 hours post-injection, individual fish


title: Spleen_FOdiet_24HPI_pIC_fish8


title: Spinal cord from newborn mouse, rep1 and 2

city: Baoshan

first: Botao

last: Zhao

state: Shanghai

address: 333 Nanchen Rd

department: college of life science

institute: Shanghai University

description:
This Sample represents 2 technical replicates, P0-1 and P0-2.
microRNA
Small RNAs were ligated to 5' and 3' adapters to generate small RNA library. Label small RNA by PCR with a Cy5-labeled 5' primer and 3' primer. Oligonucleotide probes complementary to miRNA were spotted on array.

hyb_protocol: Labeled PCR products were cleaned. Denature the PCR product at 95°C for 3 min and chill on ice immediately. Combine the PCR product with equal volume of hybridization buﬀer (8×SSC/0.2% SDS, pH 7.0) that has been heated to 48°C and mix thoroughly. Immediately, inject the mixture into the hybridization chamber. Hybridization was carried out at 48 C for 16 h. After hybridization, slides were washed (2×SSC/0.03% SDS, 2 min; 0.2×SSC, 2 min; 0.1×SSC, 1 min) at 25°C.

scan_protocol: Slides were scanned with ScanArray 5000 (Perkin-Elmer) with a scan resolution of 5μm.

data_processing: The raw data were normalized by total intensity. miRNAs with an intensity value more than 1000 in at least one sample were subject to further analysis. After p value evaluation, intensities from the triplicate probes were merged by mean value.

source_name: spinal cord, newborn

label_protocol: Small libraries were generated by sequential ligation 5' and 3' adapters to recovered small RNAs. RT-PCR was performed to transfer these ligated small RNAs to DNA. Small RNA cDNA libraries were ampliﬁed and labeled by PCR using the 5' Cy5-primer and the 3' primer.

extract_protocol: Total RNAs were extracted by Trizol reagent and resolved on 15% UREA-PAGE gel. Small RNAs of 18-26nt were recovered by gel elution.

tag: strain/background

value: spinal cord

tag: developmental stage


title: Spleen_FOdiet_24HPI_pIC_fish7


title: C57BL/6_sham_rep1

description: sham irradiated


title: H13: A_T1 vs B_T1

city: Wageningen

first: Yinghua

last: Xiao

address: Bornse Weilanden 9

institute: Wageningen University

description:
Raw data file (Cy3): SlideC_Cy3
Raw data file (Cy5): SlideC_Cy5
Meta region on slide: 1

hyb_protocol: Labeled cDNA mixtures were subsequently concentrated in a Hetovac VR-1 (Heto Lab Equipment A/S, Birkerod, Denmark), incubated at 98°C for 3 min, and cooled at room temperature for 5 min. After the addition of 2× GEX HI-RPM hybridization buffer (Agilent Technologies, Palo Alto, CA), each mixture was applied to an Agilent 4×44K array (Agilent Technologies, Palo Alto, CA).

scan_protocol: Slides were scanned with a ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA), image analysis and processing were performed using the ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA). The microarrays were scanned at different intensities. For each of the individual microarrays the best scan was selected on the basis of signal distribution (combination of a low number of saturated spots and a low number of low signal spots).

data_processing: The data were normalized using Lowess normalization as available in MicroPrep. The data were corrected for inter-slide differences on the basis of total signal intensity per slide using Postprep. The median intensity of the different probes per gene was selected as the gene expression intensity. CyberT was used to compare the different transcriptomes, taking into account the replicates of each of the conditions. This analysis resulted in a gene expression ratio and false discovery rate (FDR) for each gene. Genes with FDR values <0.05 were considered to be statistically significant.

organism: Clostridium perfringens SM101

source_name: T1 sample in experiment A

label_protocol: 3 µg of total RNA was subjected to cDNA synthesis using random nonamer priming and indirect labeling approaches following the manufacture instruction of the Cyscribe Postlabelling kit (Amersham Biosciences). For each sample at each time point, both Cy3- and Cy5-labeled cDNA was prepared.

growth_protocol: An exponential-phase inoculum was prepared by mixing 1 ml of the overnight culture and 9 ml FTM followed by 4 h incubation; the fast dividing vegetative cells produced substantial amounts of gas. An inoculum (1:10,000, v:v) was added to 500 ml of pre-reduced mDS medium and incubated at 37°C. This sporulating culture was continuously mixed using a magnetic stirrer. Samples of the sporulating culture were taken every 30 min starting 2 h after inoculation. A 3 ml mixture of acidified phenol-ethanol (v:v=1:9) was added to 12 ml culture samples immediately upon sampling. After short mixing using a vortex, this sample was kept on ice for 30 min. Cells/spores were then harvested by centrifugation at 16,000 ×g for 5 min at 4°C, and resuspended in ice cold TRIzol Reagent (Ambion, US).

extract_protocol: 0.6 ml aliquots of the mixture were transferred to Lysing Matrix B tubes prefilled with 0.1mm silica spheres. These samples were frozen in liquid N2 and kept at -80°C until use. For final RNA extraction, 0.4 ml ice-cold TRIzol Reagent was added to the frozen sample and homogenization was performed immediately  without thawing using Savant FastPrep FP120 (Qbiogene, Carlsbad, US) for 40 sec at Speed 6, in total 3 times with interval cooling on ice. After phase separation, RNA precipitation and washing was performed as described in the instructions of the manufacturer. The total RNA extracts were further purified using a RNeasy kit (QIAGEN, Hilgen, Germany). On-column DNA digestion was performed during purification using RNase-Free DNase (QIAGEN, Hilgen, Germany).

source_name: T1 sample in experiment B


title: sample350

city: Homburg

value: sarcoidosis


title: MD_Pr.26_mouse_SS_21112012_(Mouse430_2)

description: SAMPLE 10

source_name: pro-erythroblast cell line I/11

label_protocol: RNA was amplified using the Ovation Pico WTA system (Nugen) and labeled using the encore Biotin Module (Nugen). 5 ug of amplified and labeled DNA was hybridized to Affymetrix GeneChip Mouse Genome 430plus 2.0 microarrays according to the manufacturer’s recommendations (Affymetrix).

growth_protocol: The expanding erythroid progenitors (I/11) were maintained in serum-free medium (StemPro 34 plus nutrient supplement, Invitrogen) supplemented with 1 U/ml of human recombinant Erythropoietin (EPO) (Janssen-Cilag), 100 ng/ml SCF (Peprotech), 1 µM dexamethasone (Sigma) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol: RNA was isolated from 5x105 I/11 cells transfected with either scrambled or PLCg1 shRNA using TRIzol (Life Technologies).

treatment_protocol: For PLCγ1 shRNA knockdown experiments, pLKO vector system with puromycin resistance gene was used containing different shRNA sequences for PLCγ1 (RNAi Consortium Broad Range Institutes, Harvard University, Boston; or Sigma-Aldrich). HEK 293T cells were transfected using FUGENE (Roche) transfection reagent to generate lentiviral particles.  I/11 cells stably infected with either control (scr=scrambled) or PLCγ1 shRNA.

tag: cell type

value: expanding erythroid progenitors

tag: transfected with

value: PLCg1 shRNA

tag: shRNA id

value: PLCy1 sh 133

tag: time point


title: MD_Pr.27_mouse_SS_21112012_(Mouse430_2)

description: SAMPLE 11


title: Spleen_FOdiet_24HPI_pIC_fish5


title: MD_Pr.25_mouse_SS_21112012_(Mouse430_2)

description: SAMPLE 9

value: scrambled shRNA (control)

value: scr


title: Spleen_FOdiet_24HPI_pIC_fish4

value: Spleen

value: Juvenile


title: H11: A_T1 vs A_T2

description:
Raw data file (Cy3): SlideC_Cy3
Raw data file (Cy5): SlideC_Cy5
Meta region on slide: 3

source_name: T2 sample in experiment A


title: H12: B_T2 vs B_T1

description:
Raw data file (Cy3): SlideC_Cy3
Raw data file (Cy5): SlideC_Cy5
Meta region on slide: 2

source_name: T2 sample in experiment B


title: MD_Pr.28_mouse_SS_21112012_(Mouse430_2)

description: SAMPLE 12


title: MD_Pr.23_mouse_SS_21112012_(Mouse430_2)

description: SAMPLE 7


title: Spleen_FOdiet_24HPI_pIC_fish3


title: MD_Pr.24_mouse_SS_21112012_(Mouse430_2)

description: SAMPLE 8


title: Spleen_FOdiet_24HPI_pIC_fish9


title: MD_Pr.22_mouse_SS_08112012_(Mouse430_2)

description: SAMPLE 6

value: PLCy1 sh 14


title: C57BL/6_rad_rep2

description: 10 Gy irradiated


title: MD_Pr.21_mouse_SS_08112012_(Mouse430_2)

description: SAMPLE 5


title: sample348


title: H10: A_T2 vs A_T3

description:
Raw data file (Cy3): SlideD_Cy3
Raw data file (Cy5): SlideD_Cy5
Meta region on slide: 4

source_name: T3 sample in experiment A


title: H09: A_T2 vs B_T2

description:
Raw data file (Cy3): SlideC_Cy3
Raw data file (Cy5): SlideC_Cy5
Meta region on slide: 4


title: Spinal cord from 13.5-day mouse fetus, rep1 and 2

description:
This Sample represents 2 technical replicates, E13.5-1 and E13.5-2.
microRNA
Small RNAs were ligated to 5' and 3' adapters to generate small RNA library. Label small RNA by PCR with a Cy5-labeled 5' primer and 3' primer. Oligonucleotide probes complementary to miRNA were spotted on array.

source_name: spinal cord, 13.5-day fetus


title: MD_Pr.20_mouse_SS_08112012_(Mouse430_2)

description: SAMPLE 4


title: Spleen_FOdiet_24HPI_pIC_fish2

source_name: pool of RNAs from spleen tissues, all three time points (0h, 6HPI, 24HPI), both treatments (PBS and pIC), all three diets (FO, 40CO, 80CO).


title: Spleen_FOdiet_24HPI_pIC_fish1


title: H08: B_T3 vs B_T2

description:
Raw data file (Cy3): SlideB_Cy3
Raw data file (Cy5): SlideB_Cy5
Meta region on slide: 1

source_name: T3 sample in experiment B


title: Spleen_FOdiet_24HPI_PBS_fish9

source_name: Speen tissue, fish oil diet, PBS injected, 24 hours post-injection, individual fish


title: H07: A_T3 vs B_T3

description:
Raw data file (Cy3): SlideA_Cy3
Raw data file (Cy5): SlideA_Cy5
Meta region on slide: 1


title: sample345


title: Spleen_FOdiet_24HPI_PBS_fish8


title: sample346


title: Spleen_40COdiet_24HPI_PBS_fish1


title: H06: B_T4 vs B_T3

description:
Raw data file (Cy3): SlideB_Cy3
Raw data file (Cy5): SlideB_Cy5
Meta region on slide: 2

source_name: T4 sample in experiment B


title: sample344

source_name: RNA from blood

value: normal


title: H05: A_T3 vs A_T4

description:
Raw data file (Cy3): SlideA_Cy3
Raw data file (Cy5): SlideA_Cy5
Meta region on slide: 2

source_name: T4 sample in experiment A


title: MD_Pr.18_mouse_SS_08112012_(Mouse430_2)

description: SAMPLE 2


title: H04: B_T4 vs A_T4

description:
Raw data file (Cy3): SlideB_Cy3
Raw data file (Cy5): SlideB_Cy5
Meta region on slide: 3


title: sample347


title: sample342


title: sample340


title: sample341


title: Spleen_FOdiet_24HPI_PBS_fish7


title: H01: A_T5 vs B_T5

description:
Raw data file (Cy3): SlideA_Cy3
Raw data file (Cy5): SlideA_Cy5
Meta region on slide: 4

source_name: T5 sample in experiment A

source_name: T5 sample in experiment B


title: Spleen_FOdiet_24HPI_PBS_fish5


title: Spleen_FOdiet_24HPI_PBS_fish6


title: sample339


title: MD_Pr.19_mouse_SS_08112012_(Mouse430_2)

description: SAMPLE 3


title: MD_Pr.17_mouse_SS_08112012_(Mouse430_2)

description: SAMPLE 1


title: Yap1 tumor #3-off dox

description: Subcutaneous tumor#3 from Yap1 expressing iKras cells grown off-dox

growth_protocol: Subcutaneous xenografts were generated in Nude mice

treatment_protocol: All tumors from the iKras cells (expressing Gfp or Yap1) were grown on-dox for 7 days subcutaneously in Nude mice and switched to off-dox (for 24 hours for Gfp expressing iKras cells) or kept off-dox throughout (for Yap1 expressing iKras cells)

value: subcutanous tumor generated from iKras cells expressing Yap1 by bypassing tumor regression upon Kras extinction

tag: genotype

value: p48Cre tetO_LKrasG12D ROSA_rtTAL+ p53L+

tag: background

value: FVB/B6 mix

tag: treatment

value: Off Dox


title: H03: B_T5 vs B_T4

description:
Raw data file (Cy3): SlideB_Cy3
Raw data file (Cy5): SlideB_Cy5
Meta region on slide: 4


title: Spleen_FOdiet_24HPI_PBS_fish2


title: Gfi1b wild type Ter119 positive cells

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

institute: University Hospital Of Essen

description: Gene expression data from bone marrow derived Gfi1b wild type erythroid cells

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized with Affymetrix Mouse Genome 430 2.0 Arrays and Scanned using the Afymetrix scanner M10 at the BioChip laboratory of the University Hospital of Essen, Germany

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data was processed using the AltAnalyze software (www.altanalyze.org) using the default parameters.

source_name: Mouse bone marrow derived CD11b+, Gr1-low, GFP-high monocytes from heterozygous GFP:Gfi1 knock-in mouse

label_protocol: Target RNA was reverse transcried into cDNA and in-vitro transcribed using the Ovation Pico WTA system (NuGEN) according to the Manufacturers protocols from 50 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) to generate biotin-labeled cRNA.

growth_protocol: Mice were housed under Specific Pathogen Free (SPF) conditions

extract_protocol: TRIzol (Invitrogen) was used to isolate total RNA following the manufacturers instructions.

treatment_protocol: Six weeks old mice were treated five times with pIpC (500µg each) every other day and sacrificed 42 days after the first injection

value: Ter119 positive erythroid cells

tag: genotype/variation

value: Gfi1b wild type


title: Spleen_FOdiet_24HPI_PBS_fish4


title: Spleen_80COdiet_PreInjection_fish12

source_name: Spleen tissue, 80% camelina oil diet, pre-injection, individual fish


title: H02: A_T4 vs A_T5

description:
Raw data file (Cy3): SlideA_Cy3
Raw data file (Cy5): SlideA_Cy5
Meta region on slide: 3


title: Yap1 tumor #1-off dox

description: Subcutaneous tumor#1 from Yap1 expressing iKras cells grown off-dox

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

extract_protocol: Trizol extraction of total RNA followed by RNeasy column cleanup was performed according to the manufacturer's instructions.


title: Gfi1b knock-out Ter119 positive cells

description: Gene expression data from bone marrow derived Gfi1b conditional knockout erythroid cells

source_name: Mouse bone marrow derived CD11b+, Gr1-low monocytes from Gfi1 knock-out mouse

value: Gfi1b knock-out


title: Spleen_FOdiet_24HPI_PBS_fish3


title: Gfp tumor #2-off dox 24hr

description: Subcutaneous tumor#2 from Gfp expressing iKras cells taken 24 hour off-dox

source_name: Subcutaneous tumor#2 from Gfp expressing iKras cells grown on dox but taken 24 hour off-dox before harvesting

value: subcutanous tumor generated from iKras cells expressing Gfp

value: 24 hour Off Dox


title: Gfp tumor #1-off dox 24hr

description: Subcutaneous tumor#1 from Gfp expressing iKras cells taken 24 hour off-dox

source_name: Subcutaneous tumor#1 from Gfp expressing iKras cells grown on dox but taken 24 hour off-dox before harvesting


title: sample337

treatment_protocol: stored at -20 degree

tag: disease

value: sarcoidosis


title: Yap1 tumor #2-off dox

description: Subcutaneous tumor#2 from Yap1 expressing iKras cells grown off-dox


title: Spleen_FOdiet_24HPI_PBS_fish1


title: Spleen_80COdiet_PreInjection_fish11


title: sample338

value: ovarian cancer


title: sample351

value: long-lived individuals


title: sample335


title: sample336


title: sample333


title: sample334


title: Spleen_80COdiet_PreInjection_fish8


title: Spleen_80COdiet_PreInjection_fish7


title: Spleen_80COdiet_PreInjection_fish9


title: PTEN deletion Replicate3

city: Tampa

first: Ravi

last: Pathak

address: 12901 Bruce B Downs

institute: University Of South Florida

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse MOE430 chips Array. GeneChips were washed and stained in the Affymetrix

data_processing: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default settings.

source_name: PTEN Delted Mouse Lungs

growth_protocol: Compound-transgenic mice harboring Pten gene with loxP-flanked exon-V (Ptenflox/flox), SP-C–rtTAtg/−; and TetO-Cretg/- were generated. Mice harboring SPC-rtTA/Ptenflox/flox, TetO-Cretg/-/Ptenflox/flox, SPC-rtTA, or TetO-Cretg/- as controls

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

treatment_protocol: Dox treatment (E6.5 to E14.5) induced tumors in CCSP-rtTA/TetO-Cretg/-/LSL-KrasG12D/PtenΔ/Δ mice between 10-12 weeks of age

value: Lung Epithelium


title: PTEN deletion Replicate2


title: PTEN deletion Replicate1


title: Control Replicate 3

source_name: Control Mouse Lungs


title: sample332


title: sample331


title: sample349


title: sample330


title: Spleen_80COdiet_PreInjection_fish6

value: Spleen


title: Spleen_80COdiet_PreInjection_fish10

value: Juvenile


title: sample328


title: sample327


title: MTAP+/+ R4

city: Philadelphia

first: warren

last: kruger

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

hyb_protocol: Affymetrix standard proceedure

scan_protocol: Affymetrix standard proceedure

data_processing: Affymetrix data were RMA-normalized in R, with default settings

label_protocol: Affymetrix Biotin labeling

extract_protocol: RNA was isolated using TRIzol reagent

tag: Sex

value: male

value: liver

tag: age

value: between 92 and 101 days

value: MTAP+/+


title: Control Replicate 1

tag: tissue


title: Spleen_80COdiet_PreInjection_fish2

tag: life stage


title: MTAP+/+ R3


title: MTAP+/+ R2


title: sample326

value: normal


title: Control Replicate 2


title: sample325

value: Periodontitis


title: Spleen_80COdiet_PreInjection_fish3


title: MTAP+/+ R1


title: Spleen_40COdiet_PreInjection_fish11

source_name: Spleen tissue, 40% camelina oil diet, pre-injection, individual fish


title: Spleen_80COdiet_PreInjection_fish5


title: Spleen_80COdiet_PreInjection_fish4


title: Spleen_40COdiet_PreInjection_fish12


title: Spleen_80COdiet_PreInjection_fish1


title: Spleen_40COdiet_PreInjection_fish10


title: MTAP+/- R3

value: MTAP+/-


title: sample323


title: Spleen_40COdiet_PreInjection_fish9


title: sample322


title: MTAP+/- R4


title: MTAP+/- R2


title: Spleen_40COdiet_PreInjection_fish8


title: Spleen_40COdiet_PreInjection_fish6


title: Spleen_40COdiet_PreInjection_fish7


title: sample319


title: sample320


title: sample318


title: sample316


title: sample324


title: Spleen_40COdiet_PreInjection_fish2


title: Spleen_40COdiet_PreInjection_fish5


title: sample321


title: sample315


title: Spleen_40COdiet_PreInjection_fish4


title: Spleen_40COdiet_PreInjection_fish3


title: 8-Mut_1

first: Guillaume

last: Galmiche

address: 7 quai Saint-Bernard

department: Aging, stress and inflammation

description: Aorta mutant

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip450 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The raw data were analyzed with GeneChip Operationg Software version 1.4 (GCOS) and statistical analyses were carried out with the BioConductor suite.

source_name: Aorta mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: total RNA extraction using Rneasy Fibrous tissue kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Control and mutant mice were injected i.p. with 1mg of tamoxifen for 3 days for the SRF deletion.

value: Aorta

value: SRF-flex2neo -SM22CreERT2ki/+

value: smooth muscle specific SRF knockout

value: 4 month-old


title: Mut2_2

description: Aorta mutant


title: Mut1_2

description: Aorta mutant


title: sample314


title: sample343


title: Spleen_40COdiet_PreInjection_fish1

extract_protocol: Spleens were disrupted and homogenized in TRIzol (Invitrogen) using the TissueLyzer II system with 5 mm stainless steel beads (Qiagen) and total RNA was extracted from the TRIzol homogenate according to the manufacturers’ instructions. Total RNA was treated with DNAse I (Qiagen) to remove genomic DNA, and then purified using the RNeasy 96 kit (Qiagen) according to the manufacturer’s instructions for RNA cleanup using centrifugation.

source_name: pool of RNAs from spleen tissues, all three time points (0h, 6HPI, 24HPI), both treatments (PBS and pIC), all three diets (FO, 40CO, 80CO).


title: C1_2

description: Aorta control

source_name: Aorta control

value: SRF-flex2neo littermates (control)


title: Spleen_FOdiet_PreInjection_fish12

source_name: Spleen tissue, fish oil diet, pre-injection, individual fish


title: 5-C_1

description: Aorta control


title: 7-Mut_1

description: Aorta mutant


title: C2_2

description: Aorta control


title: MTAP+/- R1


title: Spleen_FOdiet_PreInjection_fish11


title: human CPE Braak-6 donor 7

city: Amsterdam

first: Sarah

last: Janssen

address: Meibergdreef 47

department: Ophthalmogenetics

institute: Netherlands Institute for Neuroscience

description: Biological CPE replicate 7 of 7 of healthy human choroid plexus

hyb_protocol: Labeled human CPE RNA and labeled human common reference sample were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent scanner, protocol GE2-v5_95_Fec07

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and linear loweless dye normalization. This resulted amongst others in normalized log ratios (test/reference) data that can be find in the Agilent Feature Extraction files.

source_name: Braak 6 Alzheimer disease stage human choroid plexus epithelium

label_protocol: aRNA samples were labeled with a Cy5 fluorescent probe (Cy5 mono-reactive dye pack, GE Healthcare UK, Little Chalfont, Buckinghamshire, UK). In short, aRNA was coupled to Cy5 (dissolved in DMSO) in 0.5 M NaHCO3 (pH 9.0) for one hour. Free dyes were quenched by the addition of 4 M hydroxylamine and removed by filtration over a Chroma Spin-30 column (DEPC-H20 Columns, Clontech Laboratories) with glycogen as a carrier.

extract_protocol: Total RNA was isolated using RNeasy Micro Kit (Qiagen Benelux, Venlo, The Netherlands). Subsequently, the mRNA component was amplified with Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion Applied Biosystems Europe B.V.).

treatment_protocol: With laser dissection microscopy, the CPE cells were specifically cut out from cryosections of the choroid plexus (10um) mounted on PEN-membrane slides

value: choroid plexus epithelium

tag: cell sampling

value: laser dissection microscopy

tag: disease state

value: Braak 6 Alzheimer disease stage

source_name: Total RNA from pooled healthy human RPE/choroid cells

value: RPE/chodoid

value: healthy


title: human CPE Braak-6 donor 6


title: 6-C_1

description: Aorta control


title: sample317

source_name: RNA from blood


title: Spleen_FOdiet_PreInjection_fish10

value: Spleen

value: Juvenile


title: sample313


title: sample310


title: sample308


title: sample312


title: Spleen_FOdiet_PreInjection_fish9


title: sample309


title: sample311


title: Spleen_FOdiet_PreInjection_fish8


title: C26 dnFoxO 4

city: Boston

first: Susan

last: Kandarian

state: MA

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

description: Whole transcript expression profiling

hyb_protocol: Fragmented biotinylated cDNA were further processed by GeneChip® Hybridization, Wash, and Stain Kit, then hybridized on mouse Affymetrix Gene 1.0 ST arrays (Santa Clara, CA, USA) to measure the expression of 28,132 well-annotated genes.

scan_protocol: A total of 16 array images were acquired by GeneChip Scanner 3000 7G and quality assessed by Affymetrix Expression Console (Santa Clara, CA).

data_processing:
Gene expression signal values were generated by the Expression File Creator module of the GenePattern platform (Broad Institute, Cambridge, MA) and robust multi-array analysis algorithm (RMA) and quantile normalization was used for data preprocessing {Bolstad, 2003 #4365}.
Brainarray MoGene 1.0 ST custom CDF file v.16 was used for probe annotation {Dai M, 2005}.

label: Btiotin

source_name: tibialis anteior muscle

label_protocol: Whole-transcript expression profiling experiments were carried out by the Boston University Medical Center Microarray Core Facility.  The GeneChip Whole-Transcript Sense Target Labeling and Control Reagents Kit was used to synthesize and amplify cDNA for biotinylation labeling per manufacturer’s instructions .

growth_protocol: CDF1 mice (~20g) were used for all experiments. Food and water were provided ad libitum.

extract_protocol: Muscles were harvested from mice anesthetized under isofluorane and were snap-frozen in liquid nitrogen.  Muscles were minced and homogenized in TRIzol for RNA extraction.

treatment_protocol: The tibialis anterior muscles of mice were injected with either AAV9-EV or AAV9-d.n.FoxO, and then assigned to a control or C26 group. To induce cancer cachexia in the C26 group, 5x105 C26 cells were subcutaneously injected into each flank on the same day as AAV delivery. Control mice received a subcutaneous injection of 1xPBS into each flank.  Muscles from C26 mice(and control mice) were harvested when the largest tumor reached 1.5 cm in diameter (~26 days post-inoculation).

value: tibialis anteior muscle

tag: sample type

value: from atrophied C26-tumor bearing mice with AAV9 dominant negative FoxO transfection

value: from atrophied C26-tumor bearing mice


title: Spleen_FOdiet_PreInjection_fish6

scan_protocol: Arrays were scanned at a resolution of 5 μm using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer).

label_protocol: 5 μg of DNAse-treated column-purified total RNA was labeled using the SuperScript Direct cDNA Labeling kit (Invitrogen) according to the manufacturer's protocol. Test samples were labeled with AlexaFluor 647, the common reference was labeled with AlexaFluor 555.


title: C26 dnFoxO 2

description: Whole transcript expression profiling

value: AAV9 dominant negative FoxO transfection


title: ΔfabR vs. Wildtype

city: Heverlee

first: Hans

last: Steenackers

address: Kasteelpark Arenberg 20, box 2460

country: Belgium

institute: KU Leuven

description: ΔfabR vs. Wildtype

hyb_protocol: Hybridizations were performed in color flip on S. Typhimurium arrays containing 70-mer oligos representing all LT2 annotated genes (Operon), spotted in duplicate on CodeLink Activated slides (Amersham Biosciences), as previously reported (Thijs et al., 2007).

scan_protocol: Scanning by Nucleomics core VIB.

data_processing: Data were Loess normalized with the LIMMA BioConductor package without performing a background correction.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

label_protocol: RNA was labeled with Cy5 and Cy3 by reverse transcription (Wang et al., 2004).

growth_protocol: Salmonella strains were cultured under free-living TSB conditions (TSB 1/20, 200 rpm, 25 °C) for 6h (ca. 2 x 108 cells).

extract_protocol: Total RNA was isolated with the Qiagen RNeasy mini kit according to the manufacturer’s protocol. Contaminating genomic DNA was removed from the RNA samples with Turbo DNA-free (Ambion). Removal of DNA was checked by PCR. Prior to labeling, the concentration of total RNA was determined by measuring the A260 with a NanoDrop spectrophotometer (ND-1000).

treatment_protocol: Samples were treated with 1/5 volume ice-cold phenol:ethanol mixture (5:95) and transferred to a microcentrifuge tube which was immediately frozen in liquid nitrogen and stored at -80 °C.

value: Wildtype

value: ΔfabR


title: ΔfabR vs. Wildtype- color flip

description: ΔfabR vs. Wildtype, color flip


title: C26 dnFoxO 3

description: Whole transcript expression profiling


title: human CPE Braak-6 donor 5


title: human CPE Braak-6 donor 2


title: human CPE Braak-6 donor 4


title: sample306

value: normal


title: C26 dnFoxO 1

description: Whole transcript expression profiling


title: Spleen_FOdiet_PreInjection_fish7

hyb_protocol: Arrays were prehybridized at 42°C in Nexterion Oligo Prehyb Buffer (Schott Nexterion) for at least 2 hours. Arrays were washed at room temperature for with 0.1% SDS for 5 minutes, followed by 3 5-minute washes with water. Slides were dried by spinning them for 5 minutes at 200x g and kept at 42°C. LifterSlips were prepared by washing them sequentially with water, water, 70% ethanol and 100% ethanol and drying them using compressed air. For each array two labeled cDNAs were combined (one sample, one reference) and 2 μl of LNA blocker (Genisphere) and 40 μl of prewarmed 2x formamide-based hybridization buffer (Genisphere) was added. These samples were incubated at 80°C for 10 minutes and then kept at 42°C. Pre-warmed arrays were put in Corning hybridization chambers, LifterSlips were applied and the samples were loaded under the LifterSlips. Hybridizations were performed overnight for ~16 hours in a water bath at 42°C. After hybridization, arrays were washed at room temperature for 15 minutes with 2xSSC/0.2% SDS which was pre-warmed at 42°C. Next slides were washed  at room temperature for 15 minutes with 2xSSC, followed by 2 15-minute washes with 0.2xSSC. Slides were dried by spinning them for 5 minutes at 200x g.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 3 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene. Logratios of duplicate spots were averaged.


title: human CPE Braak-6 donor 3


title: human CPE Braak-3 donor 5

source_name: Braak 3 Alzheimer disease stage human choroid plexus epithelium

value: Braak 3 Alzheimer disease stage


title: Spleen_FOdiet_PreInjection_fish5


title: human CPE Braak-6 donor 1


title: sample305


title: sample307


title: human CPE Braak-3 donor 6


title: C26 EV 3

description: Whole transcript expression profiling

value: from atrophied C26-tumor bearing mice with AAV9-ev transfection

value: AAV9-ev transfection


title: sample304


title: Spleen_FOdiet_PreInjection_fish4


title: Spleen_FOdiet_PreInjection_fish3


title: sample303

value: tumor of stomach


title: C26 EV 2

description: Whole transcript expression profiling


title: sample302


title: Spleen_FOdiet_PreInjection_fish2


title: C26 EV 4

description: Whole transcript expression profiling


title: human CPE Braak-3 donor 4

value: choroid plexus epithelium

value: laser dissection microscopy


title: sample301


title: Control dnFoxO 4

description: Whole transcript expression profiling

value: from healthy, non-tumor bearing mice with AAV9 dominant negative FoxO transfection

value: from healthy, non-tumor bearing mice


title: sample300


title: Spleen_FOdiet_PreInjection_fish1

value: Spleen


title: C26 EV 1

description: Whole transcript expression profiling


title: Fertilized_Eggs_Female13_dyeswap_rep2

last: Rise

department: Department of Ocean Sciences

description:
dye-swap
female13_ds_2

data_processing: Signal intensity data was extracted from tiff images using Imagene v7.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 2 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene. Logratios of duplicate spots were averaged, and logratios for the dye-swap arrays were multiplied by -1 to give all logratios the same orientation.

source_name: Fertilized egg_high quality female

label_protocol: 5 μg of DNAse-treated and column-purified total RNA was labeled using the SuperScript Direct cDNA Labeling kit (Invitrogen) according to the manufacturer's protocol. Each RNA was labeled in 4 labeling reactions: two with AlexaFluor 647 and two with AlexaFluor 555.

growth_protocol: Eggs and sperm were harvested by stripping and collected in plastic collection beakers. Eggs were transferred into 1.5 L graduated glass ‘fertilization’ beakers by gentle pouring and sperm was added using a plastic transfer pipette. The egg and sperm mixture was gently stirred using the pipette and 100 ml UV-treated, filtered seawater was added and again stirred with the pipette. The mixture was left to incubate for 1 minute after which 500 ml UV-treated, filtered seawater was added and left to incubate for 5 minutes. After this incubation, the fertilization beaker was filled to 1.4 L mark with UV-treated, filtered seawater, placed on the bench in the walk-in cold room (6°C) and left undisturbed until the embryos reached first cleavage (2-cell stage), approximately 7 hours post-fertilization (hpf). At first cleavage stage, 7hpf embryo samples were collected from the 'fertilization beaker'. A sterile transfer pipette was used to fill three 1.5 ml RNase-free tubes with 0.25 ml of floating eggs from the ‘fertilization beaker’. Seawater was removed by pipette, and samples were flash frozen in liquid nitrogen and stored at -80 °C until RNA extraction.

extract_protocol: Per female, 3 batches of 0.25 ml of eggs were homogenized in TRIzol (Invitrogen) Bio-Gen PRO200 tissue homogenizer (PRO Scientific Inc., Oxford, CT) equipped with a 5 mm x 150 mm generator tip, at speed setting 2-3 for 30 seconds or until no solids were visible. The homogenate samples were passed through QIAshredder columns (Qiagen) following the manufacturer’s instructions. Total RNA was extracted from the TRIzol homogenate according to the manufacturers’ instructions, and the triplicate extractions were pooled for each individual female. Total RNA was treated with DNAse I (Qiagen) to remove genomic DNA, and then purified using the RNeasy MinElute Cleanup kit (Qiagen) according to the manufacturer’s instructions.

value: fertilized egg

tag: developmental stage

value: 7h post-fertilization (7 hpf, ~ 2-cell stage)

tag: egg harvested from

value: high quality female

source_name: Fertilized egg_low quality female

value: low quality female


title: human CPE Braak-3 donor 3

value: RPE/chodoid

value: healthy


title: human CPE Braak-3 donor 1


title: Control dnFoxO 3

description: Whole transcript expression profiling

value: tibialis anteior muscle

value: AAV9 dominant negative FoxO transfection


title: human CPE Braak-3 donor 7

value: Braak 3 Alzheimer disease stage


title: sample329

value: normal


title: Control dnFoxO 2

description: Whole transcript expression profiling


title: Fertilized_Eggs_Female13_rep2


title: human CPE Braak-3 donor 2


title: Fertilized_Eggs_Female13_dyeswap_rep1

description:
dye-swap
female13_ds_1


title: human CPE Braak-0 donor 7

source_name: healthy human choroid plexus epithelium (Braak 0)


title: sample299


title: sample298


title: human CPE Braak-0 donor 6

description: Biological CPE replicate 6 of 7 of healthy human choroid plexus


title: Fertilized_Eggs_Female13_rep1


title: Control EV 4

description: Whole transcript expression profiling

value: from healthy, non-tumor bearing mice with AAV9-ev transfection

value: AAV9-ev transfection


title: sample297

value: tumor of stomach


title: sample296


title: Fertilized_Eggs_Female12_dyeswap_rep2

description:
dye-swap
female12_ds_2


title: human CPE Braak-0 donor 5

description: Biological CPE replicate 5 of 7 of healthy human choroid plexus

value: choroid plexus epithelium

value: laser dissection microscopy


title: sample295


title: human CPE Braak-0 donor 4

description: Biological CPE replicate 4 of 7 of healthy human choroid plexus


title: sample294

value: long-lived individuals


title: sample293


title: Control EV 2

description: Whole transcript expression profiling

value: from healthy, non-tumor bearing mice


title: human CPE Braak-0 donor 3

description: Biological CPE replicate 3 of 7 of healthy human choroid plexus