title: T_67 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589752


title: T_680

status: Public on Jun 19 2015

type: RNA

city: Paris

first: Tatiana

last: Popova

address: 26, rue d'Ulm

country: France

institute: Institute Curie

description: Gene expression data for invasive breast carcinoma

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Data were analyzed using standard AffyCDF or Brainarray HGU133Plus2_Hs_ENTREZG version 13 custom chipset definition file. Data were normalized using  Brainarray.
Gene summarized expression value obtained using Brainarray CDF and software

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast tumor sample

label_protocol: Following RNA quality and quantity control, 2 Âµg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.

growth_protocol: Tumor samples were obtained from patients treated at the hospital of Institut Curie (Biological Resource Center, Paris, France). Healthy samples were obtained from mammary plastic surgery. Cell lines were grown from the American Type Culture Collection (ATCC),

extract_protocol: Total RNA was extracted and purified from frozen tumor samples using the RNeasy Mini Kit (Qiagen) followed by the RNA clean up kit (Macherey Nagel), according to manufacturer instructions.

treatment_protocol: No

tag: gender

value: female

tag: tissue

value: invasive breast carcinoma sample

tag: molecular subtype

value: luminal


title: T_61 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589747


title: T_62 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589748


title: T_669


title: T_575

value: TNBC


title: T_56 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589745


title: T_546


title: T_570


title: T_567


title: T_580


title: T_60 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589772


title: T_540


title: T_576


title: T_577


title: T_671


title: T_542


title: T_545


title: T_561


title: T_537


title: T_533


title: T_550


title: T_532


title: T_58 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589746


title: T_55 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589743


title: T_526


title: T_556


title: T_571


title: T_538


title: T_528


title: T_523


title: T_524


title: T_530


title: T_522


title: T_535


title: T_520


title: T_512


title: T_518


title: T_511


title: T_515


title: T_510


title: T_514


title: T_513


title: T_51


title: T_509


title: T_500


title: T_507


title: T_503


title: T_502


title: T_504


title: T_519


title: T_48 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589740


title: T_46 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589739


title: T_44 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589737


title: T_416


title: T_45 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589738


title: T_41 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589733


title: T_409


title: T_49 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589741


title: T_516


title: T_501


title: T_506


title: T_417


title: T_50 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589742


title: T_39 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589732


title: T_386


title: T_383 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589704


title: T_389_dup


title: T_389


title: T_376


title: T_380 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589708


title: T_381 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589643


title: T_375 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589632


title: T_387

description: Gene expression data for invasive breast carcinoma


title: T_372


title: T_361 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589696


title: T_349 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589656


title: T_343 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589639


title: T_370


title: T_359 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589694


title: T_35 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589727


title: T_347 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589648


title: T_333 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589678


title: T_328 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589645


title: T_324


title: T_342 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589631


title: T_340 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589681


title: T_33 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589725


title: T_327 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589662


title: T_326 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589654


title: T_363 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589699


title: T_340_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589682


title: T_323_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589626


title: T_320 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589620


title: T_343_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589640


title: T_317 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589689


title: T_323

description: Gene expression data for invasive breast carcinoma


title: T_316_dup


title: T_317_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589690


title: T_32 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589723


title: T_34 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589726


title: T_316


title: T_315 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589695


title: Neuroblastoma_14_Relapse_CGH

type: genomic

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

country: Germany

institute: University Hospital Essen

description: Relapse

hyb_protocol: Labelled DNA were hybridized to oligonucleotide microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNA (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Arrays were scanned by using an Agilent G2567AA Scanner follwowing the manufacturer's protocol (Agilent Technologies).

data_processing: The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files (LogRatio column) were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies). The circular binary segmentation algorithm was applied. Ref: PMID:17234643.  Background normalization was performed using snapCGH (method "minimum").  The  normalized data  are located on the series record and contain the normalized log2 ratio Cy3/Cy5 values.

molecule: genomic DNA

source_name: Promega Reference DNA

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2 ug of sample and reference genomic DNAs (for reference were used Human Genomic DNA: male Cat G1471, female Cat G1521, Promega, Madison, WI) were separately digested with AluI/RsaI restriction enzyme mix (Promega). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (ThermoScientific) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was isolated using the DNA-Isolation Kit (Gentra) according to the manufacturer's protocol. A pool of normal male or female DNA (Promega) was used as reference.

tag: control type

value: Reference DNA

source_name: Relapse

tag: diagnosis

value: neuroblastoma


title: T_314 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589664


title: Neuroblastoma_14_Tumour_CGH

description: Tumour

source_name: Tumour


title: T_310


title: T_311 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589627


title: T_311_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589628


title: T_314_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589665


title: T_312 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589636


title: IntNorm_Cy3_G.M._MDGL_2_1

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia, and INCLIVA

description: Gene expression

hyb_protocol: The labeled cRNA was hybridized to the Agilent SurePrint G3 Rat GE 8x60K Microarray according to the manufacturer's protocol.

scan_protocol: The arrays were washed, and scanned on an Agilent G2565CA microarray scanner at 100% PMT and 3 mm resolution

data_processing: The intensity data was extracted using the Feature Extraction Software (Agilent).

organism: Rattus norvegicus

label_protocol: 100 ng of total RNA was labeled by using Low Input Quick Amp Labeling kit (Agilent) following manufacturer instructions. Briefly, the mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA. cDNAwas then in vitro transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labeled cRNA

growth_protocol: The cells were grown in NM10 (high glucose DMEM supplemented with 10% fetal bovine serum), and cultured for one week at 37C, 5% CO2

extract_protocol: RNA was extracted using the QiagenRNeasy RNA extraction kit according to the manufacturer’s instructions

treatment_protocol: OPCs were treated with CSF diluted at a 1:1 dilution in ODM supplemented with bFGF(20 ng/mL) and PDGF-AA (10 ng/mL).

tag: cell type

value: OPCs treated with MS CSF

tag: gender (ms csf)

value: Female

tag: age (ms csf)

tag: edss (ms csf)

tag: mean edss (ms csf)

tag: disease duration (yrs (ms csf))


title: T_313 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589659


title: Neuroblastoma_11_Relapse_CGH

description: Relapse


title: T_31 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589722


title: T_312_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589637


title: IntNorm_Cy3_EMPP_MSH_1_2

description: Gene expression


title: IntNorm_Cy3_EMPP_MTRB_1_4

description: Gene expression


title: IntNorm_Cy3_G.M._CSM_2_2

description: Gene expression


title: T_313_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589660


title: P14_blood

city: MADRID

first: LARA

last: RODRIGUEZ

address: PASEO DE LA CASTELLANA 261

department: GEF

institute: INGEMM

hyb_protocol: In situ hybridization on solid matrices was performed using the Cot-1 enzyme and incubated for 24 hours.

scan_protocol: Scanned on an Agilent G2505C Microarray scanner.

data_processing: Feature Extraction v.11.1. was used for data subtraction applying the algorithm DLRS (Log Ratio Spread Derivative). Then the extracted results are imported into the Agilent Genomic Workbench 7.0.4.0 and Agilent Cytogenomic 2.7.8.0 programs for image analysis. Aberration Detection Method 2 (ADM-2) algorithm was used for bioinformatic analysis and it set to  five consecutive oligos, the minimum number, to consider a change (CNV).

source_name: DNA blood sample from patient 14 (P14)

label_protocol: 1250 ng of total DNA (test/reference) were digested with Alu I and Rsa I enzymes. After that we proceeded to the enzyme-labeled using Random Primer and fluorophores Cy5-dUTP for test samples and Cy3-UTP for reference, using Agilent DNA labeling kit SureTag.

extract_protocol: DNA was isolated from peripheral blood and tumor samples following standard saline and phenol/chloroform procedures.

tag: age (months)

tag: Sex

value: Male


title: IntNorm_Cy3_G.M._AGM_1_3

description: Gene expression


title: P14_tumor

source_name: DNA tissue sample from patient 14 (P14)


title: IntNorm_Cy3_G.M._MMMP_2_4

description: Gene expression


title: IntNorm_Cy3_Control_ALEG_2_1

description: Gene expression


title: P13_tumor

source_name: DNA tissue sample from patient 13 (P13)


title: IntNorm_Cy3_EMPP_FFM_2_3

description: Gene expression


title: P12_tumor

source_name: DNA tissue sample from patient 12 (P12)


title: IntNorm_Cy3_Control_CPC_1_3

description: Gene expression


title: P11_tumor

source_name: DNA tissue sample from patient 11 (P11)


title: P12_blood

source_name: DNA blood sample from patient 12 (P12)


title: P13_blood

source_name: DNA blood sample from patient 13 (P13)


title: IntNorm_Cy3_Control_JGR_1_2

description: Gene expression


title: Neuroblastoma_9_Relapse_CGH

description: Relapse


title: T_308


title: P11_blood

source_name: DNA blood sample from patient 11 (P11)


title: T_302_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589685


title: Neuroblastoma_7_Relapse_CGH

description: Relapse


title: Neuroblastoma_7_Tumour_CGH

description: Tumour


title: Neuroblastoma_5_Relapse_CGH

description: Relapse


title: T_302


title: Neuroblastoma_5_Tumour_CGH

description: Tumour


title: Neuroblastoma_9_Tumour_CGH

description: Tumour


title: T_30 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589721


title: Neuroblastoma_2_Relapse_CGH

description: Relapse


title: T_29 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589720


title: T_299

description: Gene expression data for invasive breast carcinoma


title: UM-UC-6

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

description: SAMPLE 19

hyb_protocol: Following fragmentation,  cRNA were hybridized for 16 hr at 45C on the Affymetrix U133 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: Raw expression data from these cell lines were normalized using the R library Frozen Robust Multiarray Analysis (fRMA) method [Biostatistics 2010, 11:242-253]. We applied this method as described by the authors for multiple arrays. We read the raw data (CEL files) and used the Random effect model for preprocessing. This model let us combine data from different batches and same microarray platform for analysis. Further, to obtain a matrix of gene-level expression values we used the exprs function with parameters by default.

source_name: Bladder Cell Line_UM-UC-6

label_protocol: 500 ng of biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were cultured in RPMI supplemented with 10-20% FBS and were harvested at 70-90% confluence.

extract_protocol: RNA was isolated with Trizol according to the manufacturers instructions.

tag: cell line

value: urothelial bladder carcinoma


title: UM-UC-7

description: SAMPLE 20

source_name: Bladder Cell Line_UM-UC-7


title: Neuroblastoma_11_Tumour_CGH

description: Tumour


title: T_280


title: P09_blood

source_name: DNA blood sample from patient 9 (P09)


title: T_3


title: P10_blood

source_name: DNA blood sample from patient 10 (P10)


title: UM-UC-5

description: SAMPLE 18

source_name: Bladder Cell Line_UM-UC-5


title: P10_tumor

source_name: DNA tissue sample from patient 10 (P10)


title: P09_tumor

source_name: DNA tissue sample from patient 9 (P09)


title: UM-UC-12

description: SAMPLE 14

source_name: Bladder Cell Line_UM-UC-12


title: P06_tumor

source_name: DNA tissue sample from patient 6 (P06)


title: UM-UC-17

description: SAMPLE 16

source_name: Bladder Cell Line_UM-UC-17


title: UM-UC-15

description: SAMPLE 15

source_name: Bladder Cell Line_UM-UC-15


title: T_28 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589719

source_name: Breast tumor sample


title: Neuroblastoma_1_Relapse_CGH

description: Relapse

source_name: Promega Reference DNA

source_name: Relapse


title: UM-UC-11

description: SAMPLE 13

source_name: Bladder Cell Line_UM-UC-11


title: P08_blood

source_name: DNA blood sample from patient 8 (P08)


title: UM-UC-18

description: SAMPLE 17

source_name: Bladder Cell Line_UM-UC-18


title: P08_tumor

source_name: DNA tissue sample from patient 8 (P08)


title: Neuroblastoma_2_Tumour_CGH

description: Tumour

source_name: Tumour


title: Neuroblastoma_1_Tumour_CGH

description: Tumour


title: T_278_dup reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589668


title: UM-UC-10

description: SAMPLE 12

source_name: Bladder Cell Line_UM-UC-10


title: T_275 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589622


title: T_277 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589641


title: P05_blood

source_name: DNA blood sample from patient 5 (P05)


title: T_278 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589669


title: SW-800

description: SAMPLE 10

source_name: Bladder Cell Line_SW-800


title: P05_tumor

source_name: DNA tissue sample from patient 5 (P05)


title: P04_tumor

source_name: DNA tissue sample from patient 4 (P04)


title: SW-850

description: SAMPLE 11

source_name: Bladder Cell Line_SW-850


title: H3 unsorted cortex

city: Wako-shi

first: Junko

last: Ueda

state: Saitama-ken

address: Hirosawa 2-1

department: BSI

country: Japan

institute: RIKEN

description:
Sample 24
genomic DNA from frontal cortex of H3 (unsorted)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v3.2
Matrix signal intensities value definition: Unmethylated and methylated signal intensities.  Linked as supplementary file on Series record.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from FACS sorted cell nuclei by standard phenol-chloroform method.

tag: sorting (facs)

value: unsorted

value: liver

tag: individual


title: P04_blood

source_name: DNA blood sample from patient 4 (P04)


title: BC61

description: SAMPLE 8

source_name: Bladder Cell Line_BC61


title: LGW01 G600

description: SAMPLE 9

source_name: Bladder Cell Line_LGW01 G600


title: P02_tumor

source_name: DNA tissue sample from patient 2 (P02)


title: 97-7

description: SAMPLE 7

source_name: Bladder Cell Line_97-7


title: P01_tumor

source_name: DNA tissue sample from patient 1 (P01)


title: T_25 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589716

source_name: Breast tumor sample


title: H3 liver

description:
Sample 21
genomic DNA from liver of H3

value: frontal cortex (brain)


title: T_26 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589717


title: H2 unsorted cortex

description:
Sample 23
genomic DNA from frontal cortex of H2 (unsorted)


title: P02_blood

source_name: DNA blood sample from patient 2 (P02)


title: T_225


title: 97-24

description: SAMPLE 6

source_name: Bladder Cell Line_97-24


title: T_27 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589718


title: P01_blood

source_name: DNA blood sample from patient 1 (P01)


title: 97-18

description: SAMPLE 5

source_name: Bladder Cell Line_97-18


title: H2 liver

description:
Sample 20
genomic DNA from liver of H2


title: H1 unsorted cortex

description:
Sample 22
genomic DNA from frontal cortex of H1 (unsorted)


title: H1 liver

description:
Sample 19
genomic DNA from liver of H1


title: T_219


title: T_220


title: 97-1

description: SAMPLE 4

source_name: Bladder Cell Line_97-1


title: T_222


title: MCF10A eIF4E-silenced heavy polysome mRNA

city: New York

first: Robert

middle: J

last: Schneider

state: NY

address: 550 First Ave, MSB 238

department: Microbiology

country: USA

institute: NYU School of Medicine

hyb_protocol: 1 μg of total or polysomal RNA was converted to cRNA following the Affymetrix one-cycle protocol and hybridized to Affymetrix GeneChip Human Genome U133A 2.0 Array arrays according to the manufacturer’s recommendations for hybridization, fluidics processing, and scanning.

scan_protocol: Arrays were scanned using an HP Gene-array scanner

data_processing: Data analysis was conducted using MicroArray Suite Software from Affymetrix. To remove probe sets with insignificant differences between perfect match and mismatch data, which creates a more robust data set of greater clarity without a high level of background noise, discrimination values for each probe pair were calculated for low intensity ratios using Wilcoxon signed rank test to assess significance and data re-assigned as either changed or unchanged mRNAs. Data sets were compared using Expressionist Suite software. Significance of mRNAs were assessed using fold changes and the FDRs estimated based on t-tests.

source_name: eIF4E silenced heavy polysome RNA

label_protocol: Biotinylated cRNA prepared from 1 micgrogram of purified RNA using the Affymetrix label transcript kit

growth_protocol: MCF10A cells were obtained from ATCC and cultured in Ham’s F12/DMEM (Cellgro) supplemented with 5% horse serum (Gibco), 20 ng/ml EGF (Invitrogen), 100 ng/ml Cholera toxin (Calbiochem), 0.01 mg/ml bovine insulin (Gibco) and 500 ng/mL hydrocortisone (Sigma).

extract_protocol: Total RNA was purified as follows. Polysome-associated mRNA was isolated as follows. Polysome isolation was performed by sucrose gradietn fractionation.  Fractions 5 to 8 and fractions 9-16 were pooled to represent light and heavy polysomes, respectively.  RNA was isolated by extraction with phenol/chloroform and following chloroform extraction, precipitated overnight with isopropanol and NaOAc (pH 5.2) at -20°C. RNA was pelleted at 13,000g for 10 minutes at 4°C, washed with 70% ethanol and resuspended on 100 μl of nuclease-free water. RNA was then purified using RNAeasy mini-elute columns (QIAGEN). Total RNA was extracted using Trizol and purified through RNAeasy mini-elute columns. The RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer and Nanodrop ND-1000.

value: breast epithelial cell line


title: C1 NeuN negative

description:
Sample 16
genomic DNA from frontal cortex of C1 (NeuN negative)

organism: Pan troglodytes

value: NeuN-negative


title: MCF10A eIF4E-silenced light polysome mRNA

source_name: eIF4E silenced light polysome RNA


title: MCF10A eIF4E-silenced total polysome mRNA

source_name: eIF4E silenced total RNA


title: T_211


title: MCF10A non-silenced heavy polysome mRNA

source_name: non-silenced heavy polysome RNA


title: P03_blood

source_name: DNA blood sample from patient 3 (P03)


title: T_22 reanalysis

description: Gene expression data for invasive breast carcinoma: reanalysis GSM1589714


title: 639V

description: SAMPLE 1

source_name: Bladder Cell Line_639V


title: 96-1

description: SAMPLE 3

source_name: Bladder Cell Line_96-1


title: P03_tumor

source_name: DNA tissue sample from patient 3 (P03)


title: C2 NeuN negative

description:
Sample 17
genomic DNA from frontal cortex of C2 (NeuN negative)


title: C3 NeuN negative

description:
Sample 18
genomic DNA from frontal cortex of C3 (NeuN negative)


title: T_216


title: C3 NeuN positive

description:
Sample 15
genomic DNA from frontal cortex of C3 (NeuN positive)

value: NeuN-positive


title: P07_tumor

source_name: DNA tissue sample from patient 7 (P07)


title: C1 NeuN positive

description:
Sample 13
genomic DNA from frontal cortex of C1 (NeuN positive)


title: P07_blood

source_name: DNA blood sample from patient 7 (P07)


title: T_209

description: Gene expression data for invasive breast carcinoma


title: 92-1

description: SAMPLE 2

source_name: Bladder Cell Line_92-1


title: C2 NeuN positive

description:
Sample 14
genomic DNA from frontal cortex of C2 (NeuN positive)


title: T_208

source_name: Breast tumor sample


title: C3 liver

description:
Sample 12
genomic DNA from liver of C3


title: MCF10A non-silenced light polysome mRNA

source_name: non-silenced light polysome RNA


title: MCF10A non-silenced total mRNA

source_name: non-silenced total RNA


title: T_204


title: T_202


title: T_203


title: T_200


title: C2 liver

description:
Sample 11
genomic DNA from liver of C2


title: C3 unsorted cortex

description:
Sample 9
genomic DNA from frontal cortex of C3 (unsorted)


title: T_201


title: T_196


title: T_199


title: C1 unsorted cortex

description:
Sample 7
genomic DNA from frontal cortex of C1 (unsorted)


title: T_194


title: C2 unsorted cortex

description:
Sample 8
genomic DNA from frontal cortex of C2 (unsorted)


title: H3 NeuN negative

description:
Sample 6
genomic DNA from frontal cortex of H3 (NeuN negative)


title: C1 liver

description:
Sample 10
genomic DNA from liver of C1


title: T_192


title: H2 NeuN positive

description:
Sample 2
genomic DNA from frontal cortex of H2 (NeuN positive)


title: H3 NeuN positive

description:
Sample 3
genomic DNA from frontal cortex of H3 (NeuN positive)


title: H2 NeuN negative

description:
Sample 5
genomic DNA from frontal cortex of H2 (NeuN negative)


title: H1 NeuN negative

description:
Sample 4
genomic DNA from frontal cortex of H1 (NeuN negative)


title: T_205


title: P06_blood

source_name: DNA blood sample from patient 6 (P06)


title: H1 NeuN positive

description:
Sample 1
genomic DNA from frontal cortex of H1 (NeuN positive)


title: T_19


title: HeLa S3 RNA

city: Beijing

first: Yu-Xiang

last: Zhang

address: Fengtai-District,You-An-Men-Wai

department: Biochemistry

country: China

institute: Capital Medical University, China

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio

source_name: Human cell Line

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

extract_protocol: Total RNA was extracted from HeLa S3 cells with a ToTALLY RNA™ Total RNA Isolation Kit (Ambion)

value: HeLa S3 cells

value: cervix

value: adenocarcinoma

tag: morphology

value: epithelial

tag: growth properties

value: monolayer


title: salt 24 h, biological rep3

city: Athens

first: Eleni

last: Mavrogonatou

address: Patriarchou Grigoriou & Neapoleos

department: Institute of Biosciences and Applications

country: Greece

institute: NCSR "Demokritos"

description: Gene expression data from nucleus pulposus cells treated with salt for 24 h

hyb_protocol: Fragmented cRNA was hybridized to the GeneChip array during a 16-h incubation at 45oC. After hybridization, the array was washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using a GeneChip Scanner (Affymetrix)

data_processing: The primary analysis was performed using the Affymetrix Expression Console and PLIER algorithm

organism: Bos taurus

source_name: Nucleus pulposus intervertebral disc cells exposed to salt for 24 h

label_protocol: First-strand cDNA synthesis was performed from 2 μg of high quality RNA using an oligo(dT)-T7 primer, while biotinylated cRNA was generated by the GeneChip IVT Labeling Kit (Affymetrix)

growth_protocol: Cells were plated in DMEM supplemented with 10% FBS before the addition of salt for 5 or 24 h

extract_protocol: Total RNA was isolated with the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, including  an on-column DNase treatment (Qiagen) step to eliminate any contaminating genomic DNA

treatment_protocol: Cells were treated or not with a salt solution at a final osmolality of 500 mOsm/kg Η2Ο for 5 or 24 h before RNA extraction

tag: tissue

value: caudal intervertebral disc

tag: region

value: nucleus pulposus

tag: age

value: young calves


title: salt 24 h, biological rep2


title: T_780

tag: gender

value: female

value: invasive breast carcinoma sample

tag: molecular subtype

value: luminal


title: Neuroblastoma_9_Tumour_methylation

description: Differential methylation

hyb_protocol: DNA was fragmented, precipitated and resuspended in hybridisation buffer and subsequent steps performed according to the standard protocol supplied by the manufacturer

scan_protocol: BeadChips were coated and images on an Illumina BeadArray Reader.

data_processing:
Images were processed with BeadStudio software
Data were normalized by the Beta Mixture Quantile (BMIQ) method using the RnBeads analysis software package (Assenov et al., available at rnbeads.mpi-inf.mpg.de)
Unmethylated and methylated signal intensities are available on the series record.

label: Cy3, Cy5

source_name: Tumour

label_protocol: Bisulfite-converted DNA was used in a whole-genome amplification reaction and BeadArray protocols followed the manusfaturers instructions (Illumina)

extract_protocol: DNA was isolated using standard methods (Qiagen) and bisulfite converted using the EZ DNA Methylation Gold Kit (Zymo Research)

tag: diagnosis

value: neuroblastoma


title: genomic DNA from proton beam-treated MCF-7

city: Gyungkido

first: Byungtak

last: Kim

address: Siksadong

country: South Korea

institute: Dongguk University

description: SAMPLE 2

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

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
GenomeStudio 2011, R 3.0.2
[signals.txt] Unmethylated and methylated signal intensities

source_name: mammary gland, breast; derived from metastatic site: pleural effusion

label_protocol: Standard Illumina Protocol (Cy5 and Cy3)

growth_protocol: optional

extract_protocol: genomic DNA was extracted and purified from MCF-7 using using a ZR-Duet DNA/RNA MiniPrep (Zymo Research, Irvine, CA) according to standard instructions

treatment_protocol: optional

tag: treatment

value: proton beam


title: salt 24 h, biological rep1


title: salt 5 h, biological rep3

description: Gene expression data from nucleus pulposus cells treated with salt for 5 h

source_name: Nucleus pulposus intervertebral disc cells exposed to salt for 5 h


title: genomic DNA from MCF-7

description: SAMPLE 1

value: control


title: Neuroblastoma_9_Relapse_methylation

description: Differential methylation

source_name: Relapse


title: Neuroblastoma_4_Relapse_methylation

description: Differential methylation


title: salt 5 h, biological rep2


title: Neuroblastoma_2_Relapse_methylation

description: Differential methylation


title: Neuroblastoma_8_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_7_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_4_Tumour_methylation

description: Differential methylation


title: control cells, biological rep3

description: Gene expression data from untreated nucleus pulposus cells

source_name: Nucleus pulposus intervertebral disc cells


title: salt 5 h, biological rep1


title: Neuroblastoma_12_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_18_Relapse_methylation

description: Differential methylation


title: Neuroblastoma_15_Relapse_methylation

description: Differential methylation


title: Neuroblastoma_12_Relapse_methylation_R5

description: Differential methylation


title: Neuroblastoma_8_Relapse_methylation

description: Differential methylation


title: Neuroblastoma_5_Relapse_methylation

description: Differential methylation


title: RCC220sII

status: Public on Jun 18 2015

city: Houston

first: Kanishka

last: Sircar

state: TX

address: 1515 Holcombe Blvd., G1.3623

institute: MD Anderson Cancer Center

hyb_protocol: Illumina DASL Expression Chip Protocol

scan_protocol: Illumina Bead Array Reader DirectHyb Gene Expression

data_processing: There are 3 sets of raw data. “Data 1” contains batches 10, 11, 15 and 16. “Data 2” only contains batch 17. “Data 3” contains batches K04 and K05. “Data 1” was obtained by Illumina HumanHT-12_v3 and “Data 2” and “Data 2” were obtained by Illumina HumanHT-12_v4. We normalized data using “Data 1” and “Data 2” (“Quantile normalized Data1+Data2”). We also use all three data sets to normalize (“Quantile normalized All”). Since there are different number of probe sets between V3 and V4, we used common probes for normalization. The data were log 2 transformed and normalized using quantile normalization.

source_name: Renal Cell Carcinoma

label_protocol: Illumina DASL Protocol Inoculate PCR (one product labeled with fluorescent dye and the other is biotynylated

extract_protocol: Epicentre MasterPure Complete DNA and RNA Purification Kit

tag: sampletype

value: S

tag: data set

value: Data 3

tag: batch

tag: pretreatment

tag: chipversion

value: Illumina HumanHT-12_v4

tag: Stage

value: IV

tag: grade

value: Sarcomatoid

tag: flagged

value: FALSE


title: Neuroblastoma_13_Relapse_methylation

description: Differential methylation


title: control cells, biological rep2


title: Neuroblastoma_5_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_15_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_13_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_3_Relapse_methylation

description: Differential methylation


title: RCC220eII

value: E

value: Epithelioid


title: RCC120eII


title: RCC057sII

value: R

value: Rhabdoid


title: RCC057eII


title: control cells, biological rep1

value: caudal intervertebral disc

value: nucleus pulposus

value: young calves


title: Neuroblastoma_3_Tumour_methylation

description: Differential methylation


title: RCC051sII


title: RCC051eII


title: RCC517eII


title: Neuroblastoma_17_Relapse_methylation

description: Differential methylation


title: Neuroblastoma_17_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_2_Tumour_methylation

description: Differential methylation


title: RCC666s

value: III


title: RCC601sII


title: RCC501eII

value: Chemotherapy


title: RCC666e


title: Neuroblastoma_12_Relapse_methylation_R4

description: Differential methylation

value: neuroblastoma


title: Neuroblastoma_18_Tumour_methylation

description: Differential methylation


title: Neuroblastoma_12_Relapse_methylation_R3

description: Differential methylation


title: RCC519s


title: RCC519e


title: Neuroblastoma_7_Relapse_methylation

description: Differential methylation


title: RCC514sII


title: RCC518s


title: RCC504s

value: Sutent


title: RCC518e


title: RCC504e


title: RCC517s

value: S


title: RCC511e

value: Data 3


title: RCC517e

value: Illumina HumanHT-12_v4


title: RCC120sII

value: IV


title: RCC510e


title: RCC515s

value: Sarcomatoid


title: RCC511s

value: FALSE


title: RCC600s


title: RCC515e

value: E


title: RCC601e

value: Epithelioid


title: RCC514s


title: Neuroblastoma_12_Relapse_methylation_R2

description: Differential methylation


title: RCC514e


title: RCC503e


title: RCC601s

value: R


title: RCC512s


title: Neuroblastoma_12_Relapse_methylation_R1

description: Differential methylation


title: RCC512e


title: RCC600e


title: RCC502e


title: RCC513e


title: RCC503s


title: RCC501s


title: RCC513s


title: RCC501e


title: RCC500s


title: RCC500e


title: RCC516s


title: RCC516e


title: RCC510s


title: RCC502s


title: Neuroblastoma_11_Relapse_methylation

description: Differential methylation


title: Neuroblastoma_11_Tumour_methylation

description: Differential methylation


title: RCC186

value: E*

value: Data 2

value: I


title: RCC007


title: RCC185


title: RCC189


title: RCC236


title: RCC087


title: RCC011


title: RCC197


title: RCC238


title: RCC187


title: RCC274


title: RCC083

value: II


title: RCC288

value: III


title: RCC040


title: RCC198


title: RCC268


title: RCC234


title: RCC237


title: RCC285


title: RCC327


title: RCC332


title: Neuroblastoma_1_Relapse_methylation

description: Differential methylation


title: RCC039


title: Neuroblastoma_1_Tumour_methylation

description: Differential methylation


title: RCC259


title: RCC102


title: 412-primagraft_Vehicle treatment

city: Boston

first: Loretta

last: Li

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

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

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method using Brainarray cdf annotations (hta20hsensgcdf_18.0.0.cdf, version 18) as implemented in the BioConductor package affy (Gentleman et al., 2004). Ensemble IDs were converted to HUGO gene symbols using the biomaRt package and collapsed by their median. Cell line and primagraft data were profiled seperatly and therefore treated as different batches.

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

growth_protocol:
MHH-CALL4 cells were cultured in RPMI-1640 with 20% FBS, 1% penicillin-streptomycin, and 2mM L-alanyl-L-glutamine.
05-412, 05-440, and 05-537 CRLF2+ patient-derived xenografts were generated in NSG mice by tail vein injection.

extract_protocol: Total RNA was extracted using Trizol followed by purification on a Qiagen RNeasy column.

treatment_protocol:
MHH-CALL4 cells cultured at 1 x 10^6 cells/mL were treated with vehicle (DMSO), CHZ868 (500nM), dexamethasone (250nM), or CHZ868 + dexamethasone combination for 12 hours. Experiment was performed in triplicate.
Primary human xenografts 05-412, 05-440, and 05-537 were treated in vivo with vehicle, CHZ868 (30mg/kg/day), dexamethasone (1mg/kg/day), or CHZ868 + dexamethasone combination for three days and then sacrificed. Transcriptional profiling was performed on unselected splenocytes.

value: primary graft 05-412

value: Vehicle

tag: replicate

tag: cell type

value: splenocyte


title: 412-primagraft_DEX treatment

tag: tissue

value: DEX


title: 412-primagraft_CHZ + DEX treatment

value: CHZ + DEX


title: 440-primagraft_DEX treatment

value: primary graft 05-440


title: 440-primagraft_CHZ + DEX treatment


title: 537-primagraft_DEX treatment

value: primary graft 05-537


title: 537-primagraft_Vehicle treatment


title: 412-primagraft_CHZ treatment

value: CHZ


title: MHH-CALL4_CHZ + DEX treatment - replicate 1

tag: cell line


title: 440-primagraft_Vehicle treatment


title: 440-primagraft_CHZ treatment


title: MHH-CALL4_Vehicle treatment - replicate 2


title: 537-primagraft_CHZ + DEX treatment


title: MHH-CALL4_Vehicle treatment - replicate 3


title: Donor 105 S1P 4h

city: London

first: Grzegorz

last: Woszczek

state: London

address: 5th Floor, Tower Wing, Guy's Hospital

department: Division of Asthma, Allergy and Lung Biology

country: United Kingdom

institute: King's College London

hyb_protocol: Samples were processed with the Ambion WT Expression Kit (Applied Biosystems) according to the manufacturers’ instructions. Second cycle cDNA was fragmented, stained, and hybridized to the Affymetrix Human Exon 1.0 ST Arrays at 45°C for 17 hours using the Gene Chip WT Terminal Labelling and Hybridization Kit (Affymetrix).

scan_protocol: GeneChip fluidics station 450 (Affymetrix) was used for processing of the chips and fluorescent signals were detected with the GeneChip scanner 3000

data_processing: RMA processing and quantile normalisation was applied to GC and sequence corrected probe intensities after Median Polish gene level probeset summarisation using Partek Genomics Suite.

source_name: Airway smooth muscle cells

growth_protocol: Human airway smooth muscle cells were grown from bronchial biopsies by explant culture as previously described (Mahn K. et al. Proc Natl Acad Sci U S A 2009;106(26):10775-80).

extract_protocol: Total cellular RNA was isolated using the miRNeasy mini kit (Qiagen) and DNAase treated (Ambion).

treatment_protocol: Cultured human airway smooth muscle cells were serum starved for 18 hours before stimulation with sphingosine-1-phosphate or medium control for 4 hours.

value: Airway smooth muscle cells

tag: individual

value: Donor 105


title: MHH-CALL4_CHZ treatment - replicate 1


title: MHH-CALL4_Vehicle treatment - replicate 1


title: MHH-CALL4_CHZ treatment - replicate 3


title: MHH-CALL4_DEX treatment - replicate 2


title: MHH-CALL4_CHZ + DEX treatment - replicate 2


title: MHH-CALL4_DEX treatment - replicate 3


title: Transcriptional change of HLT013 compared to BL21

city: Seoul

first: Hyeon-Cheol

last: Lee

address: 136, Changgyeonggung-ro,Jongro-gu

department: Research center

institute: BPgene Co., Ltd.

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Escherichia coli BL21-D23_30K microarray (MYcroarray.com, USA). The arrays hybridized at 57oC for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GenoWiz 4.0 (Ocimumbiosolutions, India).

organism: Escherichia coli BL21

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 ug total RNA was mixed with WT primer mix and incubated at 65 oC for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70 oC for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: Samples of HLT013 and BL21(DE3) were taken at mid-log growth phase during batch fermentation.

extract_protocol: Total cellular RNA was extracted from mid-log phase cells with a QIAGEN RNEasy Mini Kit

tag: strain

value: Recombineered Escherichia coli BL21

tag: phenotype

value: Thymidine Producing strain


title: Donor 111 S1P 4h

label_protocol: Samples were processed with the Ambion WT Expression Kit (Applied Biosystems) according to the manufacturers’ instructions. Second cycle cDNA was fragmented, stained, and hybridized to the Affymetrix Human Exon 1.0 ST Arrays at 45°C for 17 hours using the Gene Chip WT Terminal Labelling and Hybridization Kit (Affymetrix).

value: Donor 111


title: Donor 105 control


title: MHH-CALL4_CHZ + DEX treatment - replicate 3


title: MHH-CALL4_CHZ treatment - replicate 2


title: 537-primagraft_CHZ treatment


title: MHH-CALL4_DEX treatment - replicate 1


title: Donor 116 S1P 4h

value: Donor 116


title: Donor 111 control


title: POMCMfn2KO 2_mouse_liver

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

description: Gene expression data from whole-liver of 6-week old POMCMfn2KO mouse

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.2.0.1515, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor on R language.

organism: Mus musculus

source_name: Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mice were maintained on a 12h-light/12h-dark cycle with free access to water and standard chow (2014; Teklad).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and the RNAeasy Mini kit (Qiagen).

treatment_protocol: Total RNA was extracted from whole-liver of 6-week old control and POMCMfn2KO mice.

tag: genotype

value: liver

tag: age (weeks)

value: mixed C57Bl/6J, FVB/N and 129


title: POMCMfn2KO 4_mouse_liver


title: POMCMfn2KO 5_mouse_liver


title: DNL4[EP10385]_1

city: Cambridge

first: Terry

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Slides were hybridized to custom Agilent tiling arrays and washed as per Agilent recommendations

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer's protocol

data_processing: Raw data was LOESS normalized using the Ringo package in R. The .bed files contain the normalized log2 ratio (Cy5/Cy3) representing test/reference

organism: Drosophila melanogaster

source_name: stage 13 egg chambers

label_protocol: DNA was labeled by random priming and purified with an Amicon Ultra 30K column (Millipore)

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media.

extract_protocol: Egg chambers were resupended in ChIP lysis buffer buffer (50mM HEPES/KOH pH 7.5, 140mM NaCl, 1mm EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate), dounced and sonicated in a Bioruptor 300 (Diagenode). Standard phenol/chloroform extraction followed by isopropanol precipitation was used to isolate total genomic DNA.

treatment_protocol: Ovaries were hand dissected from females fattened for 2 days on wet yeast in Grace’s media. Stage 13 egg chambers were isolated and transferred to Grace’s media on ice until 100 egg chambers were collected. Egg chambers were stored at -80ᵒC until all egg chambers from each genotype were collected.

tag: strain genotype/variation

tag: developmental stage

value: stage 13 egg chambers

source_name: Oregon R  0-2 hour embryonic diploid DNA

extract_protocol: Embryos were resupended in 1% SDS in TE, dounced and sonicated in a Bioruptor 300 (Diagenode). Standard phenol/chloroform extraction followed by isopropanol precipitation was used to isolate total genomic DNA.

value: Oregon R

tag: genotype/variation

value: wild type

value: 0-2 hour embryos


title: POMCMfn2KO 1_mouse_liver


title: Control 2_mouse_liver

description: Gene expression data from whole-liver of 6-week old control mouse

value: WT


title: DNL4[EP10385]_2


title: Donor 116 control


title: Control 1_mouse_liver


title: d18.5_placenta_restricted_267

city: Columbia

first: Laura

middle: Clamon

last: Schulz

state: MO

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: pooled from two placentas

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K Whole Mouse Genome microarrays (Design ID 026655, Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing:
Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).
Intensity values are normalized to the 75th percentile intensity of each array.

source_name: d18.5 placenta, mom 267

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

extract_protocol: Placentas were halved and frozen in Trireagent (Sigma).  After phase separation, the aqueous phase was applied to RNEasy columns (Qiagen) according to manufacturer's protocol.  Total RNA from two placentas per mother were pooled.

treatment_protocol: Mice were mated, and on pregnancy day 1.5, randomized to (1) ad libitum fed (control); (2) restricted to 50% of previous food consumption (restricted);  Mice were returned to ad libitum feed on d11.5, sacrificed on d18.5 and placentas were collected.

value: placenta

tag: maternal treatment group

value: restricted

tag: pregnancy stage


title: Control 3_mouse_liver


title: POMCMfn2KO 3_mouse_liver


title: d18.5_placenta_control_245

description: pooled from two placentas

source_name: d18.5 placenta, mom 245

value: control


title: HFD_wt_flox-rep3

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

country: Australia

institute: Garvan Institute of Medical Research

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific wildype mice, replicate 3

hyb_protocol: Amplified cRNAs were hybridized on Mouse Gene 2.0 ST Arrays (Affymetrix, Santa Clara, CA, USA) according with manufacturer’s procedures. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The arrays were processed using the oligo and pd.mogene.2.0.st packages, and normalized by Robust Multi-array Average (RMA) method and annotated by the mogene20sttranscriptcluster.db package. The limma package was applied to identify differentially expressed genes.

source_name: pancreatic islets isolated from 16 week old mice (C57BL/6 background)

label_protocol: Biotinylated cRNAs were prepared according to the Ambion WT kit (Life Technologies, CA, USA) protocol from 250 ng total RNA

extract_protocol: Total RNA from isolated pancreatic islets of 16 week old male and female animals was extracted using Qiagen RNeasy RNA extration kit.

treatment_protocol: Standard animal house treatment (chow diet) or 8 weeks of high-fat feeding (45%kcal fat) from 8-16 weeks of age

value: pancreatic islets

tag: treatment

value: HFD

value: floxed littermates


title: d18.5_placenta_control_264

description: pooled from two placentas

source_name: d18.5 placenta, mom 264


title: HFD_wt_flox-rep2

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific wildype mice, replicate 2


title: d18.5_placenta_control_249

description: pooled from two placentas

source_name: d18.5 placenta, mom 249


title: Chow_wt_flox-rep3

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific wildype mice, replicate 3

value: Chow


title: d18.5_placenta_restricted_265

description: pooled from two placentas

source_name: d18.5 placenta, mom 265


title: d18.5_placenta_restricted_253

description: pooled from two placentas

source_name: d18.5 placenta, mom 253


title: chk2/CyO_2


title: HFD_wt_flox-rep1

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific wildype mice, replicate 1


title: chk2/CyO_1


title: d18.5_placenta_control_172

description: pooled from two placentas

source_name: d18.5 placenta, mom 172


title: RCC214

tag: sampletype

value: E*

tag: data set

value: Data 1

tag: batch

tag: pretreatment

tag: chipversion

value: Illumina HumanHT-12_v3

tag: Stage

value: IV

tag: grade

value: FALSE


title: d18.5_placenta_restricted_164

description: pooled from two placentas

source_name: d18.5 placenta,  mom 164

tag: tissue


title: d18.5_placenta_control_262

description: pooled from two placentas

source_name: d18.5 placenta, mom 262


title: Chow_bTRAF3-rep3

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific TRAF3 knockout mice (TRAF3 RIP Cre), replicate 3

value: RIPCre; TRAF3loxP/loxP


title: Chow_bTRAF3-rep1

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific TRAF3 knockout mice (TRAF3 RIP Cre), replicate 1


title: Chow_wt_flox-rep2

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific wildype mice, replicate 2


title: d18.5_placenta_restricted_240

description: pooled from two placentas

source_name: d18.5 placenta, mom 240


title: Chow_bTRAF3-rep2

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific TRAF3 knockout mice (TRAF3 RIP Cre), replicate 2


title: brca2[KO]_2

value: stage 13 egg chambers

tag: strain

value: Oregon R


title: Chow_wt_flox-rep1

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific wildype mice, replicate 1

tag: genotype


title: RCC211

tag: flagged


title: brca2[KO]_1

tag: strain genotype/variation

value: wild type

value: 0-2 hour embryos


title: RCC210

value: III


title: HFD_bTRAF3-rep2

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific TRAF3 knockout mice (TRAF3 RIP Cre), replicate 2


title: HFD_bTRAF3-rep3

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific TRAF3 knockout mice (TRAF3 RIP Cre), replicate 3


title: RCC205


title: ligIV[169]_3

tag: developmental stage


title: spnA[093]_3

tag: genotype/variation


title: RCC195


title: spnA[093]_2


title: RCC178


title: RCC202


title: RCC192


title: chk2[P6]_3


title: Chow_bTRAF2-rep3

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific TRAF2 knockout mice (TRAF2 RIP Cre), replicate 3

value: RIPCre; TRAF2loxP/loxP


title: ligIV[169]_1


title: RCC175


title: RCC101


title: chk2[P6]_1


title: HFD_bTRAF3-rep1

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific TRAF3 knockout mice (TRAF3 RIP Cre), replicate 1


title: breast cancer_control [Patient 32]

city: Salzburg

first: Franz

last: Zehentmayr

address: Müllner Hauptstraße

country: Austria

institute: RadArt

hyb_protocol: hybridization time was 20h at 55° with 20rpm following cbc™ standard procedures

scan_protocol: Scanning and image acquisition followed cbc™ standard procedures; Scanner: Latest High-Resolution Microarray Scanner GS2505_C

data_processing:
The scanned images were analyzed with the latest Agilent Feature Extraction software (10.7.3.1) according to cbc™ standard procedures. To detect outliers in the samples, Hampel's rule was applied. For this purpose  all correlation coefficients were transformed using the Fisher transformation and then applied the robust test for detecting outliers. The RMA (robust multi-arra average) was used for normalization.
The RMA algorithm calculates an own background, normalizes by quantile and summarizes the data. The first step is a background correction by fitting a normal and exponential convolution model to the vector of observed intensities. The normal part represents the background, the exponential part represents the signal intensities. After background subtraction the arrays are normalized by quantile across a set of hybridizations at the probe level. Finally an estimate of the microRNA gene signal is obtained by fitting a linear model to log 2 transformed intensities. This procedure was carried out by cbcT.

source_name: patients without local relapse after breast conserving therapy in early stage breast cancer

label_protocol: 100 ng total RNA input per array, for labeling Agilent's microRNA Complete labeling and Hybridization Kit was used; the protocol followed cbc™ standard procedures

extract_protocol: slices from FFPE samples were sent to the comprehensive biomarker center (cbc™) in Heidelberg, RNA was extracted according to cbc standard procedures

treatment_protocol: breast cancer tissue from surgical procedure

tag: patient id

value: Patient 32

tag: gender

value: female

tag: tissue type

value: primary tumor

tag: sample type

value: FFPE material


title: breast cancer_relapse [Patient 31]

source_name: patients with local relapse after breast conserving therapy in early stage breast cancer

value: Patient 31


title: RCC081

source_name: Renal Cell Carcinoma

tag: sampletype

value: E*

tag: data set


title: breast cancer_control [Patient 30]

value: Patient 30


title: H2Av[ΔCT]_3

value: P{His2Av[ΔCT]}; His2Av[810]/TM6B


title: RCC043

value: Data 1

tag: batch

tag: pretreatment

value: Illumina HumanHT-12_v3

value: IV


title: Chow_bTRAF2-rep2

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific TRAF2 knockout mice (TRAF2 RIP Cre), replicate 2

value: pancreatic islets

tag: treatment

value: Chow


title: ligIV[169]_2

value: stage 13 egg chambers

value: Oregon R

value: wild type


title: breast cancer_relapse [Patient 29]

value: Patient 29


title: RCC032

tag: chipversion

tag: Stage

tag: grade

value: FALSE


title: H2Av[ΔCT]_2

tag: strain

value: 0-2 hour embryos


title: Chow_bTRAF2-rep1

description: Total RNA from pancreatic islets isolated from 16-week old chow-diet fed beta-cell specific TRAF2 knockout mice (TRAF2 RIP Cre), replicate 1

tag: tissue

tag: genotype

value: RIPCre; TRAF2loxP/loxP


title: mus101[D1]_3

tag: strain genotype/variation

tag: developmental stage


title: breast cancer_control [Patient 28]

tag: patient id

value: Patient 28

value: female

value: primary tumor

value: FFPE material


title: RCC029

value: E*

tag: flagged


title: HFD_bTRAF2-rep1

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific TRAF2 knockout mice (TRAF2 RIP Cre), replicate 1

value: HFD


title: breast cancer_relapse [Patient 27]

value: Patient 27

tag: gender

tag: tissue type


title: brca2[KO]_3

tag: genotype/variation


title: RCC028

tag: sampletype

tag: data set

value: Data 1

value: Illumina HumanHT-12_v3

value: IV


title: K02_28S

hyb_protocol: Illumina Infinium HD FFPE Protocol

scan_protocol: Illumina iScan Infinium NXT

data_processing: Log R Ratio for copy number were obtained using Illumina GenomeStudio 2011.1 software.

label_protocol: Illumina Infinium HD FFPE Protocol

value: S

tag: ChIP

value: Sarcomatoid

tag: pretreatment

tag: position on chip


title: breast cancer_control [Patient 26]

value: Patient 26

tag: sample type


title: K02_27E

value: E

tag: Stage

tag: grade

value: Epithelioid


title: RCC025

tag: batch

tag: chipversion

value: FALSE


title: chk1[1]_3

tag: strain genotype/variation

value: stage 13 egg chambers

tag: strain

value: Oregon R

value: wild type

value: 0-2 hour embryos


title: breast cancer_relapse [Patient 25]

tag: patient id

value: Patient 25

value: female

value: primary tumor

value: FFPE material


title: RCC177

value: E*

value: Data 1

value: I

tag: flagged


title: K02_26S

value: S

value: III


title: K02_25E


title: RCC003

value: Illumina HumanHT-12_v3


title: K01_03N

value: N

value: Normal

value: Chemotherapy


title: breast cancer_relapse [Patient 23]

value: Patient 23

tag: gender


title: K03_31N


title: RCC181

value: FALSE


title: HFD_bTRAF2-rep2

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific TRAF2 knockout mice (TRAF2 RIP Cre), replicate 2

tag: tissue

value: pancreatic islets

tag: treatment

value: HFD

tag: genotype

value: RIPCre; TRAF2loxP/loxP


title: K02_22S

tag: sampletype

value: IV

value: Sarcomatoid


title: breast cancer_control [Patient 22]

value: Patient 22

value: female

tag: tissue type

value: primary tumor

value: FFPE material


title: RCC240

value: E*

tag: data set

value: Data 1

tag: pretreatment

value: I


title: HFD_bTRAF2-rep3

description: Total RNA from pancreatic islets isolated from 16-week old high-fat diet fed beta-cell specific TRAF2 knockout mice (TRAF2 RIP Cre), replicate 3


title: RCC239

value: Illumina HumanHT-12_v3


title: RCC183


title: K02_20S

value: S

tag: ChIP

tag: position on chip


title: K02_21E

value: E

tag: Stage

tag: grade

value: Epithelioid


title: breast cancer_control [Patient 20]

value: Patient 20

tag: sample type


title: breast cancer_relapse [Patient 21]

value: Patient 21


title: K03_33N

value: N

value: Normal


title: breast cancer_control [Patient 24]

value: Patient 24


title: K02_19E

value: IV

value: Chemotherapy


title: RCC171

tag: batch

tag: chipversion

value: II

value: FALSE


title: RCC230

value: III


title: K03_32N


title: RCC233

value: E*


title: K02_16S

value: Sarcomatoid


title: breast cancer_relapse [Patient 15]

tag: patient id

value: Patient 15

value: female

value: primary tumor

value: FFPE material


title: breast cancer_relapse [Patient 17]

value: Patient 17


title: breast cancer_control [Patient 18]

value: Patient 18


title: breast cancer_relapse [Patient 19]

value: Patient 19


title: RCC013

value: Data 1

value: Illumina HumanHT-12_v3

value: I

tag: flagged


title: breast cancer_control [Patient 16]

value: Patient 16

tag: gender


title: RCC229


title: K02_15E

value: E

value: IV

value: Epithelioid


title: K02_14S

value: S


title: K02_13E


title: RCC015

value: E*

value: III

value: FALSE


title: RCC188


title: RCC199


title: breast cancer_control [Patient 14]

value: Patient 14

value: female


title: breast cancer_control [Patient 12]

value: Patient 12

value: primary tumor

value: FFPE material


title: RCC232


title: RCC228


title: K02_10S

value: Sarcomatoid


title: RCC120s

value: Data 1


title: K02_09E


title: breast cancer_control [Patient 10]

value: Patient 10


title: breast cancer_relapse [Patient 11]

value: Patient 11


title: RCC220s

value: Illumina HumanHT-12_v3


title: breast cancer_control [Patient 8]

value: Patient 8


title: breast cancer_relapse [Patient 9]

value: Patient 9


title: RCC120e

value: E

value: IV

value: Epithelioid


title: K01_02S

value: S


title: breast cancer_relapse [Patient 13]

value: Patient 13


title: breast cancer_relapse [Patient 7]

value: Patient 7


title: RCC109s

value: II

value: FALSE


title: breast cancer_control [Patient 6]

value: Patient 6

value: female

value: primary tumor


title: K02_06S

value: Sarcomatoid


title: K02_12S

value: III


title: breast cancer_control [Patient 4]

value: Patient 4

value: FFPE material


title: breast cancer_relapse [Patient 5]

value: Patient 5


title: K02_11E


title: RCC109e

value: Data 1

value: Illumina HumanHT-12_v3

value: TRUE


title: RCC057s

value: R

value: IV

value: Rhabdoid


title: RCC057e

value: E

value: Epithelioid


title: K02_05E


title: RCC055s

value: S


title: RCC055e

value: FALSE


title: RCC114s


title: breast cancer_relapse [Patient 3]

value: Patient 3

value: female


title: breast cancer_control [Patient 2]

value: Patient 2

value: primary tumor


title: RCC112s

value: Sarcomatoid


title: RCC220e


title: K01_01N

value: N

value: Normal


title: RCC112e

value: Data 1


title: RCC115s

value: Illumina HumanHT-12_v3


title: breast cancer_relapse [Patient 1]

value: Patient 1

value: FFPE material


title: RCC111s

value: IV


title: RCC063e


title: RCC115e


title: RCC111e

value: TRUE


title: RCC063s


title: RCC116s


title: RCC116e

value: E


title: RCC218s


title: RCC218e

value: Epithelioid


title: ILLUM RNA

value: control


title: RCC119s

value: S


title: RCC053s

value: FALSE


title: RCC053e


title: RCC126s

value: Chemotherapy


title: RCC126e


title: RCC051s


title: RCC113e

value: III


title: RCC051e


title: RCC061s


title: RCC123s


title: RCC061e


title: RCC114e


title: RCC123e


title: RCC054s


title: RCC225s


title: mus101[D1]_1

tag: strain genotype/variation

tag: developmental stage

value: stage 13 egg chambers

tag: strain

value: Oregon R

tag: genotype/variation

value: wild type

value: 0-2 hour embryos


title: RCC226e

tag: sampletype

value: Data 1

value: Sutent


title: RCC226s

tag: data set

value: Illumina HumanHT-12_v3

value: Sarcomatoid


title: RCC225e

tag: pretreatment

value: IV


title: RCC054e


title: RCC056e


title: RCC122s


title: RCC113s


title: RCC122e


title: chk2[P6]_2


title: spnA[093]_1


title: chk1[1]_2


title: chk1[1]_1


title: H2Av[ΔCT]_1

value: P{His2Av[ΔCT]}; His2Av[810]/TM6B


title: RCC056s


title: mus101[D1]_2


title: normal5

status: Public on Jun 17 2015

city: Changsha

first: Jun

last: Zhou

state: Hunan

address: 172 Tongzipo Road

department: Central South University

institute: urine

hyb_protocol: Equilibrate water bath or heat block to 100°C. Resuspend the dried sample in 17 μL of nuclease-free water when the Spike-In solution is used and 18 μL. Add 1.0 μL of the Hyb Spike-In solution (3rd Dilution) to each sample.Add 4.5 μL of the 10X GE Blocking Agent to each sample.Add 22.5 μL of 2X Hi-RPM Hybridization Buffer to each sample for a total of 45 μL.Mix well but gently on a vortex mixer. hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 1x44k 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (V.10.7) (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Pleaes note that the complete data matrix including control probesets (2,028 data rows) is linked to Series records.

source_name: normal control

label_protocol: Microarray experiments were conducted according to the manufacturer's instructions. Briefly, the miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (100 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays. Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

extract_protocol: The mirVana miRNA isolation kit (Ambion Inc, Austin, TX) was used for theextraction of total RNA from urine according to the manufacturer’s protocol. For each subject, 400 uL of urine was used for miRNA extraction.

treatment_protocol: urine was collected and directly stored -80℃.

tag: subject gender

value: female

tag: subject group

value: healthy control

tag: tissue

value: urine


title: tumor1

source_name: ovarian cancer

value: epithelial ovarian cancer patients


title: tumor5


title: tumor2


title: tumor4


title: normal3


title: normal2


title: normal4


title: normal1


title: Extensor digitorum longus 251955510008_0007_Cy5

city: Helsinki

first: Peter

last: Hackman

address: Haartmaninkatu 8

department: Dpt. of Medical Genetics

country: Finland

institute: Folkhälsan research Center/University of Helsinki

hyb_protocol: For the hybridisations, the samples were prepared according to the instructions, and reagents were provided by Agilent Technologies as follows: 5 µl of 10X blocking agent was added to 300 nanograms of each of the labelled RNA samples and diluted with nuclease-free water to 24 µl. One microliter of 25X fragmentation buffer was added, and the mixture was incubated at 60 ºC for 30 min. Twenty-five microliters of 2X GEx Hybridisation Buffer HI-RPM were added, and the mixture was centrifuged for 1 min at 13,000 rpm. Forty microliters of the mixture were hybridised on the microarray for 17 h in a +65 ºC hybridisation oven. The microchip was washed with Gene Expression Wash Buffer 1 and 2 at 37 ºC, dried, and scanned with an Axon Scanner (Molecular Devices, Sunnyvale, CA, USA), using a 5-µm pixel resolution.

scan_protocol: Image analysis was done using the GenePixPro 6.1 software (Molecular Devices)

data_processing: The local background of the spot signal was subtracted using the “normexp” method with an offset value of 50, and housekeeping genes-based loess normalisation (composite loess) was applied to logarithmic intensity ratios using the R software [40] with the Limma package [41]. The median value was calculated from replicate probes

label_protocol: The RNA samples were amplified with the Ambion Amino Allyl MessageAmpTM aRNA Amplification kit (#AM1753) (described in [39]). The aRNA was labelled using Cy3, Cy5 Mono-Reactive Dye Pack colours (GE Healthcare, Freiburg, Germany) and Alexa 488 Reactive Dye Decapack (Invitrogen). Six micrograms of aRNA were used in the dye coupling reaction, which was performed according to the instructions from the manufacturer (Life Technologies, Carlsbad, CA, USA).

extract_protocol: Total RNA was extracted from the selected samples by the Trizol reagent method according to the instructions of the manufacturer (Invitrogen Life Technologies, Burlington, Ontario, Canada). The quality of the obtained RNA was checked with BioAnalyzer equipment using the RNA 6000 Nano Assay kit (Agilent Technologies, Waldbronn, Germany).

value: Extensor digitorum longus


title: Tibialis anterior 251955510008_0007_Cy3

value: Tibialis anterior


title: tumor3


title: Peroneus longus 251955510008_0006_Cy3

value: Peroneus longus


title: Soleus 251955510008_0008_Cy5

value: Soleus


title: Tibialis posterior 251955510008_0004_Cy3

value: Tibialis posterior


title: Flexor hallucis longus 251955510008_0005_Cy5

value: Flexor hallucis longus


title: Peroneus longus 251955510008_0002_Cy5


title: Tibialis anterior 251955510008_0003_Cy5


title: Gracilis 251955510008_0001_Cy5

value: Gracilis


title: Gastrocnemius lateralis 251955510008_0004_Cy5

value: Gastrocnemius lateralis


title: Vastus medialis 251955510008_0001_Cy3

value: Vastus medialis


title: Tibialis posterior 251955510008_0006_Cy5


title: Gastrocnemius medialis 251955510008_0005_Cy3

value: Gastrocnemius medialis


title: Vastus interior 251955510008_0002_Cy3

value: Vastus interior


title: Vastus lateralis 251955510006_0008_Alexa 488

label: Alexa 488

source_name: Alexa 488

value: Vastus lateralis


title: Vastus lateralis 251955510006_0007_Alexa 488


title: Disease-BA 2

city: Philadelphia

first: Randolph

last: Matthews

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: cy3, cy5

source_name: Disease-BA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver explants using Qiagen DNeasy Kit according to standard instructions and Bisulphite converted using Qiagen Epitect Kit according to standard instructions

value: Biliary atresia

tag: subject status

value: liver explant


title: Gastrocnemius lateralis 251955510006_0008_Cy5


title: Flexor digitorum longus 251955510006_0008_Cy3

value: Flexor digitorum longus


title: Disease-BA 4


title: Gastrocnemius lateralis 251955510006_0007_Cy5


title: Extensor digitorum longus 251955510008_0003_Cy3


title: Disease Control-DC 3

source_name: Disease Control-DC

value: Disease Control

value: Acute Liver Failure


title: Disease-BA 1


title: Flexor digitorum longus 251955510006_0007_Cy3


title: Disease-BA 3


title: Disease-BA 5


title: Nondisease Control-NDC 2

source_name: Nondisease Control-NDC

value: Nondisease Control

value: Urea cycle defect


title: Disease-BA 6


title: Disease Control-DC 2

value: Alagille Syndrome


title: Gastrocnemius medialis 251955510006_0004_Alexa 488


title: Soleus 251955510006_0005_Cy3

value: Soleus


title: Flexor hallucis longus 251955510006_0004_Cy5


title: Soleus 251955510006_0001_Alexa 488


title: Peroneus longus 251955510006_0002_Cy3

value: Peroneus longus


title: Gastrocnemius medialis 251955510006_0002_Alexa 488


title: Tibialis anterior 251955510006_0002_Cy5

value: Tibialis anterior


title: Tibialis posterior 251955510006_0005_Cy5

value: Tibialis posterior


title: Extensor hallucis longus 251955510006_0003_Cy3

value: Extensor hallucis longus


title: Tibialis posterior 251955510006_0003_Alexa 488


title: Extensor digitorum longus 251955510006_0003_Cy5

value: Extensor digitorum longus


title: Semitendinosus 251955510006_0001_Cy3

value: Semitendinosus


title: Flexor hallucis longus 251955510006_0006_Alexa 488

value: Flexor hallucis longus


title: Extensor digitorum longus 251955510006_0006_Cy5


title: Semimembranosus 251955510006_0001_Cy5

value: Semimembranosus


title: Flexor hallucis longus 251955510008_0008_Cy3


title: Tibialis anterior 251955510006_0005_Alexa 488


title: Nondisease Control-NDC 3

value: Hepatoblastoma


title: Peroneus longus 251955510006_0006_Cy3


title: Flexor digitorum longus 251955510006_0004_Cy3


title: Disease Control-DC 4

value: liver explant


title: Rectus femoris 251955510005_0006_Cy5

value: Rectus femoris


title: Nondisease Control-NDC 1


title: Semitendinosus 251955510005_0006_Cy3


title: Vastus interior 251955510005_0005_Cy3

value: Vastus interior


title: Flexor hallucis longus 251955510005_0005_Alexa 488


title: Vastus interior 251955510005_0005_Cy5


title: Disease Control-DC 1

value: Disease Control

value: Primary sclerosing cholangitis


title: Semitendinosus 251955510005_0006_Alexa 488


title: sartorius 251955510005_0004_Alexa 488

value: sartorius


title: sartorius 251955510005_0004_Cy5


title: Vastus lateralis 251955510005_0001_Cy5

value: Vastus lateralis


title: Semitendinosus 251955510005_0001_Alexa 488


title: Biceps femoris 251955510005_0002_Alexa 488

value: Biceps femoris


title: Gracilis 251955510005_0001_Cy3

value: Gracilis


title: Biceps femoris 251955510005_0002_Cy3


title: Biceps femoris 251955510005_0002_Cy5


title: Gastrocnemius medialis 251955510005_0003_Alexa 488

value: Gastrocnemius medialis


title: Vastus medialis 251955510005_0003_Cy5

value: Vastus medialis


title: Gastrocnemius medialis 251955510004_0008_Cy3


title: Vastus medialis 251955510004_0007_Cy5


title: Vastus medialis 251955510004_0007_Alexa 488


title: Adductor longus 251955510004_0005_Alexa 488

value: Adductor longus


title: sartorius 251955510005_0004_Cy3


title: Vastus interior 251955510004_0008_Cy5


title: Vastus lateralis 251955510004_0006_Cy5


title: Vastus interior 251955510004_0008_Alexa 488


title: Semimembranosus 251955510004_0006_Cy3


title: Vastus lateralis 251955510004_0006_Alexa 488


title: Vastus medialis 251955510005_0003_Cy3


title: Gastrocnemius lateralis 251955510004_0005_Cy5

value: Gastrocnemius lateralis


title: Rec femoris 251955510004_0007_Cy3

value: Rec femoris


title: Soleus 251955510004_0004_Alexa 488

value: Soleus


title: Gracilis 251955510004_0003_Alexa 488


title: Flexor hallucis longus 251955510004_0003_Cy5

value: Flexor hallucis longus


title: Gracilis 251955510004_0003_Cy3


title: Semitendinosus. 251955510004_0004_Cy3

value: Semitendinosus.


title: Biceps femoris 251955510004_0002_Cy5


title: Adductor magnus 251955510004_0005_Cy3

value: Adductor magnus


title: sartorius 251955510004_0001_Alexa 488


title: Biceps femoris 251955510004_0002_Cy3


title: Rectus femoris 251955510003_0008_Cy5

value: Rectus femoris


title: Adductor longus 251955510003_0008_Cy3


title: sartorius 251955510004_0001_Cy5


title: sartorius 251955510003_0005_Alexa 488


title: Semitendinosus 251955510003_0005_Cy3

value: Semitendinosus


title: Gracilis 251955510003_0004_Alexa 488


title: sartorius 251955510003_0006_Cy3


title: biceps femoris. 251955510003_0006_Cy5

value: biceps femoris.


title: Vastus medialis 251955510003_0004_Cy5


title: Semitendinosus. 251955510004_0004_Cy5


title: Biceps femoris 251955510004_0002_Alexa 488


title: Gracilis 251955510003_0007_Cy3


title: Vastus lateralis 251955510003_0003_Alexa 488


title: Semimembranosus 251955510003_0006_Alexa 488

value: Semimembranosus


title: sartorius 251955510004_0001_Cy3

value: sartorius


title: Adductor magnus 251955510003_0004_Cy3


title: sartorius 251955510003_0007_Cy5


title: Vastus interior 251955510003_0003_Cy5

value: Vastus interior


title: Vastus medialis 251955510003_0003_Cy3


title: Vastus lateralis 251955510003_0002_Cy5

value: Vastus lateralis


title: Vastus medialis. 251955510003_0002_Alexa 488

value: Vastus medialis.


title: Adductor magnus 251955510003_0008_Alexa 488


title: Biceps femoris 251955510003_0001_Alexa 488

value: Biceps femoris


title: Gracilis 251955510003_0001_Cy5

value: Gracilis


title: Biceps femoris 251955510003_0007_Alexa 488


title: Vastus lateralis 251955510003_0001_Cy3


title: Adductor magnus 251955510003_0005_Cy5


title: Tibialis anterior  251955510002_0008_Cy3

value: Tibialis anterior


title: Peroneus longus 251955510002_0007_Cy5

value: Peroneus longus


title: Peroneus longus 251955510002_0007_Cy3


title: Extensor digitorum longus 251955510002_0004_Cy5

value: Extensor digitorum longus


title: Gastrocnemius medialis 251955510002_0004_Alexa 488

value: Gastrocnemius medialis


title: Soleus 251955510002_0007_Alexa 488

value: Soleus


title: Flexor digitorum longus 251955510002_0005_Cy3

value: Flexor digitorum longus


title: Flexor hallucis longus 251955510002_0006_Cy3

value: Flexor hallucis longus


title: Gastrocnemius medialis 251955510002_0002_Alexa 488


title: Tibialis anterior 251955510002_0008_Cy5


title: Extensor hallucis longus 251955510002_0005_Cy5

value: Extensor hallucis longus


title: Extensor hallucis longus 251955510002_0004_Cy3


title: Extensor digitorum longus 251955510002_0003_Cy3


title: Gastrocnemius lateralis 251955510002_0003_Alexa 488

value: Gastrocnemius lateralis


title: Tibialis posterior 251955510002_0002_Cy3

value: Tibialis posterior


title: Flexor hallucis longus 251955510002_0003_Cy5


title: Tibialis posterior 251955510002_0001_Cy5


title: Gastrocnemius lateralis 251955510002_0001_Alexa 488


title: Tibialis anterior  251955510002_0001_Cy3


title: Vastus interior 251955510003_0002_Cy3


title: Soleus  251955510001_0005_Cy5


title: Tibialis anterior 251955510002_0002_Cy5


title: Flexor digitorum longus  251955510001_0004_Cy3


title: Tibialis ant 251955510001_0004_Cy5

value: Tibialis ant


title: Gastrocnemius.lateralis  251955510001_0005_Cy3


title: Extensor hallucis longus  251955510001_0002_Cy5


title: Peron longus  251955510001_0003_Cy3

value: Peron longus


title: Gastr.medialis   251955510001_0002_Cy3


title: Extensor digitorum longus  251955510001_0003_Cy5


title: Tibialis Posterior 251955510001_0001_Cy5

value: Tibialis Posterior


title: Tibialis anterior  251955510001_0001_Cy3


title: xrtp6A_Human_Blood_Sample

city: Bethesda

first: Leorey

last: Saligan

state: MD

address: 3 Center Drive, Building 3, Room 5E14

department: National Institute of Nursing Research

institute: National Institutes of Health

description:
Gene expression data from prostate cancer patients
Human_xrtp6_A

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

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

data_processing: Affymetrix Microarray Suite version 5.0.  Data were RMA background corrected, quantile normalized and log-transformed data     using Partek analysis software.  Statistical analysis performed using Partek Genomic Suite.

source_name: xrtp6A at baseline

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: Not Applicable

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to the manufacturer's guide

treatment_protocol: Not Applicable

tag: individual id

tag: disease state

value: prostate cancer

tag: fatigue

value: Low

tag: treatment

value: control

tag: time

value: baseline


title: xrt12A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt12_A

source_name: xrt12 at baseline


title: xrt24F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt24_F

source_name: xrt24 at endpoint

value: EBRT

value: endpoint (days 38-42)


title: xrt25A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt25_A

source_name: xrt25 at baseline


title: xrt25F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt25_F

source_name: xrt25 at endpoint


title: xrtp6E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp6_E

source_name: xrtp6E at midpoint

value: midpoint (days 19-21)


title: xrt25E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt25_E

source_name: xrt25 at midpoint


title: xrt24E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt24_E

source_name: xrt24 at midpoint


title: xrtp6F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp6_F

source_name: xrtp6F at endpoint


title: xrtp8A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp8_A

source_name: xrtp8A at baseline

value: High


title: xrt12E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt12_E

source_name: xrt12 at midpoint


title: xrt10F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt10_F

source_name: xrt10 at endpoint


title: xrtp2A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp2_A

source_name: xrtp2A at baseline


title: xrt24A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt24_A

source_name: xrt24 at baseline


title: xrt12F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt12_F

source_name: xrt12 at endpoint


title: xrtp5A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp5_A

source_name: xrtp5A at baseline


title: xrtp5F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp5_F

source_name: xrtp5F at endpoint


title: xrtp8F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp8_F

source_name: xrtp8F at endpoint


title: xrt10A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt10_A

source_name: xrt10 at baseline


title: xrtp2F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp2_F

source_name: xrtp2F at endpoint


title: xrt27A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt27_A

source_name: xrt27 at baseline


title: xrt27F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt27_F

source_name: xrt27 at endpoint


title: xrt10E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt10_E

source_name: xrt10 at midpoint


title: xrt22F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt22_F

source_name: xrt22 at endpoint


title: xrtp8E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp8_E

source_name: xrtp8E at midpoint


title: xrtp2E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp2_E

source_name: xrtp2E at midpoint


title: xrtp5E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrtp5_E

source_name: xrtp5E at midpoint


title: xrt27E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt27_E

source_name: xrt27 at midpoint


title: xrt22E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt22_E

source_name: xrt22 at midpoint


title: xrt20F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt20_F

source_name: xrt20 at endpoint


title: xrt20E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt20_E

source_name: xrt20 at midpoint


title: xrt19F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt19_F

source_name: xrt19 at endpoint


title: xrt19A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt19_A

source_name: xrt19 at baseline


title: xrt22A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt22_A

source_name: xrt22 at baseline


title: xrt18A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt18_A

source_name: xrt18 at baseline


title: xrt18E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt18_E

source_name: xrt18 at midpoint


title: xrt20A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt20_A

source_name: xrt20 at baseline


title: Flexor digitorum longus 251955510002_0006_Cy5


title: xrt19E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt19_E

source_name: xrt19 at midpoint


title: xrt18F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt18_F

source_name: xrt18 at endpoint


title: xrt17F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt17_F

source_name: xrt17 at endpoint


title: xrt16F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt16_F

source_name: xrt16 at endpoint


title: xrt15F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt15_F

source_name: xrt15 at endpoint


title: xrt17E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt17_E

source_name: xrt17 at midpoint


title: xrt16E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt16_E

source_name: xrt16 at midpoint


title: xrt17A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt17_A

source_name: xrt17 at baseline


title: HeLa-CDK9-inhibitor-T16-2

city: emeryville

first: Zhenhai

last: Gao

state: California

address: 4560 Horton street

institute: Novartis Institute for Biomedical Research

description: CDK9 inhibitor treatment at 16hr

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor affy package (http://bioconductor.org) with RMA method and HGU133Plus2_Hs_ENTREZG custom CDF v14.1 for target gene definition (Dai et al., 2005)

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

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS. Cells were maintained at 37 °C under 5% CO2.

extract_protocol: Total RNA was extracted with RNAeasy Plus kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: HeLa cells were treated with DMSO or i-CDK9 for 2, 8 or 16 hours

tag: cell line

value: HeLa

value: CDK9 inhibitor

tag: time (hours)


title: HeLa-CDK9-inhibitor-T16-3

description: CDK9 inhibitor treatment at 16hr


title: xrt13F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt13_F

source_name: xrt13 at endpoint


title: xrt11F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt11_F

source_name: xrt11 at endpoint


title: HeLa-CDK9-inhibitor-T16-1

description: CDK9 inhibitor treatment at 16hr


title: xrt11A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt11_A

source_name: xrt11 at baseline


title: xrt15A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt15_A

source_name: xrt15 at baseline


title: xrt8E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt8_E

source_name: xrt8 at midpoint


title: xrt11E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt11_E

source_name: xrt11 at midpoint


title: xrt16A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt16_A

source_name: xrt16 at baseline


title: xrt15E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt15_E

source_name: xrt15 at midpoint


title: xrt13E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt13_E

source_name: xrt13 at midpoint


title: xrt13A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt13_A

source_name: xrt13 at baseline


title: xrt8F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt8_F

source_name: xrt8 at endpoint


title: HeLa-DMSO-T16-2

description: DMSO treatment at 16hr

value: DMSO


title: HeLa-DMSO-T16-3

description: DMSO treatment at 16hr


title: HeLa-DMSO-T8-1

description: DMSO treatment at 8hr


title: HeLa-DMSO-T16-1

description: DMSO treatment at 16hr


title: HeLa-DMSO-T8-3

description: DMSO treatment at 8hr


title: HeLa-CDK9-inhibitor-T8-2

description: CDK9 inhibitor treatment at 8hr


title: HeLa-CDK9-inhibitor-T8-1

description: CDK9 inhibitor treatment at 8hr


title: xrt8A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt8_A

source_name: xrt8 at baseline


title: HeLa-DMSO-T8-2

description: DMSO treatment at 8hr


title: HeLa-CDK9-inhibitor-T2-2

description: CDK9 inhibitor treatment at 2hr


title: HeLa-CDK9-inhibitor-T2-3

description: CDK9 inhibitor treatment at 2hr


title: whole uPA gene BD87 03

city: Tokai-mura

first: Shin-Ichiro

last: Nagatsuka

state: Ibaraki

address: 2117 Muramatsu

department: ADME/Tox Research Institute

institute: Sekisui Medical Co.

description:
19_BD87_WG++03
BD87-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, followed by Robust Multichip Averaging (RMA) normalization using Avadis (Strand Genomics, Inc.). Values for probe sets that were judged to be Absent in all 25 Chips by the MAS5.0 analysis were left blank in the Sample data tables.

label: Biotin

organism:
Homo sapiens
Mus musculus

source_name: Liver from whole uPA gene homozygous mouse with BD87 transplant

growth_protocol: Human hepatocytes were intrasplenically transplanted to SCID host mice (2-4 weeks of age), followed by periodical monitoring of human albumin concentration in the blood to estimate the replacement index of human hepatocytes in the liver.

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

treatment_protocol: Humanized liver samples were taken at around 9:00am from non-treated chimeric mice which were estimated to be more than 70% occupancy of human hepatocytes in the liver.

tag: host mouse genotype/variation

value: whole uPA gene+/+ / SCID

tag: transplanted human hepatocytes

value: humanized liver

tag: age

value: approx. 20 weeks


title: xrt6E_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt6_E

source_name: xrt6 at midpoint


title: uPA cDNA homo BD195 01

description:
20_BD195_cDNA++01
BD195-transplanted uPA cDNA +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from uPA cDNA homozygous mouse with BD195 transplant

value: uPA cDNA+/+ / SCID


title: xrt6F_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt6_F

source_name: xrt6 at endpoint


title: uPA cDNA hetero BD195 01

description:
23_BD195_cDNA+-01
BD195-transplanted uPA cDNA +/- mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.

source_name: Liver from uPA cDNA heterozygous mouse with BD195 transplant

value: uPA cDNA+/- / SCID


title: HeLa-DMSO-T2-2

description: DMSO treatment at 2hr


title: uPA cDNA homo BD195 02

description:
21_BD195_cDNA++02
BD195-transplanted uPA cDNA +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: uPA cDNA hetero BD195 03

description:
25_BD195_cDNA+-03
BD195-transplanted uPA cDNA +/- mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: HeLa-DMSO-T2-1

description: DMSO treatment at 2hr


title: whole uPA gene BD87 01

description:
17_BD87_WG++01
BD87-transplanted whole uPA gene +/+ mouse.
Liver samples had low expression of mouse parenchymal genes and moderate expression of mouse non-parenchymal genes, as only parenchymal cells were humanized.


title: xrt6A_Human_Blood_Sample

description:
Gene expression data from prostate cancer patients
Human_xrt6_A

source_name: xrt6 at baseline