title: Anti-μ heavy chain replicate 2

city: Umeå

first: Thomas

last: Grundström

address: Analysvägen 1

department: Department of Molecular Biology

institute: Umeå University

description: SAMPLE 4

hyb_protocol: Labeled cRNA (1.5 ug) were hybridized to the Sentrix MouseRef-6 Expression Beadchip for 16-18 h at 58 °C, according to the manufacturer's instructions (Illumina).

scan_protocol: Following attachment of Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences), arrays were scanned with an Illumina bead array reader.

data_processing: Signal intensities of genes were normalized by cubic spline method using beadstudio software (v.3.1.1.0).

source_name: pre-B cells_Anti-μ heavy chain treated

label_protocol: Total RNA was amplified and purified to yield biotinylated cRNA using an Ambion Illumina RNA amplification kit (Ambion).

growth_protocol: Mice were maintained for 8 weeks in a controlled environment with a 12 h dark/light cycle.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) and further purified using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Bone marrow of 8 weeks old mice was isolated and pre-B cells were purified and grown on S17 stromal cells in the presence of IL-7 for 72 hours. The pre-BCR  was  activated by incubation with goat F(ab’)2 anti-mouse IgM (Southern Biotechnologies) at 5 μg/ml for 3 hour.

tag: strain

tag: age

value: 8 weeks

value: Bone marrow

value: pre-B cells

tag: activated with

value: goat F(ab’)2 anti-mouse μ heavy chain at 5 μg/ml for 3h


title: Anti-µ heavy chain replicate 1

status: Public on Dec 31 2014

type: RNA

country: Sweden

description: SAMPLE 3

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: Untreated Cells_rep1

city: Miami

first: Annalise

last: Smith

state: FL

address: 1580 NW 10th Avenue

department: Microbiology and Immunology

country: USA

institute: University of Miami

description:
replicate 1
sample 1_untreated

hyb_protocol: Standard Illumina Hybridization protocol

scan_protocol: Standard Illumina Scanning protocol

data_processing: Each batch was individually Quantile normalized and log2 transformed to median of samples. The batch bias correction was done using the ComBat module on R/Bioconductor package

label: biotin

source_name: rat her-2/neu cells

label_protocol: Standard Illumina labeling protocol

growth_protocol: Rat her-2/neu expressing murine cells were grown in 20% FBS containing DMEM media with gentamicin and l-glutamine. All three individual replicates were completed at early passage numbers- passage 2,3 and 4

extract_protocol: Total RNA was extracted with Trizol followed by purifcation and DNase1 treatment using Qiagen miRNA easy mini kit following the manufacturers instructions. Two rounds of quality control was performed with Agilent Bioanalyzer

treatment_protocol: Cells were treated with 8μM of Withaferin A diluted in culture media for 6hrs

value: rat her-2/neu expressing murine cancer cells

tag: agent

value: Untreated


title: serum-wilms-postCT-1 (comparison 3)

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM265/2

hyb_protocol: The expression profile of 1205 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil normalized for every comparison; 1) Wilms serum pre CT vs controls 2) wilms serum post CT vs controls and 3) Wilms serum pre CT vs Wilms serum post CT

label: Cyanine 3

organism: Homo sapiens

source_name: serum-wilms-postCT

label_protocol: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

extract_protocol: Total RNA including miRNAs was isolated using the protocol from Leidinger et al. with minor modifications. In detail 100µl serum sample, 250µl nuclease-free water (Life Technologies) and 750µl Trizol LS (Life Technologies) were mixed and incubated at RT for 5min. After addition of 1µl glycogen (20mg/ml) and 5µl 5mM cel spike-in control (Qiagen) and 200µl chloroform the solution was vortexed and incubated at RT for 3min followed by centrifugation at 4°C and 14 000rpm for 15min. The upper aqueous phase was transferred into a new tube and RNA was precipitated using 1.5Vol of 100% ethanol. The solution was added to a RNA binding column from the MinElute Cleanup Kit (Qiagen) and RNA was washed and purified using the buffer from the miRNeasy kit (Qiagen). Total RNA including miRNA was eluted in 15µl nuclease-free water and stored at -80°C. RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the Small RNA kit (Agilent) on a Bioanalyzer2100.

tag: individual

value: Wilms tumor patient

tag: treatment

value: chemotherapy

tag: sample type

value: serum


title: 1444-10G_3182

type: genomic

city: Durham

first: Susan

middle: K.

last: Murphy

state: NC

address: B226 LSRC B Wing, Research Drive, Box 91012

department: Obstetrics and Gynecology

institute: Duke University Medical Center

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

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

data_processing:
Please note that raw data (beta values) was used for data analysis. Normalization or filtering was not performed since there was excellent correlation between the beta values for a substantial number of CpG sites and the methylation % for these same CpGs obtained by bisulfite pyrosequencing.  The beta values were taken directly from Illumina's Genome Studio  v2010.3 software.
The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy3, Cy5

molecule: genomic DNA

source_name: ovarian cancer

label_protocol: Standard Illumina Protocol

growth_protocol: Samples were embedded in optimal cutting temperature medium and stored at -80 degrees celsius prior to use. All sections were cut and mounted on slides to confirm ≥60% tumor content with ≤20% necrosis.

extract_protocol: DNA was extracted from frozen tissues using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen).

tag: gender

value: female

tag: histologic type

value: clear cell


title: 1444-10E_3215

value: mucinous


title: Untreated replicate 2

description: SAMPLE 2

source_name: pre-B cells_untreated


title: Primary melanoma_134

city: Lund

first: Göran

last: Jönsson

address: Scheelevägen 8

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline normalisation. Features present in <80% of assays were discarded (presence defined as detection p‐value < 0.01), leaving 12,379 features for further analysis. After log2 transformation, the data were adjusted for plate by median centering each feature to zero.Reporters with standard deviation (SD) across the replicates of at least 0.3 in at least 50% of the replicated samples were excluded (n=3,447). Replicate samples were merged by average. Missing values have been imputed by k‐nearest neighbor imputation (k=10), using the R package impute. Using principal componenet analysis (PCA) the variation of  PC1 and PC3 were removed since these were strongly associated with technical variables. Hence, the processed data represent log(2) values adjusted for technical variation.

source_name: Primary melanoma

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was extractedusing the FFPE Roche kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: melanoma

tag: mutation status

value: Sporadic

tag: thickness

tag: histology

value: LMM

tag: clark

tag: number of replicates


title: serum-wilms-postCT-10 (comparison 3)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 3: (Wilms serum pre CT vs Wilms serum post CT)
Sample name: HOM362/2


title: Primary melanoma_133

value: SSM


title: Untreated replicate 1

description: SAMPLE 1


title: Primary melanoma_132

value: NM


title: serum-wilms-postCT-9 (comparison 2)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM357/2


title: serum-wilms-postCT-8 (comparison 2)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM355/2


title: serum-wilms-postCT-7 (comparison 2)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM341/2


title: Primary melanoma_131


title: Primary melanoma_130


title: 1444-10H_2673

value: serous


title: serum-wilms-postCT-6 (comparison 2)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM320/2


title: 1444-11A_2739


title: Primary melanoma_129


title: 1444-10D_1451


title: serum-wilms-postCT-5 (comparison 2)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM315/2


title: serum-wilms-postCT-4 (comparison 2)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM301/2


title: Primary melanoma_128


title: 1444-10C_3266

value: endometrioid


title: 1444-10B_1674


title: 1444-10F_2967


title: serum-wilms-postCT-3 (comparison 2)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM296/2


title: Primary melanoma_126


title: Primary melanoma_136


title: Primary melanoma_127


title: Primary melanoma_124


title: serum-wilms-postCT-16 (comparison 2)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM396/2


title: serum-wilms-postCT-2 (comparison 2)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM285/2


title: Primary melanoma_125


title: serum-wilms-postCT-15 (comparison 2)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM388/2


title: 1444-09E_2895


title: 1444-09G_2479


title: Primary melanoma_122


title: 1444-10A_CpG:NL=1:1

source_name: universally methylated DNA mixed 1:1 with normal lymphocyte DNA

value: unknown


title: 1444-09F_2953


title: serum-wilms-postCT-13 (comparison 2)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM374/2


title: 1444-09H_NO-5

source_name: ovarian surface epithelium

value: ovarian surface epithelium


title: Primary melanoma_123


title: serum-wilms-postCT-12 (comparison 2)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM364/2


title: Differentiating monocytes at 4h-VD rep4

city: Leuven

first: Gabriela

last: Bomfim Ferreira

state: Vlaams-Brabant

address: Herestraat 49 bus 902

department: Clinical and Experimental Medicine

country: Belgium

institute: KU Leuven

description: Gene expression data from human differentiating monocytes treated for 4-24h with 1,25(OH)2D3 or ethanol.

hyb_protocol: Labeled DNA fragments were hybridized overnight to Affymetrix GeneChip® human gene 1.0 St arrays.

scan_protocol: Affymetrix 3000 GeneScanner

data_processing: Microarray image files were analyzed using the Affymetrix command console software, and the robust multichip average (RMA) algorithm was used to calculate the signal intensities for each probe cell.

source_name: Differentiating monocytes_4h_VD

label_protocol: Biotin labeling using the Ambion WT expression kit (Affymetrix, San Diego, CA), according to the manufacturer’s instructions

growth_protocol: Human monocytes were magnetically isolated from PBMCs of healthy donors (MACS, miltenyi biotec) and cultured in the presence of IL-4, GM-CSF and 1,25(OH)2D3/ethanol for 4-24h

extract_protocol: Total RNA was extracted from monocytes using the RNeasy Micro Kit (Qiagen, Hilden, Germany), according to the manufacturer's specifications

treatment_protocol: Cells were harvested and lysed using the lysis buffer containing betamercaptoethanol using the RNeasy Micro Kit (Qiagen, Hilden, Germany), according to the manufacturer's specifications

value: PBMCs from buffy coats


title: Differentiating monocytes at 24h-VD rep4

source_name: Differentiating monocytes_24h_VD


title: Primary melanoma_118


title: Primary melanoma_119


title: serum-wilms-postCT-14 (comparison 2)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM384/2


title: 1444-08H_1552


title: serum-wilms-postCT-11 (comparison 2)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM363/2


title: Differentiating monocytes at 24h-CTR rep4

source_name: Differentiating monocytes_24h_CTR


title: serum-wilms-postCT-10 (comparison 2)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM362/2


title: 1444-09D_3157


title: Primary melanoma_117


title: Primary melanoma_116


title: serum-wilms-postCT-1 (comparison 2)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: HOM265/2


title: 1444-09A_1578


title: Differentiating monocytes at 4h-CTR rep4

source_name: Differentiating monocytes_4h_CTR


title: 1444-09C_2505


title: 1444-09B_3240


title: 1444-08F_2476


title: Differentiating monocytes at 24h-VD rep3


title: 1444-08E_2904


title: Differentiating monocytes at 4h-VD rep3


title: serum-control-8 (comparison 2)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk47

source_name: serum-control

value: control

value: untreated


title: Primary melanoma_114


title: serum-control-9 (comparison 2)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk71


title: serum-control-7 (comparison 2)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: G19


title: Primary melanoma_115


title: Differentiating monocytes at 24h-CTR rep3


title: 1444-08G_NO-4


title: 1444-08C_3117


title: serum-control-6 (comparison 2)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: G16


title: 1444-08D_2802


title: Primary melanoma_112


title: Primary melanoma_120


title: serum-control-5 (comparison 2)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: G15


title: 1444-07H_2977


title: 1444-08B_2204


title: Differentiating monocytes at 4h-CTR rep3


title: 1444-08A_3177


title: Primary melanoma_111


title: Differentiating monocytes at 4h-VD rep2


title: serum-control-4 (comparison 2)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: G14


title: serum-control-3 (comparison 2)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: G9


title: Primary melanoma_110


title: 1444-07G_1024


title: Primary melanoma_109


title: 1444-07F_NO-49


title: Differentiating monocytes at 4h-CTR rep2


title: Differentiating monocytes at 24h-CTR rep2


title: Primary melanoma_108


title: Primary melanoma_107


title: Differentiating monocytes at 24h-VD rep1


title: serum-control-18 (comparison 2)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk348


title: serum-control-19 (comparison 2)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk374


title: Primary melanoma_106


title: serum-control-17 (comparison 2)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk328


title: Primary melanoma_105


title: 1444-07C_2573


title: Differentiating monocytes at 24h-CTR rep1


title: Differentiating monocytes at 4h-VD rep1


title: Differentiating monocytes at 4h-CTR rep1


title: 1444-07D_2898


title: 1444-07E_2419


title: 1444-07A_2075


title: serum-control-16 (comparison 2)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk133


title: serum-control-2 (comparison 2)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: G7


title: Primary melanoma_104


title: Primary melanoma_113


title: serum-control-15 (comparison 2)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk132


title: 1444-07B_2790


title: Primary melanoma_103


title: serum-control-14 (comparison 2)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk126


title: Primary melanoma_102


title: serum-control-13 (comparison 2)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk122


title: 1444-06H_1877


title: Primary melanoma_101


title: MDA-MB-231 control clone #5

city: Bethesda

first: Nigel

last: Crawford

state: MD

address: 50 South Drive, Room 5154

institute: Human Genome Research Institute

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to The Affymetrix Human GeneChip 1.0 ST chips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing:
Data was processed via Partek and normalized using RMA.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta probe set file: HuGene-1_0-st-v1.r4.mps

label_protocol: Labeling performed using GeneChip WT Terminal Labeling and Controls Kit according to manufacturer's protocol.

growth_protocol: MDA-MB-231 cells were incubated in 5% CO2 at 37 °C.

extract_protocol: Total RNA was isolated from cells using QIAGEN RNeasy Mini Kit with on-column DNaseI digestion.

value: breast cancer

tag: cell line


title: Differentiating monocytes at 24h-VD rep2

description: Gene expression data from human differentiating monocytes treated for 4-24h with 1,25(OH)2D3 or ethanol.


title: 1444-06E_NO-46


title: serum-control-12 (comparison 2)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk136

value: serum


title: MDA-MB-231 control clone #6


title: MDA-MB-231 control clone #4


title: 1444-06C_2893

value: female


title: 1444-06G_2435


title: Primary melanoma_99


title: serum-control-11 (comparison 2)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk106


title: MDA-MB-231 control clone #1


title: serum-control-10 (comparison 2)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: kk99


title: MDA-MB-231 control clone #3


title: 1444-06F_3250


title: MDA-MB-231 RRP1B over-expressing clone #10


title: serum-control-1 (comparison 2)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 2: (wilms serum post CT vs controls)
Sample name: G5


title: Primary melanoma_98


title: MDA-MB-231 RRP1B over-expressing clone #9


title: Primary melanoma_97


title: serum-Wilms-preCT-9 (comparison 1)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM357/1

source_name: serum-Wilms-preCT

value: Wilms tumor patient


title: Primary melanoma_100


title: Primary melanoma_96


title: 1444-06B_2542


title: MDA-MB-231 RRP1B over-expressing clone #8


title: 1444-06D_2324


title: MDA-MB-231 RRP1B over-expressing clone #7


title: serum-Wilms-preCT-8 (comparison 1)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM355/1


title: Primary melanoma_95


title: Primary melanoma_94


title: 1444-05G_1846


title: 1444-06A_2708

value: mucinous


title: MDA-MB-231 RRP1B over-expressing clone #5


title: serum-Wilms-preCT-5 (comparison 1)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM315/1


title: serum-Wilms-preCT-7 (comparison 1)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM341/1


title: Primary melanoma_93

value: melanoma


title: DAOY_SCR

city: New York

first: Colin

last: Palmer

state: New York

address: 701 W. 168th Street

department: Microbiology & Immunology

institute: Columbia University

hyb_protocol: Biotinylated DNA probe was made according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned according to the Affymetrix protocol.

data_processing: Gene level RMA

source_name: DAOY cells transduced with lentivirus encoding control non-targeting shRNA SCR

label_protocol: We used the Ambion WT Labelling Kit as per manufacturer's instructions. We used 250 ng/sample of starting total RNA.

extract_protocol: Total RNA was extracted from Trizol LS according to manufacturer's instructions.

treatment_protocol: DAOY cells were transduced for 16-24 hours with lentivirus encoding shRNA targeting ZFX (H2, H3, H4) or scrambled non-targeting shRNA (SCR). Cells were allowed to recover for 48 hours, and then were replated in 2 ug/mL puromycin selective media. Cells were collected in TriZol LS reagent for RNA for microarrays ~48 hours after start of puromycin selection.

value: DAOY

tag: genotype

value: Ctrl


title: serum-Wilms-preCT-4 (comparison 1)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM301/1


title: 1444-05E_2981


title: Primary melanoma_92

value: Sporadic

value: LMM


title: 1444-05D_NFT-5

source_name: fallopian tube epithelium

value: fallopian tube epithelium


title: DAOY_H3

source_name: DAOY cells transduced with lentivirus encoding anti-ZFX shRNA H3

value: ZFX KD


title: Primary melanoma_91

value: SSM


title: Primary melanoma_90

value: NM


title: serum-Wilms-preCT-3 (comparison 1)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM296/1


title: DAOY_H4

source_name: DAOY cells transduced with lentivirus encoding anti-ZFX shRNA H4


title: DAOY_H2

source_name: DAOY cells transduced with lentivirus encoding anti-ZFX shRNA H2


title: 1444-05F_2883

value: serous


title: 1444-05C_2198


title: serum-Wilms-preCT-2 (comparison 1)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM285/1


title: Primary melanoma_88


title: serum-Wilms-preCT-15 (comparison 1)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM388/1


title: Primary melanoma_89


title: 1444-05A_2465


title: Primary melanoma_87


title: serum-Wilms-preCT-16 (comparison 1)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM396/1


title: serum-Wilms-preCT-14 (comparison 1)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM384/1


title: Primary melanoma_86


title: Primary melanoma_85


title: serum-Wilms-preCT-13 (comparison 1)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM374/1


title: serum-Wilms-preCT-6 (comparison 1)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM320/1


title: Primary melanoma_84


title: serum-Wilms-preCT-11 (comparison 1)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM363/1


title: 1444-05B_2621

value: clear cell


title: serum-Wilms-preCT-1 (comparison 1)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM265/1

value: untreated


title: serum-Wilms-preCT-10 (comparison 1)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM362/1


title: Primary melanoma_82


title: 1444-04G_5602


title: 1444-05H_5760


title: 1444-04F_1834


title: Primary melanoma_81


title: serum-control-9 (comparison 1)

description:
US11153896_253118111390_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk71

value: control


title: Primary melanoma_80

value: Mucosal


title: 1444-04H_2424

value: female


title: Primary melanoma_79


title: 1444-04A_5530

value: endometrioid


title: 1444-04D_2422


title: 1444-04B_2046


title: 1444-03H_5331


title: 1444-04C_NFT-4


title: Primary melanoma_78


title: 1444-04E_2783


title: Primary melanoma_73


title: serum-Wilms-preCT-12 (comparison 1)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: HOM364/1

value: Wilms tumor patient

value: serum


title: Primary melanoma_75

value: nevus


title: Primary melanoma_77

value: melanoma


title: serum-control-7 (comparison 1)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: G19


title: serum-control-8 (comparison 1)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk47


title: serum-control-6 (comparison 1)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: G16


title: Primary melanoma_83

value: Sporadic


title: Primary melanoma_72


title: serum-control-3 (comparison 1)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: G9


title: serum-control-4 (comparison 1)

description:
US11153896_253118111388_S01_miRNA_1010_Sep10_2_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: G14


title: serum-control-5 (comparison 1)

description:
US11153896_253118111159_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: G15


title: serum-control-19 (comparison 1)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk374


title: serum-control-2 (comparison 1)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: G7


title: Primary melanoma_71


title: 1444-03G_2064


title: Primary melanoma_70


title: 1444-03D_1859


title: 1444-03F_5088


title: 1444-03B_NFT-3


title: serum-control-18 (comparison 1)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk348


title: Primary melanoma_69

value: LMM


title: serum-control-17 (comparison 1)

description:
US11153896_253118111160_S01_miRNA_1010_Sep10_2_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk328


title: Primary melanoma_68


title: Primary melanoma_67


title: serum-control-16 (comparison 1)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk133


title: serum-control-14 (comparison 1)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk126


title: Primary melanoma_66


title: serum-control-13 (comparison 1)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk122


title: 1444-03E_872


title: Primary melanoma_64


title: Primary melanoma_65


title: 1444-03C_1665


title: serum-control-15 (comparison 1)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_1_4.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk132


title: Primary melanoma_63


title: serum-control-12 (comparison 1)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_1_2.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk136


title: serum-control-11 (comparison 1)

description:
US11153896_253118111392_S01_miRNA_1010_Sep10_1_3.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk106


title: Primary melanoma_62


title: serum-control-10 (comparison 1)

description:
US11153896_253118111405_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: kk99


title: Primary melanoma_61


title: serum-control-1 (comparison 1)

description:
US11153896_253118111385_S01_miRNA_1010_Sep10_1_1.txt
total RNA including miRNA
Comparison 1: (Wilms serum pre CT vs controls)
Sample name: G5


title: Primary melanoma_60


title: 1444-03A_1784


title: Primary melanoma_59


title: Primary melanoma_58


title: 1444-02H_1623


title: 1444-02F_1913


title: 1444-02A_NFT-2

value: fallopian tube epithelium


title: Primary melanoma_56


title: 1444-02C_3691


title: MCF7 hGH

city: Houston

first: Xiang H.-F.

last: Zhang

state: Texas

address: One Baylor Plaza

department: Beast Center

institute: Baylor College of Medicine

description: pMT-hGH is an expression plasmid containing the wild-type hGH gene. This Sample represents 2 replicates.

hyb_protocol: The labeled miRNA was hybridized as per the manufacturer's protocol of mirVana(TM) miRNA bioarray(Invitrogen).

scan_protocol: The hybridized slides were scanned on the microarray scanner LuxScan TM 10K(CapitalBio, Ltd) at 532nm and then were processed with GenePix Pro 6.0 (Axon, Ltd) and signal intensities quantified.

data_processing: The mean of the duplicate detected intensities was taken and normalized to internal positive controls using Microsoft Excel.

source_name: MCF7 clone transfected with pMT-hGH

label_protocol: The total miRNA was labeled by useing the mirVana(TM) miRNA Labeling kit (Ambion) as per the manufacturer's protocol.

growth_protocol: MCF7-MUT and MCF7-hGH were cultured at 37 °C in 5% CO2 in completed RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol: The total RNA and miRNA was isolated from cells by using the TRIzol Reagent (Life Technologies) and mirVana(TM) Isolation Kit (Invitrogen).

treatment_protocol: MCF-MUT and MCF-hGH were cultured for a total of 24 h in serum-free medium before processing for RNA preparation.

value: Breast cancer

tag: transfection

value: pMT-hGH


title: MCF7 MUT hGH

description: ATG start site of hGH gene was disabled via a mutation to TTG in pMT-MUT hGH plasmid. This Sample represents 2 replicates.

source_name: MCF7 clone transfected with pMT-MUT hGH

value: pMT-MUT hGH


title: 1444-02E_5003

source_name: ovarian cancer


title: Primary melanoma_54

source_name: Primary melanoma

value: NM


title: 1444-01H_5277

value: mucinous


title: Primary melanoma_55


title: Primary melanoma_53


title: Recurrence_patient-62_SCC_str_bio-rep2

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description:
Sample 144.
Biological replicate for sample 128.

hyb_protocol: Hybridizations and washes were performed according to the Exiqon® miRCURY™ LNA microRNA Array Instruction manual using an HS4800 hybridization station (Tecan®, Grödig, Austria). This work was performed as a commercial service by Exiqon®.

scan_protocol: Arrays were scanned using the G2565BA Microarray Scanner System (Agilent®), and image analysis was carried out using the ImaGene™ software (version 9; BioDiscovery®, Hawthorne, CA). This work was performed as a commercial service by Exiqon®.

data_processing:
Raw Hy3™ and Hy5™ signal data for all 136 arrays were processed together in R (version 2.15.1) using the limma Bioconductor package (version 3.12.3) on Mac OS X 10.6.8. Briefly, background signals were adjusted for using the 'normexp' method with 'offset' value of 10. Array data was then subjected to within-array global loess normalization with a 'span' value of 1/3. This was followed by between-array 'quantile' normalization. Probe-set summarization for Hy3™/Hy5™ ratio values (test RNA/reference RNA) was then performed, using the mean value from replicate probe-spots when the maximum was <1.5x minimum value, using the median value otherwise.

Raw data files:
1_Exiqon*:  Hy3
0_Exiqon*: Hy5

source_name: Recurrence case, patient-62, SCC, stromum

label_protocol: The miRCURY™ LNA microRNA Hi-Power Labeling kit from Exiqon® was used to label 350 ng of test RNA with the Cy3-like Hy3™ dye. The reference RNA (350 ng) was similarly labeled with the Cy5-like Hy5™ dye. Artificial small RNAs were spiked in to test and reference RNA samples before labeling. This work was performed as a commercial service by Exiqon®.

growth_protocol: Formalin-fixed and paraffin-embedded, resected, stage I, human lung cancer tumor tissue samples were provided by the Department of Pathology of Roswell Park Cancer Institute, Buffalo, NY, USA.

extract_protocol: Total RNA was extracted from microdissectates using the FFPE RNA Purification kit (catalog# 25300, Norgen-Biotek®, Thorold, ON, Canada) following the kit manufacturer's guidelines. The kit uses silicon carbide spin-columns. The extracted RNA preparations were not treated with DNase. The low-range Quant-iT™ Ribogreen assay (Life Technologies®, Carlsbad, CA) was used to estimate RNA concentration using yeast tRNA as the standard. Refer to Patnaik et al., BMC Research Notes, 2012, 5:40 (PMID 22260539) for details on RNA isolation and quantitation. The reference RNA, a human 'universal reference total RNA,' was obtained by Exiqon® from Ambion® (catalog# AM6000; Austin, TX).

treatment_protocol: Laser capture microdissection was performed to isolate epithelial or stromal compartments of tumors using hematoxylin-eosin-stained tissue sections. Refer to Patnaik et al., BMC Research Notes, 2012, 5:40 (PMID 22260539) for details on tissue section preparation and microdissection.

value: squamous cell carcinoma stroma

tag: patient

tag: recurrence

value: Y

value: SCC

value: F

tag: race

value: White

value: former

value: S

source_name: Reference RNA

value: reference


title: 1444-02B_1615

value: female

value: serous


title: Recurrence_patient-62_SCC_epi_bio-rep2

description:
Sample 143.
Biological duplicate for samples 5 & 127.

source_name: Recurrence case, patient-62, SCC, epithelium

tag: tissue

value: squamous cell carcinoma epithelia

value: E


title: 1444-02G_3511

value: endometrioid


title: Primary melanoma_52

value: melanoma

value: Sporadic

value: LMM


title: Primary melanoma_51

value: NM


title: 1444-01C_3107


title: Non-recurrence_patient-78_SCC_epi

description: Sample 141.

source_name: Non-recurrence case, patient-78, SCC, epithelium

value: N


title: Non-recurrence_patient-78_SCC_str

description: Sample 142.

source_name: Non-recurrence case, patient-78, SCC, stromum

value: squamous cell carcinoma stroma


title: iMSC#3, Day 28 osteogenic differentiation (June)

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard IIlumina hyb protocol

scan_protocol: Standard IIlumina scan protocol

data_processing: Data extraction and initial quality control of the bead summary raw data were performed using GenomeStudio v2011.1 and the Methylation module v1.9, both provided by Illumina.

label: Biotin and dinitrophenyl

source_name: iMSC#3 , Day 28 osteogenic differentiaiton  (June)

label_protocol: Standard IIlumina label protocol

growth_protocol: The iMSC3 cells were culture in minimum essential medium alpha (MEM alpha) (Invitrogen) supplemented with 10% fetal calf serum (FCS) and glutamax (growth mediun; GM). For osteogenic differentiation GM was supplemented with 67 µM ascorbic acid 2-phosphate (Sigma-Aldrich), 3.5 mM β-glycerol phosphate (Sigma-Aldrich) and 10 nM dexamethasone (Sigma-Aldrich) (differentiation medium; DM) and cells were cultured for 28 days.

extract_protocol: DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA).

tag: sample origin

value: Human bone marrow-derived mesenchymal stromal cell

value: Male

value: osteogenic differentiaiton


title: Primary melanoma_50


title: 1444-01B_1605


title: Primary melanoma_57

value: SSM


title: 1444-01D_3722

value: clear cell


title: 1444-01G_1590


title: 1444-01E_1858


title: 1444-01F_3488


title: Primary melanoma_45


title: Primary melanoma_46


title: 1444-02D_3142


title: Recurrence_patient-71_AC_str

description: Sample 136.

source_name: Recurrence case, patient-71, AC, stromum

value: adenocarcinoma stroma

value: Y

value: AC

value: M

value: Black

value: former

value: S

value: reference


title: Recurrence_patient-72_AC_epi

description: Sample 137.

source_name: Recurrence case, patient-72, AC, epithelium

value: adenocarcinoma epithelia

value: F

value: White

value: E


title: Immortalized human bone marrow-derived mesenchymal stromal cell line DNA methylation [iMSC#3 (Culture II)]

source_name: iMSC#3 (Culture II)

growth_protocol: Primary hMSCs were obtained from the hip of a healthy donor after informed consent. Mononuclear cells from the bone marrow were isolated using standard density centrifugation and cultured in minimum essential medium (MEM) Alpha medium (cat. no. 22561) supplemented with 20% FBS (PAA Laboratories), GlutaMAX, penicillin (100U/mL), and streptomycin (100 mg/mL) (all from Life Technologies) at 37C and 5% CO2. Non-adherent cells were removed after approximately 24 h by replacement of the medium. Subsequently, the adherent cells were allowed to expand until 70% confluence (5–6 days) before they were harvested and further expanded. iMSC#3 were grown under the same condition as hMSCs, but the medium was supplemented with 10% FBS.

value: Human bone marrow-derived mesenchymal stromal cell


title: Human none marrow-derived mesenchymal stromal primary culture DNA methylation [hMSC_Male]

tag: cell type

value: hMSC

value: Male


title: Primary melanoma_48

value: melanoma

value: Sporadic

value: NM


title: Primary melanoma_42


title: Primary melanoma_47

value: SSM


title: Primary melanoma_43


title: Recurrence_patient-71_AC_epi

description: Sample 135.

source_name: Recurrence case, patient-71, AC, epithelium

value: Y

value: AC

tag: sample type


title: Primary melanoma_41


title: Recurrence_patient-70_AS_str

description: Sample 134.

source_name: Recurrence case, patient-70, AS, stromum

value: adenosquamous carcinoma stroma

value: AS

tag: gender

value: M

value: current


title: Primary melanoma_40


title: Recurrence_patient-70_AS_epi

description: Sample 133.

source_name: Recurrence case, patient-70, AS, epithelium

value: adenosquamous carcinoma epithelia

value: reference


title: Primary melanoma_49


title: Primary melanoma_39


title: Human none marrow-derived mesenchymal stromal primary culture DNA methylation [hMSC_Female]

value: Female


title: Non-recurrence_patient-67_SCC_str

description: Sample 132.

source_name: Non-recurrence case, patient-67, SCC, stromum

value: squamous cell carcinoma stroma

value: N

value: SCC

value: F

value: White

value: S


title: Non-recurrence_patient-64_SCC_str

description: Sample 130.

source_name: Non-recurrence case, patient-64, SCC, stromum

value: former


title: Non-recurrence_patient-77_AC_epi

description: Sample 139.

source_name: Non-recurrence case, patient-77, AC, epithelium

value: adenocarcinoma epithelia

value: never

value: E


title: iMSC#3, Undifferentiated Day 0 osteogenic differentiation (June)

source_name: iMSC#3 , Undifferentiated Day 0 osteogenic differentiaiton (June)

value: Human bone marrow-derived mesenchymal stromal cell

value: Male

tag: treatment

value: undifferentiated


title: Primary melanoma_37

source_name: Primary melanoma

value: melanoma

tag: mutation status

value: Sporadic

value: SSM


title: Primary melanoma_38

tag: thickness


title: Non-recurrence_patient-64_SCC_epi

description: Sample 129.

source_name: Non-recurrence case, patient-64, SCC, epithelium

value: squamous cell carcinoma epithelia

tag: histology

value: M

value: reference


title: Recurrence_patient-62_SCC_str

description: Sample 128.

source_name: Recurrence case, patient-62, SCC, stromum

value: squamous cell carcinoma stroma

value: Y

value: SCC

source_name: Reference RNA


title: Primary melanoma_36

tag: clark


title: Recurrence_patient-72_AC_str

description: Sample 138.

source_name: Recurrence case, patient-72, AC, stromum

value: adenocarcinoma stroma

value: AC

value: F

value: White

value: S


title: Non-recurrence_patient-61_AC_str

description: Sample 126.

source_name: Non-recurrence case, patient-61, AC, stromum

value: N

value: current


title: Non-recurrence_patient-77_AC_str

description: Sample 140.

source_name: Non-recurrence case, patient-77, AC, stromum

value: never


title: Recurrence_patient-62_SCC_epi

description: Sample 127.

source_name: Recurrence case, patient-62, SCC, epithelium

value: former

value: E


title: Primary melanoma_44

value: melanoma

value: Sporadic

value: SSM

tag: number of replicates


title: Non-recurrence_patient-61_AC_epi

description: Sample 125.

source_name: Non-recurrence case, patient-61, AC, epithelium

value: adenocarcinoma epithelia

value: M

value: reference


title: 1444-01A_860

source_name: ovarian cancer

value: female

tag: histologic type

value: serous


title: Primary melanoma_35


title: Primary melanoma_34

value: NM


title: Primary melanoma_33

value: nevus


title: Immortalized human bone marrow-derived mesenchymal stromal cell line DNA methylation [iMSC#3 (Culture I)]

source_name: iMSC#3 (Culture I)

tag: cell line

value: Human bone marrow-derived mesenchymal stromal cell

value: Male


title: Primary melanoma_32


title: Non-recurrence_patient-60_SCC_epi

description: Sample 123.

source_name: Non-recurrence case, patient-60, SCC, epithelium

value: squamous cell carcinoma epithelia

value: N

value: SCC

value: White


title: Non-recurrence_patient-60_SCC_str

description: Sample 124.

source_name: Non-recurrence case, patient-60, SCC, stromum

value: squamous cell carcinoma stroma

value: current

value: S


title: Non-recurrence_patient-59_SCC_str

description: Sample 122.

source_name: Non-recurrence case, patient-59, SCC, stromum

value: F

value: American Indian

value: former


title: Non-recurrence_patient-59_SCC_epi

description: Sample 121.

source_name: Non-recurrence case, patient-59, SCC, epithelium

value: E

value: reference


title: Recurrence_patient-58_AC_str

description: Sample 120.

source_name: Recurrence case, patient-58, AC, stromum

value: adenocarcinoma stroma

value: Y

value: AC


title: Primary melanoma_29

value: melanoma

value: Sporadic

value: SSM


title: Non-recurrence_patient-57_SCC_str

description: Sample 118.

source_name: Non-recurrence case, patient-57, SCC, stromum

value: N


title: Primary melanoma_28

source_name: Primary melanoma


title: Non-recurrence_patient-57_SCC_epi

description: Sample 117.

source_name: Non-recurrence case, patient-57, SCC, epithelium

value: squamous cell carcinoma epithelia

value: SCC


city: Philadelphia

first: Hiroshi

last: Nakagawa

state: PA

address: 415 Curie Blvd.

department: Gastroenterology Division

institute: University of Pennsylvania

description: EPC2-T-ICN1 (#22) with DOX plus recombinant human TGF-beta1 treatment EPC2-T-ICN1 (#22) with DOX plus recombinant human TGF-beta1 treatment DOXTGF2

hyb_protocol: Hybridization of cRNAs to Affymetrix chips were performed according manufacturer's instructions

scan_protocol: Scanning of Affymetrix chips were performed according manufacturer's instructions

data_processing: .CEL files (probe level data) were exported from Affymetrix® GeneChip® Operating Software which was also used to calculate detection flags, which were exported in .chp files. Probe level data (.CEL files) were imported with Partek Genomics Suite (v. 6.4, Partek, Inc., St. Louis, MO). The data were normalized and summarized to the probe set level using GC-RMA, yielding log2 intensities for all probe sets on the array.

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

growth_protocol: All cells were grown under regular conditions (21% O2, 5% CO2, 95% humidity) at 37°C in serum free medium (Keratinocyte-SFM)(Invitrogen) supplemented with 1 ng/ml epidermal growth factor and 50 µg/ml bovine pituitary extract.

extract_protocol: RNeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Cells were treated for 10 days either with or without 2.5 ng/ml recombinant human TGF-beta1 (TGF) along with or without 0.5 µg/ml doxycycline (DOX).

tag: source tissue

value: esophagus

value: transformed epithelial cells (keratinocytes)

tag: transgene


title: Primary melanoma_30


title: Primary melanoma_26


title: Non-recurrence_patient-56_BAC_epi

description: Sample 115.

source_name: Non-recurrence case, patient-56, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia

tag: patient

tag: recurrence

value: BAC

value: M

value: White


description: EPC2-T-ICN1 (#22) with DOX plus recombinant human TGF-beta1 treatment EPC2-T-ICN1 (#22) with DOX plus recombinant human TGF-beta1 treatment DOXTGF3


description: EPC2-T-ICN1 (#22) with DOX plus recombinant human TGF-beta1 treatment EPC2-T-ICN1 (#22) with DOX plus recombinant human TGF-beta1 treatment DOXTGF1


title: Primary melanoma_31

tag: tissue

value: nevus


title: Non-recurrence_patient-67_SCC_epi

description: Sample 131.

source_name: Non-recurrence case, patient-67, SCC, epithelium

value: F

tag: race

value: current

value: E

source_name: Reference RNA

value: reference


description: EPC2-T-ICN1 (#22) with recombinant human TGF-beta1 treatment EPC2-T-ICN1 (#22) with recombinant human TGF-beta1 treatment TGF2

tag: cell type

value: recombinant human TGF-beta1 treatment


description: EPC2-T-ICN1 (#22) with DOX treatment EPC2-T-ICN1 (#22) with DOX treatment DOX1

source_name: EPC2-T-ICN1 (#22) with DOX treatment

value: DOX treatment


description: EPC2-T-ICN1 (#22) with DOX treatment EPC2-T-ICN1 (#22) with DOX treatment DOX2


description: EPC2-T-ICN1 (#22) with DOX treatment EPC2-T-ICN1 (#22) with DOX treatment DOX3


description: EPC2-T-ICN1 (#22) with recombinant human TGF-beta1 treatment EPC2-T-ICN1 (#22) with recombinant human TGF-beta1 treatment TGF3


title: Recurrence_patient-55_SCC_str

description: Sample 114.

source_name: Recurrence case, patient-55, SCC, stromum

value: squamous cell carcinoma stroma

value: Y

value: former

value: S

tag: sample type


title: muscle cell line (C2C12) at day 8 replication 3

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description:
replication 3
miRNA expression data from mouse muscle lcell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip miRNA arrays. GeneChips were washed and processed to detect biotin-containing transcripts by Streptavidin-PE (Phycoerythrin) conjugate.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Expression Console and quantify by med polish

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag™ Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix® GeneChip® miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

tag: time

value: day 8


title: Recurrence_patient-54_SCC_str

description: Sample 112.

source_name: Recurrence case, patient-54, SCC, stromum

value: SCC

tag: gender


title: Recurrence_patient-55_SCC_epi

description: Sample 113.

source_name: Recurrence case, patient-55, SCC, epithelium

value: squamous cell carcinoma epithelia


title: muscle cell line (C2C12) at day 4 replication 3

value: day 4


title: Primary melanoma_24

tag: mutation status


description: EPC2-T-ICN1 (#22) with recombinant human TGF-beta1 treatment EPC2-T-ICN1 (#22) with recombinant human TGF-beta1 treatment TGF1

value: esophagus

value: transformed epithelial cells (keratinocytes)

tag: treatment


title: Primary melanoma_23

value: nevus

tag: thickness

tag: histology


description: EPC2-T-ICN1 (#22) with no treatment EPC2-T-ICN1 (#22) with no treatment cont3

source_name: EPC2-T-ICN1 (#22) with no treatment

value: no treatment


title: muscle cell line (C2C12) at day 8 replication 2

description:
replication 2
miRNA expression data from mouse muscle lcell line


title: Primary melanoma_25

value: melanoma

value: Sporadic

value: SSM

tag: clark

tag: number of replicates


title: Primary melanoma_22


description: EPC2-T-ICN1 (#22) with no treatment EPC2-T-ICN1 (#22) with no treatment cont2

tag: cell line


title: Primary melanoma_21


title: Recurrence_patient-54_SCC_epi

description: Sample 111.

source_name: Recurrence case, patient-54, SCC, epithelium

value: M

value: White

value: E

value: reference


title: Non-recurrence_patient-53_AC_str

description: Sample 110.

source_name: Non-recurrence case, patient-53, AC, stromum

value: adenocarcinoma stroma

value: N

value: AC

value: F

value: never


title: Non-recurrence_patient-52_AC_str

description: Sample 108.

source_name: Non-recurrence case, patient-52, AC, stromum

value: former

value: S


title: Primary melanoma_20


title: muscle cell line (C2C12) at day 8 replication 1

description:
replication 1
miRNA expression data from mouse muscle lcell line

value: day 8


title: muscle cell line (C2C12) at day 0 replication 3

value: day 0


title: muscle cell line (C2C12) at day 4 replication 2

value: day 4


title: Non-recurrence_patient-52_AC_epi

description: Sample 107.

source_name: Non-recurrence case, patient-52, AC, epithelium

value: adenocarcinoma epithelia


description: EPC2-T-ICN1 (#22) with no treatment EPC2-T-ICN1 (#22) with no treatment cont1

tag: source tissue

value: esophagus

value: transformed epithelial cells (keratinocytes)

value: no treatment


title: Primary melanoma_19

value: melanoma

value: Sporadic

value: NM


description: CD24-low/CD44-high (CD44H) cell fraction CD24-low/CD44-high (CD44H) EPC2 cell fraction 44H3

treatment_protocol: To analyze CD24 and CD44 expression, cells were detached by Trypsin-EDTA [0.05% Trypsin, 0.53 mM EDTA-4Na] and incubated with Allophycocyanin-conjugated anti-human CD44 (BD Bioscience) and PE/Cy7-conjugated anti human CD24 (Biolegend, San Diego, CA) on ice for 30 min. The cells were washed with Hank's Buffered Salt Solution (HBSS) containing 1% bovine serum albumin (BSA) twice and then detected by FACSCalibur (BD Bioscience). The CD24/CD44 stained cells were sorted at the Flow cytometry facility of the University of Pennsylvania.

tag: phenotype

tag: transgene

value: EGFR-cyclin D1-p53R175H-hTERT


description: CD24-low/CD44-high (CD44H) cell fraction CD24-low/CD44-high (CD44H) EPC2 cell fraction 44H1


title: Non-recurrence_patient-53_AC_epi

description: Sample 109.

source_name: Non-recurrence case, patient-53, AC, epithelium

tag: patient

tag: recurrence

value: N

value: White

value: E

value: reference


title: muscle cell line (C2C12) at day 4 replication 1


title: Recurrence_patient-51_BAC_str

description: Sample 106.

source_name: Recurrence case, patient-51, BAC, stromum

tag: tissue

value: bronchioloalveolar carcinoma stroma

value: Y

value: BAC

value: M

tag: race

value: never


title: muscle cell line (C2C12) at day 0 replication 2

value: day 0


title: muscle cell line (C2C12) at day 0 replication 1


description: CD24-low/CD44-high (CD44H) cell fraction CD24-low/CD44-high (CD44H) EPC2 cell fraction 44H2

value: esophagus

tag: cell type


description: CD24-high/CD44-low (CD44L) cell fraction CD24-high/CD44-low (CD44L) EPC2 cell fraction 44L3

value: transformed epithelial cells (keratinocytes)


title: Primary melanoma_17

value: SSM


title: Non-recurrence_patient-50_BAC_str

description: Sample 104.

source_name: Non-recurrence case, patient-50, BAC, stromum

value: F

value: S

tag: sample type


title: Recurrence_patient-51_BAC_epi

description: Sample 105.

source_name: Recurrence case, patient-51, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia

tag: gender


title: Primary melanoma_16

source_name: Primary melanoma

value: melanoma

tag: mutation status

value: Sporadic

value: LMM


title: Primary melanoma_18


description: CD24-high/CD44-low (CD44L) cell fraction CD24-high/CD44-low (CD44L) EPC2 cell fraction 44L1

value: EGFR-cyclin D1-p53R175H-hTERT


title: Primary melanoma_15


title: Non-recurrence_patient-50_BAC_epi

description: Sample 103.

source_name: Non-recurrence case, patient-50, BAC, epithelium

value: N

value: White

value: E

value: reference


title: Recurrence_patient-49_SCC_str

description: Sample 102.

source_name: Recurrence case, patient-49, SCC, stromum

value: squamous cell carcinoma stroma

value: Y

value: SCC

value: Black

value: former


title: Primary melanoma_14

value: SSM


title: Recurrence_patient-49_SCC_epi

description: Sample 101.

source_name: Recurrence case, patient-49, SCC, epithelium

value: squamous cell carcinoma epithelia

value: F

source_name: Reference RNA


title: Recurrence_patient-47_AC_epi

description: Sample 97.

source_name: Recurrence case, patient-47, AC, epithelium

value: adenocarcinoma epithelia

value: AC


title: Primary melanoma_13

value: melanoma

value: Sporadic


title: Primary melanoma_10


title: Non-recurrence_patient-46_AC_str

description: Sample 96.

source_name: Non-recurrence case, patient-46, AC, stromum

value: adenocarcinoma stroma

value: M

value: S


title: Primary melanoma_9


title: Primary melanoma_12


description: CD24-high/CD44-low (CD44L) cell fraction CD24-high/CD44-low (CD44L) EPC2 cell fraction 44L2

value: esophagus

value: transformed epithelial cells (keratinocytes)

value: EGFR-cyclin D1-p53R175H-hTERT


title: CD24-high/CD44-low (CD44L) cell fraction 1

treatment_protocol: To analyze CD24 and CD44 expression, cells were detached by Versene (0.02% Tetrasodium ethylenediaminetetraacetate in Phosphate Buffered Saline) and incubated with Allophycocyanin-conjugated anti-human CD44 (BD Bioscience) and PE/Cy7-conjugated anti human CD24 (Biolegend, San Diego, CA) on ice for 30 min. The cells were washed with Hank's Buffered Salt Solution (HBSS) containing 1% bovine serum albumin (BSA) twice and then detected by FACSCalibur (BD Bioscience). The CD24/CD44 stained cells were sorted at the Flow cytometry facility of the University of Pennsylvania.

tag: cell fraction

tag: genotype

value: EGFR-cyclin D1-p53R175H-hTERT-DNMAML1


title: CD24-high/CD44-low (CD44L) cell fraction 2


title: CD24-high/CD44-low (CD44L) cell fraction 3


title: Primary melanoma_8

tag: thickness

tag: histology

value: NM


title: Recurrence_patient-45_AC_str

description: Sample 94.

source_name: Recurrence case, patient-45, AC, stromum

value: Y

value: White

value: never

value: reference


title: Recurrence_patient-47_AC_str

description: Sample 98.

source_name: Recurrence case, patient-47, AC, stromum

value: F

value: former


title: Primary melanoma_11

value: SSM

tag: clark

tag: number of replicates


title: Primary melanoma_7

value: melanoma


title: CD24-low/CD44-high (CD44H) cell fraction 2


title: CD24-low/CD44-high (CD44H) cell fraction 3


title: Primary melanoma_6

value: Sporadic


title: Kidney_lupus NZM2410 (remission_Ad-BAFF-R-Ig) rep6

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
Sample name: Baff6_VO4RL
Kidney from lupus NZM2410 mouse (remission after Ad-BAFF-R-Ig)
Gene expression data from NZM2410 kidney after remission with Ad-BAFF-R-Ig

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChip arrays (Santa Clara, CA) according to the manufacturer protocol.

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Mouse Entrez Gene custom CDF annotation version 10 were used for the normalization; and Combat for batch correction within the NZB/W mouse model and the NZM2410 mouse model.

source_name: Kidney from NZM2410 mouse under remission

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix). GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated using Trizol and manufacturer's instructions

tag: strain

tag: treatment

value: Ad-BAFF-R-Ig

tag: disease state

value: remission

value: Whole kidney


title: Kidney_lupus NZM2410 (remission_Ad-BAFF-R-Ig) rep5

description:
Sample name: Baff5_VO3LU
Kidney from lupus NZM2410 mouse (remission after Ad-BAFF-R-Ig)
Gene expression data from NZM2410 kidney after remission with Ad-BAFF-R-Ig

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.


title: Kidney_lupus NZM2410 (remission_Ad-BAFF-R-Ig) rep3

description:
Sample name: Baff3_MP1RL
Kidney from lupus NZM2410 mouse (remission after Ad-BAFF-R-Ig)
Gene expression data from NZM2410 kidney after remission with Ad-BAFF-R-Ig


title: CD24-low/CD44-high (CD44H) cell fraction 1

value: esophagus


title: Non-recurrence_patient-46_AC_epi

description: Sample 95.

source_name: Non-recurrence case, patient-46, AC, epithelium

value: adenocarcinoma epithelia

tag: patient

value: N

value: AC

value: M

value: E


title: Kidney_lupus NZM2410 (remission_Ad-BAFF-R-Ig) rep2

description:
Sample name: Baff2_MP1O
Kidney from lupus NZM2410 mouse (remission after Ad-BAFF-R-Ig)
Gene expression data from NZM2410 kidney after remission with Ad-BAFF-R-Ig


title: Primary melanoma_5


title: Recurrence_patient-44_AC_str

description: Sample 92.

source_name: Recurrence case, patient-44, AC, stromum

value: adenocarcinoma stroma

tag: recurrence

value: Y

value: White

value: current

value: S


title: Primary melanoma_2

tag: tissue

value: NM


title: Non-recurrence_patient-43_AC_str

description: Sample 90.

source_name: Non-recurrence case, patient-43, AC, stromum

value: F

tag: race

value: reference


title: Primary melanoma_4

value: melanoma

value: Sporadic

value: Mucosal


title: Primary melanoma_3

value: SSM


title: Recurrence_patient-45_AC_epi

description: Sample 93.

source_name: Recurrence case, patient-45, AC, epithelium

value: adenocarcinoma epithelia

value: never


title: Recurrence_patient-44_AC_epi

description: Sample 91.

source_name: Recurrence case, patient-44, AC, epithelium

value: AC


title: Non-recurrence_patient-43_AC_epi

description: Sample 89.

source_name: Non-recurrence case, patient-43, AC, epithelium

value: N


title: Primary melanoma_1


title: P48

type: SRA

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

library_source: transcriptomic

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing using the Picard ExtractIlluminaBarcodes algorithm.
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC hg19 RepeatMasker track (downloaded March 14, 2011).
Remaining reads are aligned using TopHat2 (default parameters except for --mate-inner-dist (average size with adapters 355, range 268-465, measured for each sample individually) --mate-std-dev 100 --library-type fr-firststrand --keep-fasta-order --no-coverage-search) to the human genome reference GRCh37/hg19 (with b37 masked chromosome Y and hs37d5 decoy sequences) together with 80,884 transcript annotations from the UCSC knownGenes table (downloaded September 10, 2012).
Cufflinks v2.1.1 is used to calculate expression levels, fragments per kilobase of exon per million mapped reads (FPKM), using default settings except --frag-bias-correct --multi-read-correct --library-type fr-firststrand --compatible-hits-norm.
Gene expression data were pre-processed by collapsing on 27,979 unique gene symbols (sum of FPKM values of each matching transcript), adding to each expression measurement 0.1 FPKM, performing a log2 transformation, and centering the gene expression values by subtracting the row-wise (gene) median (calculated across the 49 primary data sets) from the values in each row of data.
Subtyping was performed on the normalized expression matrix using the genefu R package and the published gene lists PAM50, Sorlie and Hu.
Genome_build: Human genome reference GRCh37/hg19 (with b37 masked chromosome Y and hs37d5 decoy sequences).

molecule: polyA RNA

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 instrument.

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: P49

value: Basal


title: P47

value: Normal


title: P46-replicate


title: P46


title: Kidney_lupus NZM2410 (remission_Ad-BAFF-R-Ig) rep4

description:
Sample name: Baff4_MP1RU
Kidney from lupus NZM2410 mouse (remission after Ad-BAFF-R-Ig)
Gene expression data from NZM2410 kidney after remission with Ad-BAFF-R-Ig

tag: strain

tag: treatment

value: Ad-BAFF-R-Ig

tag: disease state

value: remission

value: Whole kidney


title: Recurrence_patient-42_BAC_str

description: Sample 88.

source_name: Recurrence case, patient-42, BAC, stromum

tag: tissue

value: bronchioloalveolar carcinoma stroma

tag: patient

tag: recurrence

value: Y

tag: histology

value: BAC

tag: gender

value: F

value: White

value: former

value: S

tag: sample type

value: reference


title: Recurrence_patient-40_BAC_str

description: Sample 84.

source_name: Recurrence case, patient-40, BAC, stromum

tag: race

value: current


title: Recurrence_patient-41_AC_epi

description: Sample 85.

source_name: Recurrence case, patient-41, AC, epithelium

value: adenocarcinoma epithelia

value: AC

value: M

value: E


title: P45

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

value: Positive

value: Negative


title: Recurrence_patient-42_BAC_epi

description: Sample 87.

source_name: Recurrence case, patient-42, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia


title: Recurrence_patient-40_BAC_epi

description: Sample 83.

source_name: Recurrence case, patient-40, BAC, epithelium

value: Y

source_name: Reference RNA


title: Recurrence_patient-41_AC_str

description: Sample 86.

source_name: Recurrence case, patient-41, AC, stromum

value: adenocarcinoma stroma


title: P44

tag: er status

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: kmt2c mutations

tag: pik3ca mutations

tag: pten mutations

tag: tp53 mutations


title: P43

tag: tissue

value: Basal


title: Recurrence_patient-39_SCC_str

description: Sample 82.

source_name: Recurrence case, patient-39, SCC, stromum

value: squamous cell carcinoma stroma

tag: patient

tag: recurrence

tag: histology

value: SCC

tag: gender

value: F

tag: race

value: White

tag: sample type


title: P42

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

tag: cdh1 mutations

tag: map3k1 mutations


title: Recurrence_patient-39_SCC_epi

description: Sample 81.

source_name: Recurrence case, patient-39, SCC, epithelium

value: squamous cell carcinoma epithelia

value: current

value: reference


title: Kidney_lupus NZB/W (late remission_Ad-TACI-Ig+CTLA4Ig) rep5

description:
Sample name: Late5_E18RU
Kidney from lupus NZB/W mouse (late remission after Ad-TACI-Ig+CTLA4Ig)
Gene expression data from NZB/W kidney after late remission with Ad-TACI-Ig+CTLA4Ig

source_name: Kidney from NZB/W mouse under late remission

tag: strain

value: NZB/W

tag: treatment

tag: disease state

value: late remission

value: Whole kidney


title: Ovary,Mouse190,control

city: Chapel Hill

first: Jonathan

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description: OV190 2c

hyb_protocol: The Beckman Coulter Biomek FXP Laboratory Automation Workstation with the Target Express set up was used to prepare the samples with these two kits. Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays.

scan_protocol: Hybridization, washing, staining and scanning of the Affymetrix Mouse Gene 2.1 ST peg plate arrays was carried out using the Affymetrix GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control. Affymetrix Expression Console Software was used for basic data analysis and quality control.

data_processing: Affymetrix CEL files were normalized using the Robust Multichip Average normalization method. Expression changes (tumor versus control) were determined using Linear Models for Microarray Data Analysis (LIMMA) or Significance Analysis of Microarray (SAM) analysis. Probes with a false discovery rate (FDR) of 0% were considered statistically significant.

source_name: control ovary

label_protocol: Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.

growth_protocol: All mice were maintained at the University of North Carolina at Chapel Hill, Animal Facility using standard techniques in accordance with protocols approved by the University of North Carolina at Chapel Hill Institutional Animal Care and Use Committee.

extract_protocol: Total RNA was extracted from pulverized tumor samples or ovarian epithelial cells using the TRIzol method (Invitrogen), followed by an RNA cleanup step and on-column DNA digestion using the RNAeasy mini prep kit (Qiagen) according to the manufacturers’ instructions. The WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.

treatment_protocol: To induce genetic recombination in the ovarian surface epithelium (OSE), we employed a modified version of the ex-vivo AdCRE intrabursal delivery method. Briefly, AdCRE particles (obtained from the University of Iowa Gene Transfer Core) were diluted in sterile 1X Dulbeccos’s phosphate buffered saline (dPBS) containing 8 μg/mL polybrene. Deeply anesthetized 8-10 week old mice were given a single 5 μL injection of AdCRE particles (2.5E7 plaque-forming units or pfu) into the right ovarian bursal cavity of the surgically exposed ovary using a sterile 31 gauge needle. Immediately following AdCRE injection, the surgically excised ovaries were washed thoroughly with sterile 1X dPBS and placed back into the abdominal cavity. The surgeries were performed on multiple occasions. Age- and genotype-matched, non-littermate animals were randomized prior to AdCRE injection. The surgeon was blinded to the genotypes prior to surgery and AdCRE injection. All surgical procedures were performed in accordance with protocols approved by the University of North Carolina at Chapel Hill Institutional Animal Care and Use Committee.

value: outbred

tag: mouse id

value: mouse 190

tag: genotype/variation

tag: injected with

value: none(the left control ovary)

tag: tissue type

value: Healthy ovary


title: Non-recurrence_patient-38_AC_str

description: Sample 80.

source_name: Non-recurrence case, patient-38, AC, stromum

tag: tissue

tag: patient

tag: recurrence

value: N

tag: histology

value: AC

tag: gender

tag: race

value: Black

value: former

value: S

tag: sample type


title: Ovary,Mouse190,tumor

description: OV190 1T

source_name: tumor

value: AdCRE virus particles (the right ovary)

value: Ovarian clear cell carcinoma


title: Ovary,Mouse179,control

description: OV179 2c

value: mouse 179


title: P41-replicate

value: primary breast tumor

tag: ht12 subtype pam50

value: LumB

tag: ht12 subtype sorlie

tag: ht12 subtype hu

value: Normal

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

value: Basal

tag: er status

value: Positive

tag: pgr status

value: Negative

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: pik3ca mutations

tag: tp53 mutations


title: Kidney_lupus NZB/W (late remission_Ad-TACI-Ig+CTLA4Ig) rep3

description:
Sample name: Late3_E18LU
Kidney from lupus NZB/W mouse (late remission after Ad-TACI-Ig+CTLA4Ig)
Gene expression data from NZB/W kidney after late remission with Ad-TACI-Ig+CTLA4Ig

tag: strain

value: NZB/W

tag: treatment

tag: disease state

value: late remission

tag: tissue

value: Whole kidney


title: Kidney_lupus NZB/W (late remission_Ad-TACI-Ig+CTLA4Ig) rep4

description:
Sample name: Late4_E18RL
Kidney from lupus NZB/W mouse (late remission after Ad-TACI-Ig+CTLA4Ig)
Gene expression data from NZB/W kidney after late remission with Ad-TACI-Ig+CTLA4Ig


title: P41

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

value: LumA


title: Non-recurrence_patient-38_AC_epi

description: Sample 79.

source_name: Non-recurrence case, patient-38, AC, epithelium

value: adenocarcinoma epithelia

tag: patient

tag: recurrence

value: N

tag: histology

value: AC

tag: gender

value: F

tag: race

value: E

tag: sample type

value: reference


title: Primary melanoma_27

source_name: Primary melanoma

value: melanoma

tag: mutation status

value: Sporadic

tag: thickness

value: SSM

tag: clark

tag: number of replicates


title: Kidney_lupus NZM2410 (remission_Ad-BAFF-R-Ig) rep1

description:
Sample name: Baff1_MP1LL
Kidney from lupus NZM2410 mouse (remission after Ad-BAFF-R-Ig)
Gene expression data from NZM2410 kidney after remission with Ad-BAFF-R-Ig

source_name: Kidney from NZM2410 mouse under remission

value: Ad-BAFF-R-Ig

value: remission


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep8

description:
Sample name: CRM8_V8RU
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154

source_name: Kidney from NZB/W mouse under early remission

value: triple therapy CTX+CTLA4Ig+anti-CD154

value: early remission


title: Non-recurrence_patient-37_SCC_epi

description: Sample 77.

source_name: Non-recurrence case, patient-37, SCC, epithelium

value: squamous cell carcinoma epithelia

value: SCC

value: White

value: current


title: Ovary,Mouse153,tumor

description: OV153 1T

value: outbred

tag: mouse id

value: mouse 153

tag: genotype/variation

tag: injected with

value: AdCRE virus particles (the right ovary)

tag: tissue type

value: Ovarian clear cell carcinoma


title: Ovary,Mouse166,tumor

description: OV166 1T

tag: strain

value: mouse 166


title: Kidney_lupus NZB/W (late remission_Ad-TACI-Ig+CTLA4Ig) rep2

description:
Sample name: Late2_E18LL
Kidney from lupus NZB/W mouse (late remission after Ad-TACI-Ig+CTLA4Ig)
Gene expression data from NZB/W kidney after late remission with Ad-TACI-Ig+CTLA4Ig

value: NZB/W

tag: treatment

tag: disease state

value: late remission

tag: tissue

value: Whole kidney


title: Ovary,Mouse153,control

description: OV153 2c

value: none(the left control ovary)

value: Healthy ovary


title: P39

source_name: Primary breast tumor

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

value: LumB

tag: ht12 subtype hu

value: Normal

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

tag: erbb2 status

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: apc mutations

tag: tp53 mutations


title: P40

tag: erbb2 mutations

tag: pik3ca mutations


title: Ovary,Mouse139,control

tag: strain

tag: mouse id

value: mouse 139

tag: genotype/variation

tag: injected with

tag: tissue type


title: P38

tag: tissue

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie


title: P37

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: sf3b1 mutations


title: Recurrence_patient-36_AC_str

description: Sample 76.

source_name: Recurrence case, patient-36, AC, stromum

value: adenocarcinoma stroma

tag: patient

tag: recurrence

value: Y

tag: histology

value: AC

tag: gender

value: M

tag: race

value: White

value: current

value: S

tag: sample type

value: reference


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep7

description:
Sample name: CRM7_BG10_0
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154

tag: strain

value: NZB/W

tag: treatment

value: triple therapy CTX+CTLA4Ig+anti-CD154

tag: disease state

value: early remission

tag: tissue

value: Whole kidney


title: Non-recurrence_patient-37_SCC_str

description: Sample 78.

source_name: Non-recurrence case, patient-37, SCC, stromum

value: squamous cell carcinoma stroma

value: N

value: SCC

value: F


title: Recurrence_patient-35_AC_str

description: Sample 74.

source_name: Recurrence case, patient-35, AC, stromum

value: former


title: Kidney_lupus NZB/W (late remission_Ad-TACI-Ig+CTLA4Ig) rep1

description:
Sample name: Late1_E5O
Kidney from lupus NZB/W mouse (late remission after Ad-TACI-Ig+CTLA4Ig)
Gene expression data from NZB/W kidney after late remission with Ad-TACI-Ig+CTLA4Ig

value: late remission


title: Recurrence_patient-36_AC_epi

description: Sample 75.

source_name: Recurrence case, patient-36, AC, epithelium

value: adenocarcinoma epithelia

value: Y

value: E

source_name: Reference RNA


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep6

description:
Sample name: CRM6_BG8LL
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep3

description:
Sample name: CRM3_GG10
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: Recurrence_patient-35_AC_epi

description: Sample 73.

source_name: Recurrence case, patient-35, AC, epithelium

value: AC

value: M

value: White


title: P36

value: primary breast tumor

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

value: Positive

value: Negative

tag: lymphocyte content (1

tag: pik3ca mutations


title: P35

value: LumB

tag: er status

tag: pgr status

tag: erbb2 status

value: Amplified

tag: nottingham grade

tag: tumor cell content (1

tag: tp53 mutations


title: Ovary,Mouse137,control

tag: strain

value: outbred

tag: mouse id

value: mouse 137

tag: genotype/variation

tag: injected with

value: none(the left control ovary)

tag: tissue type

value: Healthy ovary


title: Ovary,Mouse139,tumor

description: OV139 1T

value: mouse 139

value: AdCRE virus particles (the right ovary)

value: Ovarian clear cell carcinoma


title: Ovary,Mouse166,control

description: OV166 2c

value: mouse 166


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep2

description:
Sample name: CRM2_GG2L
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154

value: NZB/W

tag: treatment

value: triple therapy CTX+CTLA4Ig+anti-CD154

tag: disease state

value: early remission

tag: tissue

value: Whole kidney


title: Ovary,Mouse137,tumor

description: OV137 1T


title: Ovary,Mouse179,tumor

description: OV179 1T

value: mouse 179


title: Ovary,Mouse129,tumor

value: mouse 129


title: P34

value: primary breast tumor

tag: ht12 subtype pam50

value: LumA

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

value: Positive

value: Negative


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep4

description:
Sample name: CRM4_GG1RL
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep1

description:
Sample name: CRM1_BG9RL
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: P33

value: LumB

value: Basal

tag: er status

tag: pgr status

tag: erbb2 status

value: Amplified

tag: nottingham grade

tag: lymphocyte content (1

tag: sf3b1 mutations


title: Ovary,Mouse129,control

tag: strain

value: outbred

tag: mouse id

tag: genotype/variation

tag: injected with

value: none(the left control ovary)

value: Healthy ovary


title: Recurrence_patient-34_SCC_str

description: Sample 72.

source_name: Recurrence case, patient-34, SCC, stromum

tag: tissue

value: squamous cell carcinoma stroma

tag: patient

tag: recurrence

value: Y

tag: histology

value: SCC

tag: gender

value: M

tag: race

value: Black

value: former

value: S

tag: sample type

value: reference


title: Ovary,Mouse127,control

description: OV127 c

value: mouse 127

tag: tissue type


title: Recurrence_patient-33_AC_str

description: Sample 70.

source_name: Recurrence case, patient-33, AC, stromum

value: adenocarcinoma stroma

value: AC

value: White


title: Recurrence_patient-34_SCC_epi

description: Sample 71.

source_name: Recurrence case, patient-34, SCC, epithelium

value: squamous cell carcinoma epithelia

value: E


title: P32

value: primary breast tumor

tag: ht12 subtype pam50

value: Basal

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Positive

tag: pgr status

value: Negative

tag: tumor cell content (1

tag: pik3ca mutations

tag: tp53 mutations


title: P31

tag: tissue

value: LumA

tag: erbb2 status

tag: nottingham grade

tag: lymphocyte content (1

tag: kmt2c mutations


title: Recurrence_patient-33_AC_epi

description: Sample 69.

source_name: Recurrence case, patient-33, AC, epithelium

value: adenocarcinoma epithelia

tag: patient

tag: recurrence

value: Y

tag: histology

tag: gender

tag: race

tag: sample type


title: Ambion normal uterus cell line

city: Helsinki

first: Johanna

last: Lotsari-Salomaa

address: Haartmaninkatu 8

department: Department of Medical Genetics

country: Finland

institute: University of Helsinki

hyb_protocol: The slides were hyridized in 2X Hi-RPM Hybridization Buffer for 20 hours in +55 ̊C in the Microarray Hybridization Chamber.

scan_protocol: After hybridization the slides were washed and scanned on an Agilent Technologies DNA Microarray G2505C Scanner. Signal intensities of fluorescence were calculated by Agilent's Feature Extraction software (version 10.7.3.1). Microarrays were investigated in duplicates for each cell lines.

data_processing:
GeneSpring GX software (version 11.0.2, Agilent Technologies) was used for miRNA data analysis. Data was normalized by quantile normalization.
Statistically significant differentially expressed miRNA were identified by T-test unpaired combined with the Benjamini and Hochberg correction for multiple testing and using filters based on p-value cut-off 0.05 and fold change cut-off +/- 2.00.

source_name: human normal uterus cell line

label_protocol: Agilent's human miRNA arrays (8x15K from Agilent Technologies, G4470B) containing 723 human and 76 human viral miRNAs sources from the Sanger miRBase, v.10.1 were used according to the protocol. 100 ng of RNA were used in Microarrays and samples were labelled with Cyanine3-pCp (Cy3).

growth_protocol: All cell lines were purchased from the American Type Culture Collection (Rockville, MD, USA) or JCRB and cultured according to the suppliers' protocol.

extract_protocol: Total RNA was extracted with miRNAeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol:
Cells were treated with 5 uM 5-aza-2' deoxycytidine (5-Aza, Sigma, A3656) for 96 hours and with 200nM trichostatin (TSA, Sigma, T1952) for 18 hours. All treatments were performed in duplicates.
The efficiency of the drug treatments was confirmed by expressional (Taqman) and methylation (SALSA MS-MLPA ME001-C1 Tumor Suppressor-1 kit, MRC-Holland, Amsterdam, the Netherlands) analyses of selected tumor suppressor genes in all cell lines, as well as by IHC analysis of MLH1 in RKO.

tag: cell line

value: uterus

tag: treatment


title: Amsbio Dr P Set normal uterus cell line


title: Kidney_lupus NZB/W (30 weeks old) rep7

description:
Sample name: 30wks7_BG10RL
Kidney from lupus NZB/W mouse (30 weeks old)
Gene expression data from NZB/W non-proteinuric kidney (30 weeks old)

source_name: Kidney from non-proteinuric NZB/W mouse

tag: disease state

value: non-proteinuric

tag: strain

value: NZB/W

tag: age

value: 30 weeks old

value: Whole kidney


title: Non-recurrence_patient-32_AC_str

description: Sample 68.

source_name: Non-recurrence case, patient-32, AC, stromum

value: adenocarcinoma stroma

value: N

value: F

value: former

value: S

value: reference


title: Kidney_lupus NZB/W (30 weeks old) rep5

description:
Sample name: 30wks5_BG9LL
Kidney from lupus NZB/W mouse (30 weeks old)
Gene expression data from NZB/W non-proteinuric kidney (30 weeks old)


title: Kidney_lupus NZB/W (30 weeks old) rep3

description:
Sample name: 30wks3_BG4RU
Kidney from lupus NZB/W mouse (30 weeks old)
Gene expression data from NZB/W non-proteinuric kidney (30 weeks old)


title: Ovary,Mouse122,control

description: OV122 2c

source_name: control ovary

value: outbred

tag: mouse id

value: mouse 122

tag: genotype/variation

tag: injected with

value: none(the left control ovary)

tag: tissue type

value: Healthy ovary


title: Kidney_lupus NZB/W (30 weeks old) rep6

description:
Sample name: 30wks6_BG9RL
Kidney from lupus NZB/W mouse (30 weeks old)
Gene expression data from NZB/W non-proteinuric kidney (30 weeks old)

tag: tissue


title: Amsbio Dr P Set normal colon cell line

source_name: human normal colon cell line

value: colon


title: Non-recurrence_patient-32_AC_epi

description: Sample 67.

source_name: Non-recurrence case, patient-32, AC, epithelium

value: adenocarcinoma epithelia

value: AC

value: White

value: E


title: Amsbio normal uterus pool

source_name: human normal uterus cell line, pool of 5 donors

value: uterus


title: Kidney_lupus NZB/W (30 weeks old) rep4

description:
Sample name: 30wks4_BG8RU
Kidney from lupus NZB/W mouse (30 weeks old)
Gene expression data from NZB/W non-proteinuric kidney (30 weeks old)

value: non-proteinuric

value: NZB/W

value: 30 weeks old

value: Whole kidney


title: P29

source_name: Primary breast tumor

value: primary breast tumor

tag: ht12 subtype pam50

value: Basal

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

tag: er status

value: Negative

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: nf1 mutations

tag: tp53 mutations


title: Ovary,Mouse127,tumor

description: OV127 1T

source_name: tumor

tag: strain

value: outbred

tag: mouse id

value: mouse 127

tag: genotype/variation

tag: injected with

value: AdCRE virus particles (the right ovary)

value: Ovarian clear cell carcinoma


title: Kidney_lupus NZB/W (early remission_CTX+CTLA4Ig+anti-CD154) rep5

description:
Sample name: CRM5_BG1LL
Kidney from lupus NZB/W mouse (early remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after early remission with triple therapy CTX+CTLA4Ig+anti-CD154

source_name: Kidney from NZB/W mouse under early remission

tag: treatment

value: triple therapy CTX+CTLA4Ig+anti-CD154

tag: disease state

value: early remission

tag: tissue


title: P28

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

value: LumB

value: Positive


title: Non-recurrence_patient-31_BAC_str

description: Sample 66.

source_name: Non-recurrence case, patient-31, BAC, stromum

value: bronchioloalveolar carcinoma stroma

tag: patient

tag: recurrence

value: N

tag: histology

value: BAC

tag: gender

value: M

tag: race

value: White

value: former

value: S

tag: sample type

value: reference


title: Amsbio normal colon pool

source_name: human normal colon cell line, pool of 5 donors

tag: cell line

value: colon


title: Ambion normal colon cell line


title: Non-recurrence_patient-31_BAC_epi

description: Sample 65.

source_name: Non-recurrence case, patient-31, BAC, epithelium

value: bronchioloalveolar carcinoma epithelia

value: E

source_name: Reference RNA


title: P30

value: primary breast tumor

value: LumA

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: erbb2 status

value: Negative

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: pik3ca mutations


title: P27

tag: tissue

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50


title: HEC59 human endometrioid adenocarcinoma, untreated cell line 2

description: MMR-deficient

value: JCRB JCRB1120

value: uterus

tag: treatment


title: P26

value: LumB

tag: rna-seq subtype sorlie

value: Positive


title: P25

value: Basal

tag: kmt2c mutations

tag: tp53 mutations


title: Non-recurrence_patient-30_AC_str

description: Sample 64.

source_name: Non-recurrence case, patient-30, AC, stromum

value: adenocarcinoma stroma

tag: patient

tag: recurrence

value: N

tag: histology

value: AC

tag: gender

value: F

tag: race

value: current

tag: sample type


title: Ovary,Mouse122,tumor

description: OV122 1T

tag: strain

value: outbred

tag: mouse id

value: mouse 122

tag: genotype/variation

tag: injected with

value: AdCRE virus particles (the right ovary)

tag: tissue type

value: Ovarian clear cell carcinoma


title: P24-replicate

tag: tissue

value: primary breast tumor

tag: ht12 subtype pam50

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype hu

tag: er status

tag: pgr status

tag: erbb2 status

value: Amplified

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: Non-recurrence_patient-30_AC_epi

description: Sample 63.

source_name: Non-recurrence case, patient-30, AC, epithelium

value: adenocarcinoma epithelia

tag: patient

tag: recurrence

tag: histology

tag: gender

tag: race

value: White

value: E

tag: sample type

value: reference


title: HEC59 human endometrioid adenocarcinoma, untreated cell line 1

description: MMR-deficient

tag: cell line

value: JCRB JCRB1120

tag: tissue

value: uterus

tag: treatment


title: HEC59 human endometrioid adenocarcinoma, treated cell line 2

description: MMR-deficient

value: cultured with 5-Aza and TSA


title: Non-recurrence_patient-29_SCC_epi

description: Sample 61.

source_name: Non-recurrence case, patient-29, SCC, epithelium

value: squamous cell carcinoma epithelia

value: N

value: SCC

value: M

value: former


title: Non-recurrence_patient-29_SCC_str

description: Sample 62.

source_name: Non-recurrence case, patient-29, SCC, stromum

value: squamous cell carcinoma stroma

value: S


title: P24

tag: ht12 subtype pam50

value: LumB

tag: ht12 subtype sorlie

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

value: Positive


title: HEC59 human endometrioid adenocarcinoma, treated cell line 1

description: MMR-deficient


title: Kidney_lupus NZB/W (30 weeks old) rep2

description:
Sample name: 30wks2_BG4LU
Kidney from lupus NZB/W mouse (30 weeks old)
Gene expression data from NZB/W non-proteinuric kidney (30 weeks old)

source_name: Kidney from non-proteinuric NZB/W mouse

tag: disease state

value: non-proteinuric

tag: strain

value: NZB/W

tag: age

value: 30 weeks old

value: Whole kidney


title: P23-replicate

value: primary breast tumor

value: LumA

tag: rna-seq subtype hu

tag: er status

tag: pgr status

value: Negative

tag: erbb2 status

value: Amplified

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1


title: AN3CA human endometrium adenocarcinoma cell line, untreated cell line 2

description: MMR-deficient

tag: cell line

value: ATCC HTB-111

tag: tissue

value: uterus


title: Non-recurrence_patient-28_SCC_epi

description: Sample 59.

source_name: Non-recurrence case, patient-28, SCC, epithelium

value: squamous cell carcinoma epithelia

tag: patient

tag: recurrence

value: N

tag: histology

value: SCC

tag: gender

tag: race

value: White

value: E

tag: sample type

value: reference


title: Non-recurrence_patient-28_SCC_str

description: Sample 60.

source_name: Non-recurrence case, patient-28, SCC, stromum

value: squamous cell carcinoma stroma

value: M

value: former

value: S


title: Kidney from lupus NZW/BXSB mouse, rep1

description:
8wks1_PK84LU
Gene expression data from NZW/BXSB prenephritic kidney (8 weeks old, non-proteinuric).

scan_protocol: GeneChip arrays were scanned by the GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using the GenePattern pipeline: The RMA method and Mouse Entrez Gene custom CDF annotation version 10 were used for the normalization, and Combat for batch correction within the NZB/W mouse model and the NZW/BXSB mouse model.

source_name: Kidney from prenephritic mouse, NZW/BXSB, 8 weeks old

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

growth_protocol: None.

extract_protocol: Total RNA was isolated using Trizol and the manufacturer's instructions.

treatment_protocol: None.

tag: strain

value: NZW/BXSB

value: 8 weeks

tag: disease status

value: prenephritic, non-proteinuric

value: whole kidney


title: P23

value: primary breast tumor

tag: ht12 subtype pam50

value: LumB

tag: ht12 subtype sorlie

value: LumA

tag: ht12 subtype hu

tag: rna-seq subtype pam50

tag: rna-seq subtype sorlie

tag: rna-seq subtype hu

value: Positive

value: Negative

value: Amplified

tag: tp53 mutations


title: P22

tag: er status

tag: pgr status

tag: erbb2 status

tag: nottingham grade

tag: tumor cell content (1

tag: lymphocyte content (1

tag: nf1 mutations


title: Kidney from lupus NZW/BXSB mouse, rep3

description:
8wks3_PK84RL
Gene expression data from NZW/BXSB prenephritic kidney (8 weeks old, non-proteinuric).

tag: age

tag: tissue


title: AN3CA human endometrium adenocarcinoma cell line, untreated cell line 1

description: MMR-deficient

tag: cell line

value: ATCC HTB-111

value: uterus

tag: treatment


title: Kidney from lupus NZB/W mouse, rep7

description:
Young7_grp1_M7
Gene expression data from NZB/W prenephritic kidney (6 weeks old, non-proteinuric).

source_name: Kidney from prenephritic mouse, NZB/W, 6 weeks old

tag: strain

value: NZB/W

value: 6 weeks

tag: disease status


title: Kidney from lupus NZW/BXSB mouse, rep2

description:
8wks2_PK84O
Gene expression data from NZW/BXSB prenephritic kidney (8 weeks old, non-proteinuric).


title: Kidney from lupus NZB/W mouse, rep5

description:
Young5_grp1_M5
Gene expression data from NZB/W prenephritic kidney (6 weeks old, non-proteinuric).


title: AN3CA human endometrium adenocarcinoma cell line, treated cell line 2

description: MMR-deficient

value: cultured with 5-Aza and TSA