title: 1 uM FK506 Mouse 6

city: Bilthoven

first: Mirjam

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

description: quality control: approved

hyb_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit  According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

scan_protocol: According to Affymetrix protocols, using a GeneChip HT Array Plate Scanner (Affymetrix)

data_processing: The raw data were subjected to a set of quality control checks. After passing array quality control, the arrays were annotated according to de Leeuw et al. (2008) and expression values were calculated using the robust multi-array average (RMA) algorithm (Affy package, version 1.22.0; Irizarry et al. 2003) available from the Bioconductor project (http://www.bioconductor.org) for the R statistical language (http://cran.r-project.org)). The normalized data was statistically analyzed for differential gene expression using a mixed linear model with coefficients for block (random) and each experimental group (fixed) (Smyth 2004; Wolfinger et al. 2001). A contrast analysis was applied to compare each exposure with the corresponding vehicle control. For hypothesis testing, a permutation-based Fs test was used (Cui et al. 2005). False discovery rate (FDR) correction was performed globally across all contrasts according to Storey and Tibshirani (2003). Only the annotated genes were used for further analysis.

source_name: Primary mouse hepatocytes Mouse #6

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

growth_protocol: Primary mouse hepatocytes were isolated from 8-10 weeks old male C57BL/6 mice by a modified two-step collagenase perfusion technique. Cells were cultured in a sandwich configuration in 6-wells  at 1.3 x 10^6 cells per well.

extract_protocol: RNA was extracted using QIAzol and purified using the miRNeasy mini kit and the QIAcube (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Hepatocytes were exposed for 24 hours to a concentration range of Cyclosporin A or Tacrolimus or the vehicle control DMSO (0,5%). After 24 hours of exposure, cells were collected in 1 ml RNAprotect (QIAgen) and stored at -80˚C for RNA isolation.

tag: age

value: 8-9 weeks

tag: chemical

value: Tacrolimus

tag: abbreviation

tag: concentration

value: 1 uM FK506


title: 20mGyT2/ reference male mouse4

status: Public on Dec 23 2016

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

molecule: genomic DNA

organism: Mus musculus

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain

tag: tissue

value: tail

source_name: reference male mouse4


title: 3 uM FK506 Mouse 6

type: RNA

middle: M

description: quality control: approved

label: biotin

molecule: total RNA

tag: gender

value: Male

value: 3 uM FK506


title: reference male mouse4/ 20mGyT2

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: A9-Low responder

city: Tokyo

first: Fumika

last: Shigiyama

address: 6-11-1, Omori Nishi, Otaku

department: Internal Medicine

institute: Toho University

scan_protocol: GeneChip were scaned by GeneChip Scaner 3000(Affymetrix 690036) using GeneChip Command Console Software ver3.2(Affymetrix 702569). The procedure of scan is followed by  Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）

data_processing: Data is processed by RMA-Skech algorythm using Expression ConsoleTM Softwere ver.1.3（Affymetrix 702387）

organism: Homo sapiens

source_name: Low responder_liver biopsy sample

label_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）. 100ng Total RNA was used for this assay.

extract_protocol: Total RNA was extracted from flash frozen ~10 mg liver biopsy using the RNeasy mini kit (Qiagen, Tokyo, Japan). RNA was reverse-transcribed into cDNA using the QuantiTect Reverse Transcription Kit (Qiagen, Hilden, Germany).

tag: subject status

value: Nonalcoholic fatty liver disease (NAFLD)

tag: insuline response

value: Low responder

value: liver biopsy


title: A8-Low responder

hyb_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）

value: Female


title: reference male mouse4/ 20mGyT1


title: 3_premet_Ctrl_rep2

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

hyb_protocol: MAGEX DNA array slides were briefly rinsed in a plastic coplin jar containing WB2 buffer (0.1x SSC, 0.1% (w/v) SDS) and subsequently incubated with 90 mL of PB1 buffer (5x SSC, 0.2% (w/v) BSA, and 0.2% (w/v) SDS) at 48°C for 45 min.  Each slide was dried by centrifugation in a 50 ml falcon tube for 3 min at 200x g.  Dried Lifterslip CS/3 coverslips (Erie Scientific Company) prerinsed with dH2O and 100% ethanol were placed over each DNA array region and the preheated cDNA/UDR samples added to each array. MAGEX array slides were placed in a slide rack and 300µL of dH2O was added to the humidity filter prior to chamber assembly. Hybridization was done for 18 h at 42°C in a Hybex Microsample Incubator (SciGene).  All buffers used in washing were prewarmed at 48°C prior to use. Following hybridization, coverslips were removed and each slide washed for 5 min with WB1 buffer (1x SSC and 0.1% (w/v) SDS). Two subsequent washes were performed with WB2 buffer followed by a wash with WB3 buffer (0.01x SSC and 0.1% (w/v) SDS). Slides were dried by centrifugation for 3 min at 200x g and stored in the dark in a Scienceware autodessicator.

scan_protocol: MAGEX DNA array image data were collected at 5 µm from each slide using a Scan Array Express (Packard Bioscience Co.) as recommended by the manufacturer and at a PMT gain of 70% and laser level of 90% for both Cy5 and Cy3 channels.  Spot intensity levels were obtained via ImaGene Version 9.0 (BioDiscovery Inc.) as per the manufacturer’s protocol using the UDR to align the spot grid.

data_processing: Data normalization involved use of the geometric means derived from the total robust and high quality gene signals obtained for each sample. This resulted in normalization factors between 1.00 and 1.21. An appropriate background signal was determined by evaluating the empty and buffer-only spot positions interspersed throughout each array. The universal floor was set at 2 robust standard deviations greater than the highest median background signal across all arrays, helping to minimize false positives due to low signal intensities.  Data was log2 transformed to minimize heteroscedasticity.

organism: Xenopus laevis

source_name: liver, premet, Ctrl

label_protocol: The DecaLabel DNA Labelling Kit was used to incorporate Cy3-dCTP (GE Healthcare Bio-Sciences Corp.) into cDNA according to manufacturer’s specification (Fermentas). To aid in microarray data collection, a universal DNA reference (UDR) containing amplicons representative of all gene sequences present on the MAGEX microarray was  labeled as above with Cy5-dCTP (GE Healthcare Bio-Sciences Corp.).  Labelled DNA was purified with the GeneJET PCR Purification Kit, and sufficient fluorophore incorporation was determined with the Nanodrop UV-Vis spectrophotometer (ND-1000, Thermo Scientific).  Labelled DNA was precipitated with sequential addition of 20 μg glycogen (ThermoFisher Scientific), 5 µl of 3 M sodium acetate (pH 5.2), and 150 µl of chilled 100% ethanol. Samples were incubated at -20 °C for a minimum of 60 min followed by centrifugation at 13,000 x g at 4 °C for 20 min. The DNA pellet was washed once with 300 µL 75% ethanol and air dried for 10 min prior to addition of 7 µl (samples) or 30 µl (UDR) dH2O, and stored at -20°C in 1.5 ml amber tubes. For hybridization, Cy5-labeled UDR (1 µL) was mixed with each Cy3-labeled cDNA (5.5 µL) and incubated at 95°C for 3 min followed by cooling on ice and a brief centrifugation to collect the denatured material. For each sample, a 33 µL hybridization solution was prepared that contained 5x SSC, 25% (v/v) deionized formamide, 0.02% (w/v) BSA, 1 µg A45 oligonucleotide, 0.1% (w/v) SDS, 5% (w/v) dextran, and 6.5 µL denatured labelled DNA and warmed briefly at 37°C prior to application onto the covered MAGEX array.

growth_protocol: Laboratory populations of X. laevis were housed at the Outdoor Aquatic Unit at the University of Victoria, BC.  All animals were treated and maintained in accordance with the guidelines of the Canadian Council on Animal Care and the Animal Care Committee guidelines of the University of Victoria.  Mature adults were bred by injection of human chorionic gonadotropin (Sigma-Aldrich, Oakville, ON, Cat#CG10) at 500 and 1000 IU into males and females, respectively.  Eggs and newly hatched tadpoles were kept in tadpole rearing water consisting of dechlorinated water treated with NaHCO3 and synthetic sea salts (Instant Ocean sea salt, Aquarium Systems Inc, Mentor, OH, USA) to a pH of 7.4-7.8 and salinity of 0.4 ppt.  A pump was used to circulate water and keep dissolved oxygen (DO) >90%.  After initiation of feeding behaviour and throughout the exposures tadpoles were fed Nasco frog brittle (Nasco, Modesto, CA, USA; Cat#:SA05961), ground and suspended at 10% (w/v) in untreated tap water.  Tadpoles were monitored until sufficient numbers reached the appropriate developmental stage for each exposure (n=200).  Conditions were based on the Organisation for Economic Co-operation and Development (OECD) guidelines for the Amphibian Metamorphosis Assay (AMA; Guideline 231, 2009).  In brief, four replicate exposure tanks (2 L glass beakers) were used within each treatment for a total of 20 tanks/exposure. Ten tadpoles were acclimated in each tank containing 2L tadpole rearing water for 24 h prior to treatment addition. Tadpole density was maintained at approximately 5 tadpoles/L, and water adjusted to 1.2L after removal of 4 tadpoles/tank on experimental day 2. Temperature was kept at 20.3 ±0.2°C with a photoperiod of 12/12 h light/dark. Glass pipettes were used as aerators to maintain high DO, prevent stagnation, and ensure treatments were thoroughly dispersed after chemical addition.  Nitrogenous wastes were monitored throughout the exposure with Aquacheck strips (Nitrate/Nitrite test strips; Ammonium test strips; Elkhart, IN, USA) to prevent toxic concentrations. Animals were euthanized with 0.1% (w/v) tricaine methanesulfonate (MS-222; Syndel Laboratories Ltd, Vancouver, BC) in tadpole rearing water with 25 mM NaHCO3.

extract_protocol: Total RNA was extracted from whole livers with TRIzol reagent (Invitrogen) according to manufacturer’s protocol. Premetamorphic tadpole livers were homogenized in 200 µl TRIzol manually with a micropestle, while prometamorphic livers were homogenized in 300 µl TRIzol using a 1mm tungsten-carbide bead and a Retsch MM301 mixer mill at 20 Hz for 6 min.  To increase RNA yield, 20 µg glycogen was added prior to isopropanol precipitation. Isolated RNA was resuspended in 40 and 60 µl diethyl pyrocarbonate (DEPC)-treated RNase-free water for the pre- and prometamorphic livers, respectively. Total RNA was quantified using Nanodrop UV- Vis spectrophotometer (ND-1000, Thermo Scientific), and stored at -80°C. cDNA was prepared using the SMARTer PCR cDNA Synthesis Kit as per manufacturer’s protocol (Clontech Laboratories Inc.) with subsequent purification of amplified cDNA with the GeneJET PCR Purification Kit (Fermentas), and stored at -20°C.

treatment_protocol: Two 48 h exposure sets were conducted with either pre- or prometamorphic tadpoles starting at NF51 and NF56 (Nieuwkoop and Faber, 1994), respectively. In each exposure, tadpoles were immersed in tadpole rearing water containing 1 of 5 treatments: negative control with 50 nM NaOH (Ctrl), T3 positive control (10 nM T3 in 50 nM NaOH), or 3 concentrations of nAg (0.018, 0.18 or 1.8 µg/L by Ag content), referred to here as Lo, Med or Hi nAg. After 48 h exposure tadpoles were euthanized in 0.1% (w/v) MS-222 and preserved whole in RNAlater (Life Technologies) as described by the manufacturer. The preserved tissue was stored at -20°C until dissection of tadpole liver prior to isolation of total RNA.

tag: developmental stage

value: Nieuwkoop and Faber stage 53

tag: unique animal number

value: liver


title: RAT_AP_34d_1

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

description:
Peripheral blood mononuclear cells from AP after 34 days therapy, replicate 1
small RNA expression data from RA rats after 34 days acupuncture therapy

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing: The scanned the image were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data were normalized by robust  multiple array average (RMA) using R package  Agi MicroRna.

organism: Rattus norvegicus

source_name: RAT Peripheral blood mononuclear cells

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Blood sampling was carried out before any therapy in RA (RA_T0) and NORA  (NORA_T0) groups whereas in the other groups (AP/MEC, MTX,ANE, PLA and NORA) at 1hour and  at 34 days after therapy. Animals were induced in deep general anesthesia and after total blood drawing (5ml), sacrificed by neck dislocation.

extract_protocol: Total RNA was extracted and purified using mirVanaTM mRNA and miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) checked for the RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were freshly isolated on Ficoll gradient (Histopaque®-1077, Sigma Aldrich, USA) according to the manufacture procedures. Separated cell were maintained in RNA Later (Ambion, USA) at -80ºC until the end of the study and then processed in a whole batch for the following extraction.

value: Wistar

value: RAT Peripheral blood mononuclear cells


title: RAT_AP_34d_2

description:
Peripheral blood mononuclear cells from AP after 34 days therapy, replicate 2
small RNA expression data from RA rats after 34 days acupuncture therapy


title: 10 uM FK506 Mouse 6

description: quality control: approved


title: 37_premet_HiAg_rep1

source_name: liver, premet, HiAg


title: A7-High responder

source_name: High responder_liver biopsy sample

value: High responder


title: RAT_NORA_34d_2

description:
Peripheral blood mononuclear cells from NORA after 1 hour therapy, replicate 2
small RNA expression data from healthy rats at 34 days after therapy


title: 30 uM FK506 Mouse 6

description: quality control: approved


title: A2-Low responder


title: DMSO Mouse 6

description: quality control: approved

value: DMSO controle

value: DMSO


title: A4-High responder


title: reference male mouse4/ 20mGyTF


title: A1-High responder


title: 20mGyTF/ reference male mouse4


title: 20mGyTM/ reference male mouse4


title: RAT_NORA_34d_1

description:
Peripheral blood mononuclear cells from NORA after 1 hour therapy, replicate 1
small RNA expression data from healthy rats at 34 days after therapy


title: 1 uM CSA Mouse 6

description: quality control: approved

value: 8-9 weeks

value: Cyclosporin A

value: CSA

value: 1 uM CSA


title: RAT_PLA_1h_2

description:
Peripheral blood mononuclear cells from PLA after 1 hour therapy, replicate 2
small RNA expression data from RA rats after 1 hour placebo therapy


title: 0.3 uM CSA Mouse 6

description: quality control: approved

value: Male

value: 0.3 uM CSA


title: nTreg AZA 3

city: St louis

first: John

middle: F

last: DiPersio

state: MO

address: 660 South Euclid Ave

country: USA

institute: Washington University

description: WT PICO

hyb_protocol: 3.8 ug of fragmented and labeled ssDNA was hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 2.0 ST Array. Affymetrix Gene 2.0 microarrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: nTreg

label_protocol: Biotinylated ssDNA were prepared according to Affymetrix  Genechip WT Pico Reagent kit from 100 pg-2 ng total RNA.   Following fragmentation and labeling of 5 ug of ssDNA with WT pico reagent kit

growth_protocol: To distinguish between nTregs and AzaC generated Tregs, nTregs were purified from the spleens of B6.Foxp3GFP mice and Treg depleted T cells were obtained from B6. Foxp3GFP x B6.CAGDSRED. T Cells were co-cultured at a 1:10 ratio of nTreg to Teff and were activated for 2 days in the presence of anti-CD3/CD28 beads (bead:cell 1:1; Invitrogen) and Xcyte medium supplemented with L-glutamine (4mM), penicillin (100 U/mL), streptomycin (100 µg/mL), and human recombinant IL-2 (hIL-2; 500 U/mL).

extract_protocol: RNA was extracted from T cells using the RNA nucleospin XS Kit (Macheray-Nagel, Düren Germany).

treatment_protocol:
1uM AzaC
The activated T cells were incubated in the presence of AzaC (1µM) (Sigma-Aldrich) or PBS for an additional 2 days.  Cells were sorted using FACS Aria II (BD) to isolate nTreg (CD4+DSRED-FOXP3GFP+), CD4+ Teff (CD4+DSRed+FOXP3GFP-), CD8+ Teff (CD8+DSRed+FOXP3GFP-).

tag: cell type

value: In vitro activated nTreg


title: 20mGyS3/ reference male mouse4

value: tail


title: RAT_PLA_1h_1

description:
Peripheral blood mononuclear cells from PLA  after 1 hour therapy, replicate 1
small RNA expression data from RA rats after 1 hour placebo therapy


title: RAT_ANE_1h_1

description:
Peripheral blood mononuclear cells from ANE  after 1 hour therapy, replicate 1
small RNA expression data from RA rats after 1 hour ANE therapy


title: 20mGyS2/ reference male mouse4


title: 10 uM CSA Mouse 6

description: quality control: approved

value: 10 uM CSA


title: nTreg AZA 2

description: WT PICO


title: nTreg PBS 3

description: WT PICO

treatment_protocol:
PBS
The activated T cells were incubated in the presence of AzaC (1µM) (Sigma-Aldrich) or PBS for an additional 2 days.  Cells were sorted using FACS Aria II (BD) to isolate nTreg (CD4+DSRED-FOXP3GFP+), CD4+ Teff (CD4+DSRed+FOXP3GFP-), CD8+ Teff (CD8+DSRed+FOXP3GFP-).


title: 30 uM CSA Mouse 6

description: quality control: approved

value: 30 uM CSA


title: 3 uM CSA Mouse 6

description: quality control: approved

value: 3 uM CSA


title: nTreg AZA 1

description: WT PICO


title: 20mGyS1/ reference male mouse4


title: RAT_MTX_1h_2

description:
Peripheral blood mononuclear cells from MTX  after 1 hour therapy, replicate 2
small RNA expression data from RA rats after 1 hour MTX therapy

value: Female


title: reference male mouse4/ 20mGyS2


title: RAT_MTX_1h_1

description:
Peripheral blood mononuclear cells from MTX after 1 hour therapy, replicate 1
small RNA expression data from RA rats after 1 hour MTX therapy

value: Wistar


title: nTreg PBS 1

description: WT PICO


title: 3 uM FK506 Mouse 5

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #5

value: Tacrolimus

value: 3 uM FK506


title: reference male mouse4/ 20mGyS1


title: RAT_AP_1h_2

description:
Peripheral blood mononuclear cells from AP after 1 hour therapy, replicate 2
small RNA expression data from RA rats after 1 hour acupuncture therapy

value: RAT Peripheral blood mononuclear cells


title: RAT_AP_1h_1

description:
Peripheral blood mononuclear cells from AP after 1 hour therapy, replicate 1
small RNA expression data from RA rats after 1 hour acupuncture therapy


title: reference male mouse4/ 20mGySF


title: RAT_ANE_1h_2

description:
Peripheral blood mononuclear cells from ANE after 1 hour therapy, replicate 2
small RNA expression data from RA rats after 1 hour ANE therapy


title: 20mGySM/ reference male mouse4


title: DMSO Mouse 5

description: quality control: approved

value: DMSO controle

value: DMSO


title: CD4 AZA 3

description: WT PICO

source_name: CD4+ T cell

value: In vitro activated CD4+ T cell


title: RAT_NORA_1h_2

description:
Peripheral blood mononuclear cells from NORA after 1 hour therapy, replicate 2
small RNA expression data from healthy rats at 1 hour after therapy


title: 30 uM FK506 Mouse 5

description: quality control: approved

value: 8-9 weeks


title: 0.3 uM CSA Mouse 5

description: quality control: approved

value: Cyclosporin A

value: CSA


title: CD4 AZA 1

description: WT PICO


title: CD4 PBS 3

description: WT PICO


title: 20mGySF/ reference male mouse4


title: reference male mouse4/ 20mGySM


title: reference male mouse4/ 20mGyS3


title: 1 uM CSA Mouse 5

description: quality control: approved

value: Male

value: 1 uM CSA


title: RAT_RA_T0_1

description:
Peripheral blood mononuclear cells from RA before therapy, replicate 1
small RNA expression data from RA rats before therapy


title: CD4 PBS 1

description: WT PICO


title: CD4 PBS 2

description: WT PICO


title: 3 uM CSA Mouse 5

description: quality control: approved


title: reference male mouse4/ 20mGyTM

value: tail


title: 20mGyR3/ reference male mouse4


title: 20mGyR4/ reference male mouse4


title: 1 uM FK506 Mouse 5

description: quality control: approved

value: 1 uM FK506


title: reference male mouse4/ 20mGyR3


title: c2c12 10% FBS, 10nM BTZ rep1

city: suzhou

first: congcong

last: shen

address: renai road

country: China

institute: suzhou university

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

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

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

source_name: c2c12 10% FBS  10nM BTZ

label_protocol: Total RNA were amplified, labeled and purified by using Affymetrix  WT Amplication Kit(Cat#902224， Affymetrix, Santa Clara, CA, US) and GeneChip  WT Terminal Labeling Kit(Cat#900671, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: c2c12 cells are culcured in DMEM with 10%FBS.

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

treatment_protocol: c2c12 cells cultured with different conditions were selected  for RNA extraction and hybridization on Affymetrix microarrays. Culture conditions: 10C(cultured with 10%FBS);10B(cultured with 10%FBS,treated with 10 nM BTZ for 24h);10T(cultured with 10%FBS,treated with 50ng/ml TNF-α for 24h);2C(cultured with 10%FBS,then add 2% differentiation medium, harvest at 5th day);2B(cultured with 10%FBS,then add 2% differentiation medium, treated with 10 nM BTZ at 4th day, harvest at 5th day);2T(cultured with 10%FBS,then add 2% differentiation medium, treated with 50ng/ml TNF-α at 4th day, harvest at 5th day)

value: c2c12 myoblasts


title: nTreg PBS 2

description: WT PICO

value: In vitro activated nTreg


title: RAT_RA_T0_2

description:
Peripheral blood mononuclear cells from RA before therapy, replicate 2
small RNA expression data from RA rats before therapy

value: Female


title: reference male mouse4/ 20mGyR2


title: 10 uM CSA Mouse 5

description: quality control: approved

value: 10 uM CSA


title: RAT_NORA_1h_1

description:
Peripheral blood mononuclear cells from NORA after 1 hour therapy, replicate 1
small RNA expression data from healthy rats at 1 hour after therapy

value: Wistar


title: RAT_NORA_T0_1

description:
Peripheral blood mononuclear cells from NORA before therapy, replicate 1
small RNA expression data from healthy rats before therapy


title: 10 uM FK506 Mouse 5

description: quality control: approved

value: Tacrolimus


title: reference male mouse4/ 20mGyR4


title: 30 uM CSA Mouse 5

description: quality control: approved

value: 30 uM CSA


title: c2c12 10% FBS rep1


title: 1 uM FK506 Mouse 4

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #4


title: c2c12 10% FBS, 50ng/ml TNF-α rep1

source_name: c2c12 10% FBS  50ng/ml TNF-α


title: c2c12 2% differention medium, 50ng/ml TNF-α rep1

source_name: c2c12 2% differention medium，50ng/ml TNF-α


title: 3 uM FK506 Mouse 4

description: quality control: approved

value: 3 uM FK506


title: 20mGyR2/ reference male mouse4


title: c2c12 2% differention medium, 10nM BTZ rep1

source_name: c2c12 2% differention medium，10nM BTZ


title: c2c12 2% differention medium rep1

source_name: c2c12 2% differention medium


title: 10 uM FK506 Mouse 4

description: quality control: approved


title: CD4 AZA 2

description: WT PICO


title: reference male mouse4/ 20mGyRF


title: 1 uM CSA Mouse 4

description: quality control: approved


title: 20mGyRF/ reference male mouse4


title: reference male mouse4/ 20mGyR1


title: 0.3 uM CSA Mouse 4

description: quality control: approved

value: 0.3 uM CSA


title: Skin_Pnpla1_WT_P0

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: WT skin at P0

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA extracted from P0 newborns was purified using a RNeasy Mini Kit (QIAGEN). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

tag: strain background

tag: genotype/variation

value: Pnpla1+/+ (wild type)

value: skin


title: 10 uM CSA Mouse 4

description: quality control: approved

value: 8-9 weeks

value: Cyclosporin A


title: DMSO Mouse 4

description: quality control: approved

value: Male

value: DMSO controle

value: DMSO


title: Skin_Pnpla1_KO_P0

source_name: KO skin at P0

value: Pnpla1-/- (knockout)


title: 3 uM CSA Mouse 4

description: quality control: approved

value: CSA

value: 3 uM CSA


title: 30 uM CSA Mouse 4

description: quality control: approved


title: reference male mouse4/ 20mGyRM

source_name: reference male mouse4

value: tail


title: 20mGyRM/ reference male mouse4


title: RAT_NORA_T0_2

description:
Peripheral blood mononuclear cells from NORA before therapy, replicate 2
small RNA expression data from healthy rats before therapy

value: Female

value: RAT Peripheral blood mononuclear cells


title: 20mGyQ4/ reference male mouse3

source_name: reference male mouse3


title: 1 uM FK506 Mouse 3

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #3

value: Tacrolimus

value: 1 uM FK506


title: 3 uM FK506 Mouse 3

description: quality control: approved

value: 3 uM FK506


title: 10 uM FK506 Mouse 3

description: quality control: approved


title: hES+Dox at d6, biological rep2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Gene expression data from differentiation human ES cells with Tet-on GCNF inducible expression system treated with Dox

hyb_protocol: Standard Affymetrix hybridization protocol performed by The Baylor College of Medicine Microarray Core Facility

scan_protocol: Standard Affymetrix chip scanning protocol performed by The Baylor College of Medicine Microarray Core Facility

data_processing: dChip version 2010, default settings

source_name: H9 human embryonic stem cells with overexpression GCNF

label_protocol: Standard Affymetrix labeling protocol performed by The Baylor College of Medicine Microarray Core Facility

growth_protocol: Undifferentiation hES cells were culture on metrigel-coat plates with mTeSR medium. To induce hES cell differentiation, DMEM/F12 medium supplied with 15% FBS, NAA and glutamine was used in the experiments

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instruction.

treatment_protocol: Undifferentiation hES cells were treated with 1 ug/ml Dox for 4 days. Differentiation hES cells were treated with 1 uM retinoic acid or 1 ug/ml Dox, respectively, for 6 days.

tag: cell line

value: differentiated

tag: treatment

value: treated with 1 ug/ml doxycycline

tag: passages

value: passages 28-35


title: 0.3 uM CSA Mouse 3

description: quality control: approved

tag: age

value: 8-9 weeks

value: 0.3 uM CSA


title: reference male mouse3/ 20mGyQ3


title: DMSO Mouse 3

description: quality control: approved

value: Male

tag: chemical


title: hES+RA at d6, biological rep3

description: Gene expression data from differentiation human ES cells with Tet-on GCNF inducible expression system treated with RA

value: treated with 1 uM RA


title: hES+Dox at d6, biological rep3


title: hES+RA at d6, biological rep2


title: 1 uM CSA Mouse 3

description: quality control: approved

value: Cyclosporin A

tag: abbreviation

value: 1 uM CSA


title: 20mGyQ2/ reference male mouse3


title: 30 uM FK506 Mouse 4

description: quality control: approved

tag: concentration


title: hES+RA at d6, biological rep1


title: reference male mouse3/ 20mGyQ4

tag: strain


title: 3 uM CSA Mouse 3

description: quality control: approved

value: CSA


title: 20mGyR1/ reference male mouse4

tag: tissue


title: reference male mouse3/ 20mGyQ1


title: hES+Dox at d6, biological rep1


title: hES+Dox at d0, biological rep3

description: Gene expression data from undifferentiation human ES cells with Tet-on GCNF inducible expression system treated with Dox

value: undifferentiated


title: 10 uM CSA Mouse 3

description: quality control: approved

tag: gender

value: 10 uM CSA


title: 20mGyQ1/ reference male mouse3

value: tail


title: hES+Dox at d0, biological rep2


title: hES+Dox at d0, biological rep1


title: 30 uM CSA Mouse 3

description: quality control: approved

value: 30 uM CSA


title: 20mGyQM/ reference male mouse3


title: reference male mouse3/ 20mGyQ2


title: hES at d0, biological rep3

description: Gene expression data from undifferentiation human ES cells with Tet-on GCNF inducible expression system


title: hES at d0, biological rep2


title: reference male mouse3/ 20mGyQF


title: 20mGyQF/ reference male mouse3


title: hES at d0, biological rep1


title: reference male mouse3/ 20mGyQM


title: reference male mouse3/ 20mGyO6


title: 30 uM FK506 Mouse 3

description: quality control: approved

value: Tacrolimus


title: 20mGyO5/ reference male mouse3


title: CD34+_5μM_12days

city: Guangzhou

first: Boxuan

last: Liang

state: Guangdong

address: Zhongshan second road

institute: Sun Yat-sen University

description: Labeling spike-in RNA and Hyb spike-in RNA(Agilent) was spotted for quality control.

hyb_protocol: Total RNA was hybridized with miRNA Complete Labeling and Hyb Kit (Agilent) following the manufacturer’s recommended protocol.

scan_protocol: After washed, slides were scaned by Agilent Scanner (G2565CA)

data_processing: data were extracted by Agilent Feature Extraction (v10.7), and then normalized by Agilent GeneSpring. T test or ANOVA were used for analysing the differences between or in groups

source_name: CD34+ cell

label_protocol: Total RNA was labeled with miRNA Complete Labeling and Hyb Kit (Agilent) following the manufacturer’s recommended protocol.

growth_protocol: CD34+ cells were seeded into complete medium immediately after isolation and cultured for 24h.Complete culture media consisted of Iscove’s Modified Dulbecco’s Medium with 30% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, 50 ng/mL SCF, 20ng/mL IL-3, 20 ng/mL GM-CSF, 50 ng/mL G-CSF and 3U/mL EPO (all cytokines from Peprotech, London, UK). All cytokines were added to the medium to stimulate hematopoietic progenitor cell growth and induce cell differentiation towards granulocytes, monocyte/macrophages, and erythrocytes.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) from cultured cells following the manufacturer’s recommended protocol.

treatment_protocol: Hydroquinone dissolved in PBS (PH 7.4) was added to the complete medium to reach final concentrations of 0, 1, 2.5 and 5.0 µM after culture initiation. During the additional 12 days culture period, cultures were maintained by addition of fresh medium and fresh hydroquinone

value: human cord blood

value: CD34+ cells

tag: treated with

value: 5.0 µM hydroquinone

tag: time point

value: 12 days


title: reference male mouse3/ 20mGyO5


title: Cancer and normal tissue from patient 5

city: Beijing

first: shuang

last: liu

address: No.6, Fucheng Road, Haidian district

institute: Navy general hospital

description: Cancer and normal tissue from patient 5

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

source_name: Cancer tissue from patient 5

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: glioblastoma

tag: patient id

source_name: Adjacent normal tissue from patient 5

value: brain

tag: patiet id

tag: disease state

value: Adjacent normal tissue


title: 20mGyQ3/ reference male mouse3


title: 20mGyO6/ reference male mouse2

source_name: reference male mouse2


title: CD34+_2.5μM_12days

tag: cell type

value: 2.5µM hydroquinone


title: Cancer and normal tissue from patient 4

description: Cancer and normal tissue from patient 4

source_name: Cancer tissue from patient 4

source_name: Adjacent normal tissue from patient 4


title: CD34+_1μM_12days

value: 1µM hydroquinone


title: CD34+_0μM_12days

value: 0µM hydroquinone


title: Cancer and normal tissue from patient 2

description: Cancer and normal tissue from patient 2

source_name: Cancer tissue from patient 2

source_name: Adjacent normal tissue from patient 2


title: 20mGyO4/ reference male mouse3


title: CD34+_5μM_8days

value: 8 days


title: reference male mouse3/ 20mGyO4


title: CD34+_2.5μM_8days


title: CD34+_0μM_8days


title: CD34+_2.5μM_5days

value: 5 days


title: reference male mouse3/ 20mGyO2


title: CD34+_1μM_5days


title: 20mGyO3/ reference male mouse3


title: CD34+_5μM_5days


title: CD34+_1μM_8days


title: CD34+_0μM_5days


title: 20mGyO1/ reference male mouse3


title: reference male mouse3/ 20mGyO3


title: 20mGyO2/ reference male mouse3


title: reference male mouse3/ 20mGyO1


title: reference male mouse3/ 20mGyOF


title: 20mGyN6/ reference male mouse3


title: 20mGyOM/ reference male mouse3


title: 20mGyOF/ reference male mouse3


title: reference male mouse3/ 20mGyOM


title: DC XCR1-, replicate 2

status: Public on Dec 22 2016

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: After hybridization of the cRNA on the custom- designed array, the chips were washed according to the manufacturer’s protocol.

scan_protocol: The chips were then scanned by using a G2565CA scanner (Agilent Technologies) at the resolution of 3 µm.

data_processing: The raw expression values were bakground corrected using the normexp method, and quantile normalized, using the limma package in an R statistical environment.

organism: Sus scrofa

source_name: DC XCR1-, replicate 2

label_protocol: Each RNA sample (50 ng) was amplified and cyanin 3 (Cy3)- labeled, the complementary RNA (cRNA) was checked for quality on Nanodrop and Agilent 2100 Bioanalyzer. Subsequently, the cRNA (600 ng) was fragmented and used for hybridization on custom- designed Agilent porcine arrays.

extract_protocol: Total RNA from cell sorted subsets were extracted using the Arcturus PicoPure RNA Isolation Kit and checked for quality with an Agilent 2100 Bioanalyzer using RNA 6000 Nano or Pico Kits. All RNA samples had a RNA integrity number (RIN) above 8.5. When insufficient total RNA amounts for hydridization were obtained (< 50 ng), the RNA from the sorted cell subsets of distinct animal were mixed. RNA amplification and labeling was performed using the one-color Low Input Quick Amp Labeling kit.

treatment_protocol: PBMC were obtained from pig peripheral blood buffy coat samples by 1.076 g/ml density Percoll gradient centrifugation. For B cell sorting, PBMC were surface-labelled with 2µg/ml primary MAb against IgL followed by Alexa647-conjugated goat anti-mouse IgG2a antibodies. For pDC sorting, PBMC were surface-labeled with 2µg/ml primary MAb anti-pig CD4, CD3, CD14 and CD172A followed by Alexa488, phycoerythrin (PE) or Alexa647-conjugated goat anti-mouse isotype-specific antibodies. Blood pDC candidates were sorted as CD3- CD14- CD4+ CD172int cells. For cDC candidates and Mo sorting, PBMC were surface-labeled with 2µg/ml mAb anti-pig IgL, anti-pig IgG, anti-pig IgM , anti-pig CD4, anti-human and pig cross-reacting CD14, anti-pig CD172A , anti-artiodactyl MHC class II, and chicken anti-human and artiodactyl cross-reacting CADM1. The primary antibodies were revealed with Alexa488, PE or Alexa647-conjugated goat anti-mouse isotype-specific antibodies and with donkey anti-chicken IgY Peridinin Chlorophyll Protein Complex (PerCP)- conjugated IgG. The XCR1- cDC candidates were isolated as FSChi IgL- IgG- IgM- CD4- CD14- MHC class II+ CADM1- CD172hi or CD172int cells. The XCR1+ cDC candidates were isolated as FSChi IgL- IgG- IgM- CD4- CD14- MHC class II+ CADM1+ CD172lo cells. Mo candidates were sorted as MHC class II- CD172hi cells. Non relevant antibodies (IgG1, IgG2a, IgG2b, IgM) were systematically used as controls to measure the level of non-specific background signal caused by primary antibodies. The cell subsets were sorted by flow cytometry on the ImaGif Cytometry platform using the analyzer-sorter MoFlo XDP cytometer and the Summit 5.2 software from Beckman Coulter.

tag: source

value: peripheral blood

value: XCR1- DC


title: reference male mouse3/ 20mGyN6

value: tail


title: Neurofibroma Schwann cells_patient 3_tumor 2_genotype NF1+/-_ForskoBack_144_S34Tu11+ForskoBack

city: Turku

first: Eeva-Mari

last: Jouhilahti

address: Kiinamyllynkatu 10

department: Department of Cell Biology and Anatomy

country: Finland

institute: University of Turku

hyb_protocol: labelled cRNA was then hybridized into the Illumina Sentrix Human HT-12 v.3 Epression BeadChips at 58C overnight (17 h) following the standard Illumina hybridization protocol

scan_protocol: Arrays were scanned with Illumina’s Bead Array Scanner (Factor=1.5, PMT=552, Filter=100%) following the standard Illumina scanning protocol

data_processing:
the basic NF1-/- vs. NF1+/- and forskolin data sets were normalized separately using quantile normalization with limma in R
Raw data: The numerical results were extracted with GenomeStudio Gene Expression Module v. 1.0.6 without any normalization or background subtraction. Normalized data: Normalized using quantile normalisation with limma in R

source_name: neurofibroma Schwann cells, NF1+/-

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

growth_protocol: The neurofibromas were cut into small pieces (3 mm x 3 mm) in sterile conditions, preincubated for one week and finally, chemically and mechanically dissociated to produce cell suspension with mixed cell types (Rosenbaum T, Rosenbaum C, Winner U, Müller H, Lenard H, Hanemann C: Long-term culture and characterization of human neurofibroma-derived Schwann cells., J Neurosci Res 2000, 61:524-532)

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with BioRad Experion system.

treatment_protocol: Cells were maintained in proliferation medium containing DMEM with 10% FCS, 100 U/ml penicillin/streptomycin, 0.5 mM IBMX, 10 nM beta1-heregulin, 0.5 uM forskolin and 2.5 ug/ml insulin. The Schwann cells were enriched into NF1+/- and NF1-/- cell lines according to the protocol described in (Serra E, Rosenbaum T, Winner U, Aledo R, Ars E, Estivill X, Lenard H, Lázaro C: Schwann cells harbor the somatic NF1 mutation in neurofibromas: evidence of two different Schwann cell subpopulations., Hum Mol Genet 2000, 9:3055-3064)

value: female

tag: patient number

value: patient 3

tag: tumor number

value: tumor 2

value: cutaneous neurofibroma

tag: genotype

tag: forskolin

value: present


title: reference male mouse3/ 20mGyN5


title: plasmacytoid DC, replicate 1

source_name: plasmacytoid DC, replicate 1

value: pDC


title: Neurofibroma Schwann cells_patient 3_tumor 1_genotype NF1+/-_ForskoBack_140_S34Tu10+ForskoBack

value: tumor 1


title: DC XCR1+, replicate 1

source_name: DC XCR1+, replicate 1

value: XCR1+ DC


title: 20mGyN4/ reference male mouse3


title: 20mGyN3/ reference male mouse3


title: Neurofibroma Schwann cells_patient 3_tumor 3_genotype NF1+/-_wo forskolin_woForsko_137_S34Tu13+woForsko

value: tumor 3

value: absent for 24h


title: Neurofibroma Schwann cells_patient 2_tumor 3_genotype NF1+/-_ForskoBack_85_E27Tu7+ForskoBack

value: male

value: patient 2


title: DC XCR1+, replicate 2

source_name: DC XCR1+, replicate 2


title: plasmacytoid DC, replicate 2

source_name: plasmacytoid DC, replicate 2


title: Neurofibroma Schwann cells_patient 3_tumor 2_genotype NF1+/-_wo forskolin_woForsko_135_S34Tu11+woForsko


title: 20mGyN5/ reference male mouse3

source_name: reference male mouse3


title: DC XCR1-, replicate 1

source_name: DC XCR1-, replicate 1


title: Neurofibroma Schwann cells_patient 2_tumor 1_genotype NF1+/-_ForskoBack_81_E27Tu5+ForskoBack


title: Neurofibroma Schwann cells_patient 3_tumor 3_genotype NF1+/-_ForskoBack_145_S34Tu13+ForskoBack


title: reference male mouse3/ 20mGyN3


title: Neurofibroma Schwann cells_patient 3_tumor 1_genotype NF1+/-_wo forskolin_woForsko_130_S34Tu10+woForsko


title: reference male mouse3/ 20mGyN4


title: reference male mouse3/ 20mGyN1


title: Neurofibroma Schwann cells_patient 2_tumor 2_genotype NF1+/-_wo forskolin_woForsko_74_E27Tu6+woForsko


title: 20mGyNM/ reference male mouse3


title: 20mGyN2/ reference male mouse3


title: Neurofibroma Schwann cells_patient 2_tumor 1_genotype NF1+/-_Forskolin_62_E27Tu5+Forskolin


title: Neurofibroma Schwann cells_patient 3_tumor 1_genotype NF1-/-_-/-_98_S34Tu10-/-

source_name: neurofibroma Schwann cells, NF1-/-

value: absent


title: Neurofibroma Schwann cells_patient 3_tumor 3_genotype NF1+/-_Forskolin_127_S34Tu13+Forskolin


title: Neurofibroma Schwann cells_patient 2_tumor 3_genotype NF1+/-_Forskolin_69_E27Tu7+Forskolin


title: reference male mouse3/ 20mGyN2


title: Neurofibroma Schwann cells_patient 2_tumor 2_genotype NF1+/-_Forskolin_66_E27Tu6+Forskolin


title: 20mGyNF/ reference male mouse3


title: Neurofibroma Schwann cells_patient 1_tumor 3_genotype NF1-/-_-/-_28_E8Tu8-/-

value: patient 1


title: reference male mouse3/ 20mGyNM


title: Neurofibroma Schwann cells_patient 3_tumor 1_genotype NF1+/-_Forskolin_121_S34Tu10+Forskolin


title: Neurofibroma Schwann cells_patient 2_tumor 2_genotype NF1-/-_-/-_47_E27Tu6-/-


title: Neurofibroma Schwann cells_patient 3_tumor 3_genotype NF1+/-_112_S34Tu13


title: Neurofibroma Schwann cells_patient 1_tumor 2_genotype NF1-/-_-/-_17_E8Tu7-/-


title: Neurofibroma Schwann cells_patient 3_tumor 2_genotype NF1+/-_Forskolin_124_S34Tu11+Forskolin


title: Neurofibroma Schwann cells_patient 2_tumor 1_genotype NF1+/-_wo forskolin_woForsko_72_E27Tu5+woForsko


title: Neurofibroma Schwann cells_patient 3_tumor 3_genotype NF1-/-_-/-_116_S34Tu13-/-


title: Neurofibroma Schwann cells_patient 2_tumor 3_genotype NF1+/-_wo forskolin_woForsko_76_E27Tu7+woForsko


title: Neurofibroma Schwann cells_patient 1_tumor 1_genotype NF1-/-_-/-_8_E8Tu6-/-


title: 20mGyN1/ reference male mouse3


title: Neurofibroma Schwann cells_patient 3_tumor 2_genotype NF1+/-_101_S34Tu11


title: Neurofibroma Schwann cells_patient 3_tumor 2_genotype NF1-/-_-/-_106_S34Tu11-/-


title: Neurofibroma Schwann cells_patient 2_tumor 3_genotype NF1+/-_54_E27Tu7


title: Neurofibroma Schwann cells_patient 2_tumor 1_genotype NF1-/-_-/-_39_E27Tu5-/-


title: Neurofibroma Schwann cells_patient 2_tumor 3_genotype NF1-/-_-/-_59_E27Tu7-/-


title: Neurofibroma Schwann cells_patient 3_tumor 1_genotype NF1+/-_94_S34Tu10


title: reference male mouse3/ 20mGyNF


title: Neurofibroma Schwann cells_patient 2_tumor 2_genotype NF1+/-_41_E27Tu6


title: Neurofibroma Schwann cells_patient 2_tumor 1_genotype NF1+/-_34_E27Tu5


title: Neurofibroma Schwann cells_patient 1_tumor 3_genotype NF1+/-_23_E8Tu8


title: Neurofibroma Schwann cells_patient 1_tumor 1_genotype NF1+/-_4_E8Tu6


title: DC XCR1-, replicate 3

hyb_protocol: cRNA (600 ng) was fragmented and used for hybridization on custom designed Agilent ovine arrays (ID 29915)

scan_protocol: standard Agilent protocol

organism: Ovis aries

source_name: DC XCR1-, replicate 3

label_protocol: Each RNA sample (25 to 50 ng) was amplified and cyanin 3 (Cy3) labeled,using the one-color Low Input Quick Amp Labeling kit (Agilent Technologies)

growth_protocol: Three independent cultures of sheep MoDC were produced with GM-CSF, as described in PMID: 18718839

extract_protocol: Total RNA from cell sorted subsets were extracted using the Arcturus PicoPure RNA Isolation Kit and checked for quality with an Agilent 2100 Bioanalyzer using RNA 6000 Nano or Pico Kits. All RNA samples had a RNA integrity number (RIN) above 8.5. When insufficient total RNA amounts for hydridization were obtained (< 25 ng), the RNA from the sorted cell subsets of distinct animal were mixed. RNA amplification and labeling was performed using the one-color Low Input Quick Amp Labeling kit.

treatment_protocol: Sheep PBMC were loaded on 1.065 density iodixanol gradient (Optiprep, Nycomed Pharma) to isolate low density cells from blood. Sheep pDC candidates were isolated by flow cytometry. For isolating sheep cDC candidates, the low density PBMC from several sheep were reacted with anti-CD11c mAb  followed by a saturating concentration of pacific blue-labeled anti-mouse IgG donkey Fab (50µg/ml). After extensive wash, cells were further incubated anti-CD172A mAb followed by a saturating concentration of Alexa488-labeled anti-mouse IgG donkey Fab (50µg/ml). After extensive wash, cells were incubated with 2µg/ml primary MAbs anti-ruminant B cells , CD11b , TCR1γ/δ receptor, CD45RB and chicken anti-human and artiodactyl cross-reacting CADM1. The IgM and IgG2a primary antibodies were revealed with PE-conjugated goat anti-mouse isotype-specific antibodies, the IgG1 anti-CD45RB primary antibody was revealed with Alexa647-conjugated goat anti-mouse IgG1 antibody and the anti-CADM1 with anti-IgY PerCP-conjugated IgG. The XCR1- cDC candidates were isolated by flow cytometry as B- CD11b- TCR1- CD45RB- CD11c+ CADM1lo CD172hi FSChi cells. The XCR1+ cDC candidates were isolated by flow cytometry as B- CD11b- TCR1- CD45RB- CD11c+ CADM1hi CD172lo FSChi cells. B cells and macrophages were sorted by flow cytometry from isolated sheep spleen cells using the anti-ruminant B cell and anti-CD14 respectively.

value: blood


title: DC XCR1+, replicate 1


title: DC XCR1-, replicate 2

value: XCR1- DC


title: DC XCR1-, replicate 1


title: MoDC, replicate 2

source_name: MoDC, replicate 2

value: in vitro derived

value: MoDC


title: Neurofibroma Schwann cells_patient 2_tumor 2_genotype NF1+/-_ForskoBack_83_E27Tu6+ForskoBack


title: MoDC, replicate 3

source_name: MoDC, replicate 3


title: Neurofibroma Schwann cells_patient 1_tumor 2_genotype NF1+/-_14_E8Tu7


title: macrophage, replicate 1

source_name: macrophage, replicate 1

value: spleen

value: Macrophage


title: macrophage, replicate 3

source_name: macrophage, replicate 3


title: A549 E2BSA+TAM

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

hyb_protocol: RNA was hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), using the HGU133A plus 2 chip, analyzing a total of 54675 transcripts.

scan_protocol: Signals were detected by an Affymetrix microarray chip reader.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: A549-182 cells treated with 1μM 17-β-estradiol-BSA plus 10μM Tamoxifen

label_protocol: RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual).

growth_protocol: HTB-182 (H) and A549 (A) cells were grown in RPMI 1640 supplemented with 10% FBS and passaged weakly. All experiments were performed with cells that were at less than 10 passages after defrost.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

treatment_protocol: HTB-182 (H) and A549 (A) cells after a 4h incubation with medium containing 10% charcoal stripped FBS were incubated with vehicle (Ethanol 0.1% (1)), E2 (1μM)(2), E2 (1μM) plus tamoxifen (10μM) (3), E2-BSA (1μM)(4) and E2-BSA (1μM) plus tamoxifen (10μM)(5) in RPMI 1640 supplemented with 10% charcoal stripped FBS, for 3 hours.

value: Non-Small Cell Lung Carcinoma (adenocarcinoma)

tag: cell line


title: HTB E2BSA

source_name: HTB-182 cells treated with 1μM 17-β-estradiol-BSA

value: Non-Small Cell Lung Carcinoma (squamous cell)


title: MoDC, replicate 1

source_name: MoDC, replicate 1


title: macrophage, replicate 2

source_name: macrophage, replicate 2


title: A549 E2

source_name: A549-182 cells treated with 1μM 17-β-estradiol


title: A549 vehicle

source_name: A549-182 cells in medium containing 0.1% Ethanol (vehicle)


title: HTB E2

source_name: HTB-182 cells treated with 1μM 17-β-estradiol


title: HTB vehicle

source_name: HTB-182 cells in medium containing 0.1% Ethanol (vehicle)


title: iPS cell derived hepatocyte, neg. sort, biological rep2

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: iHep_SLC10A1 Neg. sort_2

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (GeneChip 3' IVT PLUS Reagent Kit User Guide, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data analysis was performed using the Partek Genomic Suite Statistical Analysis Software using RMA as normalization method

source_name: iPS cell derived hepatocyte, neg. sort

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip 3' IVT PLUS Reagent Kit User Guide, Affymetrix)

growth_protocol:
iPS cells reprogrammed from human foreskin fibroblasts
Human iPS cells were differentiated into hepatocyte-like cells using a 20 day differentiation protocol (Si-Tayeb et al., Hepatology, 2010; Mallanna and Duncan, Curr. Prot. Stem Cell Biology, 2013)

extract_protocol: Total RNA was extracted using RNeasy Plus Micro kit (Qiagen; Cat. No. 74034) according to the manufacturer's instrucitons

treatment_protocol: Human iPS cell derived hepatocyte-like cells were dissociated into single cell suspension using Collagenase XI, blocked using 1% BSA, incubated with SLC10A1 antibody and appropriate PE conjugated secondary antibody followed by FACS sorting

value: iPS cell derived hepatocytes

tag: sorted cell population

value: SLC10A1 negative sort


title: A549 E2BSA

source_name: A549-182 cells treated with 1μM 17-β-estradiol-BSA


title: iPS cell derived hepatocyte, neg. sort, biological rep1

description: iHep_SLC10A1 Neg. sort_1


title: iPS cell derived hepatocyte, neg. sort, biological rep4

description: iHep_SLC10A1 Neg. sort_4


title: HTB E2BSA+TAM

source_name: HTB-182 cells treated with 1μM 17-β-estradiol-BSA plus 10μM Tamoxifen


title: A549 TAM

source_name: A549-182 cells treated with 1μM 17-β-estradiol plus 10μM Tamoxifen


title: HTB TAM

source_name: HTB-182 cells treated with 1μM 17-β-estradiol plus 10μM Tamoxifen


title: iPS cell derived hepatocyte, neg. sort, biological rep3

description: iHep_SLC10A1 Neg. sort_3


title: plasmacytoid DC, replicate 2

source_name: plasmacytoid DC, replicate 2

value: pDC


title: plasmacytoid DC, replicate 3

source_name: plasmacytoid DC, replicate 3


title: B lymphocyte, replicate 4

source_name: B lymphocyte, replicate 4

value: B lymphocyte


title: plasmacytoid DC, replicate 1

source_name: plasmacytoid DC, replicate 1


title: B lymphocyte, replicate 2

source_name: B lymphocyte, replicate 2


title: B lymphocyte, replicate 1

source_name: B lymphocyte, replicate 1


title: B lymphocyte, replicate 3

source_name: B lymphocyte, replicate 3


title: iPS cell derived hepatocyte, pos. sort, biological rep2

description: iHep_SLC10A1 Pos. sort_2

source_name: iPS cell derived hepatocyte, pos. sort

value: SLC10A1 positive sort


title: iPS cell derived hepatocyte, pre sort, biological rep3

description: iHep_Pre sort_3

source_name: iPS cell derived hepatocyte, pre sort

value: pre-sort


title: iPS cell derived hepatocyte, pre sort, biological rep1

description: iHep_Pre sort_1


title: iPS cell derived hepatocyte, pre sort, biological rep4

description: iHep_Pre sort_4


title: iPS cell derived hepatocyte, pos. sort, biological rep3

description: iHep_SLC10A1 Pos. sort_3


title: iPS cell derived hepatocyte, pos. sort, biological rep1

description: iHep_SLC10A1 Pos. sort_1


title: iPS cell derived hepatocyte, pos. sort, biological rep4

description: iHep_SLC10A1 Pos. sort_4


title: Sphere GBM T86 cells, biological rep 1

city: Odense

first: Sune

last: Munthe

address: Sdr. Boulevard 29

country: Denmark

institute: Odense University Hospital

hyb_protocol: According to Affymetrix protocol

scan_protocol: Affymetrix

data_processing: The microarray data were normalized at probe set level by using  quantile normalization , before the expression indexes were calculated by use of the Robust Multiarray Average (RMA) package in R

source_name: Sphere GBM cells

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

extract_protocol: Qiagen Rneasy

value: Sphere GBM cells


title: vince-00013: DCIS22

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Breast

tag: diseasestate

value: Breast Carcinoma

tag: celltype

value: Ductal carcinoma in situ

tag: organismpart

value: Breast

tag: nuclear grade

value: HG

tag: ihc_her2 (%)

tag: her2 status (acgh)

value: AMP

tag: ihc_er (%)

tag: er status

value: NEG

tag: ihc_pr (%)

tag: pr status


title: vince-00013: DCIS24

scan_protocol: See mage-tab files linked to series entry for additional details


title: vince-00013: DCIS26

data_processing: See mage-tab files linked to series entry for additional details

value: nd

value: POS


title: vince-00013: DCIS23

label_protocol: See mage-tab files linked to series entry for additional details


title: Sphere GBM T87 cells, biological rep 1

tag: cell type


title: vince-00013: DCIS19

extract_protocol: See mage-tab files linked to series entry for additional details


title: vince-00013: DCIS25

value: NAMP


title: iPS cell derived hepatocyte, pre sort, biological rep2

description: iHep_Pre sort_2


title: Migrating GBM T78 cells, biological rep 1

source_name: Migrating GBM cells

value: Migrating GBM cells


title: Migrating GBM T86 cells, biological rep 1


title: vince-00013: DCIS20


title: Migrating GBM T113 cells, biological rep 1


title: Sphere GBM T113 cells, biological rep 1


title: vince-00013: DCIS17

value: NHG


title: Migrating GBM T87 cells, biological rep 1


title: vince-00013: DCIS18


title: vince-00013: DCIS15


title: vince-00013: DCIS21


title: Sphere GBM T78 cells, biological rep 1


title: Migrating GBM T111 cells, biological rep 1


title: Sphere GBM T111 cells, biological rep 1


title: vince-00013: DCIS14


title: topal-00242: TCGA-24-1552-01A

source_name: Primary solid tumor

value: Serous Cystadenocarcinoma

value: Ovary

tag: age

tag: Sex

value: Female

tag: individual

tag: diseasestaging

value: IIIC

tag: external id

tag: tumorgrading


title: topal-00242: TCGA-61-2614-01A

tag: diseasestate

value: NOT SPECIFIED

value: UNKNOWN


title: topal-00242: TCGA-24-1427-01A


title: topal-00242: TCGA-13-1404-01A


title: topal-00242: TCGA-36-1576-01A


title: 3

city: Chongqing

first: Jian

last: Li

address: No.30 Gaotanyan Street, Shapingba District

institute: Southwest Hospital, Third Military Medical University

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

source_name: pancreatic cancer cell line

extract_protocol: Total RNA was isolated from three independent cultures of AsPC-1/miR-506 cells or AsPC-1/vector cells. RNA quantity and purity were determined using the Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA) and denaturing gel electrophoresis.

treatment_protocol: miR-506 was ectopically expressed via a lentiviral infection system to establish stable AsPC-1 pancreatic cancer cell lines. The cells were incubated in a humidified 5% CO2 atmosphere at 37°C.

tag: cell line

tag: sample type

value: miR-506 overexpressed


title: 6

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

value: negative control


title: topal-00242: TCGA-24-1928-01A

tag: organismpart


title: 4


title: 5


title: vince-00013: DCIS13

value: Breast Carcinoma

tag: celltype

value: Ductal carcinoma in situ

value: Breast

tag: nuclear grade

tag: ihc_her2 (%)


title: vince-00013: DCIS6

tag: her2 status (acgh)

tag: ihc_er (%)

tag: er status


title: topal-00242: TCGA-20-1682-01A

value: GX


title: vince-00013: DCIS11

value: nd

tag: ihc_pr (%)

tag: pr status


title: vince-00013: DCIS5

value: HG

value: POS


title: 2


title: 1


title: vince-00013: DCIS10

value: NAMP


title: topal-00242: TCGA-04-1349-01A

tag: age

tag: Sex

value: IV


title: vince-00013: DCIS8

value: NHG

value: AMP

value: NEG


title: vince-00013: DCIS9


title: vince-00013: DCIS12


title: trich-00099: B649

source_name: Muscle

value: Alive

tag: histology

value: Alveolar

tag: diseaselocation

value: Nasopharynx

value: male

value: III

tag: diseasestage

value: Stage 3

value: primary tumor

value: Muscle


title: vince-00013: DCIS4

tag: diseasestate

value: Breast Carcinoma

value: Ductal carcinoma in situ

value: Breast


title: topal-00242: TCGA-24-1423-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

tag: individual

tag: diseasestaging

value: IIIC

tag: external id

tag: tumorgrading


title: trich-00099: A434

value: Neck

value: IV

value: Stage 4

tag: celltype

tag: organismpart


title: vince-00013: DCIS3

tag: nuclear grade

value: NHG

tag: ihc_her2 (%)

tag: her2 status (acgh)

value: AMP

value: NEG

value: POS


title: topal-00242: TCGA-24-1558-01A


title: trich-00099: A864

value: Embryonal

value: Testis-Paratestis

value: male

value: Stage 1


title: vince-00013: DCIS2

value: Breast Carcinoma

value: Ductal carcinoma in situ

value: NAMP

tag: ihc_er (%)

tag: er status

tag: ihc_pr (%)


title: vince-00013: DCIS1

value: Breast

tag: pr status


title: topal-00242: TCGA-13-0761-01A

value: Serous Cystadenocarcinoma

value: Ovary

tag: age

tag: Sex

value: Female


title: topal-00242: TCGA-30-1880-01A

value: IIIC


title: trich-00099: B757

value: Alive

tag: histology

tag: diseaselocation

value: Other H&N & PM Extension

value: female

value: IIA

tag: diseasestage

value: Stage 3

value: primary tumor

value: Muscle


title: trich-00099: A444

tag: diseasestate

value: Dead

value: Alveolar

value: male

value: III


title: trich-00099: A340

value: Undifferentiated Sarcoma

value: Neck

value: Stage 1


title: topal-00242: TCGA-61-1743-01A

value: Serous Cystadenocarcinoma

value: Ovary

tag: individual

tag: diseasestaging

value: IIC

tag: external id


title: vince-00013: DCIS7

value: Breast Carcinoma

tag: celltype

value: Ductal carcinoma in situ

tag: organismpart

value: Breast

value: HG

value: nd

value: AMP

value: NEG


title: trich-00099: A372

value: Alive

value: Embryonal

value: Orbit

value: female

tag: tumorgrading

value: IIA

value: primary tumor

value: Muscle


title: topal-00242: TCGA-13-0885-01A

value: Serous Cystadenocarcinoma

value: Female

value: IIIC


title: trich-00099: B747

value: Spindle

value: Other Head & Neck

value: III

value: Stage 2


title: topal-00242: TCGA-24-1850-01A

value: Ovary


title: trich-00099: B777

value: Parapharyngeal Area

value: male

value: Stage 3


title: topal-00242: TCGA-24-2267-01A

value: IIB


title: trich-00099: A613

value: Alive

value: Alveolar

value: Forearm

value: IV

value: Stage 4


title: topal-00242: TCGA-24-0970-01B

value: Serous Cystadenocarcinoma


title: topal-00242: TCGA-13-0751-01A

value: Female

value: GX


title: trich-00099: A367

value: Leg

value: female

value: primary tumor

value: Muscle


title: trich-00099: B755

value: III


title: trich-00099: A527

value: Embryonal

value: Eye


title: trich-00099: A362

value: Nasopharynx

value: male

value: Stage 3


title: trich-00099: B734

value: Dead


title: topal-00242: TCGA-24-1467-01A

value: Ovary

value: IIIC


title: topal-00242: TCGA-25-2391-01A


title: topal-00242: TCGA-10-0936-01A


title: topal-00242: TCGA-29-1695-01A


title: topal-00242: TCGA-09-2054-01A


title: trich-00099: A535

value: Alveolar

value: Hand

value: UNKNOWN


title: topal-00242: TCGA-10-0930-01A

value: Serous Cystadenocarcinoma

value: Female


title: trich-00099: A361

value: Alive

value: Pelvis, Site Indeterminate

value: IV

value: Stage 4


title: trich-00099: A375

value: Middle Ear

value: female

value: III

value: primary tumor

value: Muscle


title: topal-00242: TCGA-24-0980-01A


title: trich-00099: B753

value: Dead

value: Leg

value: male


title: topal-00242: TCGA-13-2071-01A

value: NOT SPECIFIED

value: Ovary


title: topal-00242: TCGA-13-0764-01A


title: trich-00099: B737

value: Embryonal

value: Testis-Paratestis

value: IA

value: Stage 1


title: topal-00242: TCGA-29-1766-01A

value: Serous Cystadenocarcinoma

value: PERITONEUM (OVARY)

value: Female

value: IIIC


title: topal-00242: TCGA-24-1413-01A


title: trich-00099: B650

value: Alveolar

value: female

value: IIB

value: Stage 3


title: topal-00242: TCGA-31-1955-01A


title: topal-00242: TCGA-25-1323-01A


title: topal-00242: TCGA-36-1574-01A


title: trich-00099: V3

value: UNKNOWN

value: tumor cell line

value: Muscle


title: trich-00099: A423

value: Alive

value: Other

value: Testis

value: male

value: primary tumor


title: topal-00242: TCGA-04-1652-01A

value: Ovary


title: trich-00099: A398

value: Embryonal

value: Liver

value: IV

value: Stage 4


title: trich-00099: A358

value: Other Head & Neck

value: IA

value: Stage 1


title: trich-00099: C337

value: Alveolar


title: trich-00099: A551

value: Dead

value: Mixed Alv/Emb

value: Chest Wall


title: topal-00242: TCGA-29-1694-01A

value: Serous Cystadenocarcinoma

value: Female

value: IIIC

value: GX


title: trich-00099: P7F3

value: UNKNOWN

value: tumor cell line

value: Muscle


title: topal-00242: TCGA-13-0791-02A

source_name: Recurrent Solid Tumor

value: Ovary


title: topal-00242: TCGA-13-0801-01A


title: trich-00099: A529

value: Alive

value: Embryonal

value: Abdominal mass

value: male

value: primary tumor


title: topal-00242: TCGA-29-2434-01A

value: NOT SPECIFIED


title: trich-00099: A406

value: Dead

value: Retroperitoneum

value: IV

value: Stage 4


title: topal-00242: TCGA-13-0791-01A

value: Serous Cystadenocarcinoma

value: Female


title: trich-00099: A391

value: Orbit

value: IIA

value: Stage 1


title: trich-00099: A433

value: Alveolar

value: Leg

value: female

value: Stage 3

value: Muscle


title: topal-00242: TCGA-13-0919-01A

value: Ovary

value: IIIC


title: topal-00242: TCGA-36-1575-01A

value: IIIB


title: trich-00099: A420

value: Alive

value: Forearm

value: IA

value: primary tumor


title: topal-00242: TCGA-25-1626-01A

value: Serous Cystadenocarcinoma


title: topal-00242: TCGA-24-1471-01A

value: Female


title: trich-00099: A437

value: Embryonal

value: Paranasal Sinus

value: III


title: trich-00099: A462

value: Dead

value: Heart

value: male

value: IV

value: Stage 4


title: trich-00099: A547

value: Mixed Alv/Emb

value: Arm

value: Muscle


title: topal-00242: TCGA-24-1469-01A

value: Ovary

value: IIIC


title: topal-00242: TCGA-13-1819-01A

value: IIC


title: topal-00242: TCGA-25-1632-01A


title: trich-00099: A459

value: Alive

value: Bladder

value: female

value: IA

value: Stage 3

value: primary tumor


title: trich-00099: A428

value: Embryonal

value: Nasopharynx

value: III


title: topal-00242: TCGA-13-0913-02A

value: Serous Cystadenocarcinoma

value: Female


title: topal-00242: TCGA-13-0913-01A


title: topal-00242: TCGA-13-0727-01A


title: topal-00242: TCGA-24-1849-01A


title: trich-00099: V2

value: UNKNOWN

value: tumor cell line


title: topal-00242: TCGA-59-2372-01A

value: NOT SPECIFIED


title: trich-00099: A347

value: Spindle

value: Testis-Paratestis

value: male

value: Stage 1

value: Muscle


title: trich-00099: B635

value: Dead

value: Alveolar

value: Cheek

value: IV

value: Stage 4


title: trich-00099: B763

value: Alive

value: Thigh

value: Stage 3

value: primary tumor


title: topal-00242: TCGA-13-1497-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IIIC


title: trich-00099: A541

value: Foot

value: female


title: topal-00242: TCGA-04-1335-01A

value: IB


title: trich-00099: P3F1

value: Embryonal

value: UNKNOWN

value: tumor cell line

value: Muscle


title: topal-00242: TCGA-25-1314-01A

value: IV


title: topal-00242: TCGA-61-2110-01A

value: NOT SPECIFIED


title: trich-00099: A376

value: Alive

value: Bladder

value: male

value: III


title: trich-00099: RH28-1

value: Alveolar


title: trich-00099: A343

value: Stage 3

value: primary tumor


title: topal-00242: TCGA-04-1638-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: topal-00242: TCGA-09-1674-01A

value: IIIC


title: trich-00099: A523

value: Axillary Mass

value: female


title: trich-00099: A425

value: Botryoid

value: Paranasal Sinuses


title: topal-00242: TCGA-13-0714-01A

value: IV


title: topal-00242: TCGA-13-1412-01A


title: trich-00099: A356

value: Dead

value: Foot

value: Stage 4

value: Muscle


title: topal-00242: TCGA-13-1819-02A

value: IIC


title: trich-00099: A354

value: Undifferentiated Sarcoma

value: Other Head & Neck

value: IA

value: Stage 1


title: topal-00242: TCGA-23-2649-01A

value: NOT SPECIFIED

value: UNKNOWN

value: Ovary


title: topal-00242: TCGA-59-2351-01A

value: Serous Cystadenocarcinoma

value: Female

value: IIIC


title: trich-00099: C343

value: Alive

value: Alveolar

value: Stage 3

value: primary tumor


title: topal-00242: TCGA-29-1704-01B


title: topal-00242: TCGA-29-1704-02A


title: topal-00242: TCGA-61-1901-01A

value: IV


title: trich-00099: A378

value: Hand

value: male

value: Stage 2

value: Muscle


title: trich-00099: A465

value: Embryonal

value: Uterus

value: female

value: IA


title: trich-00099: A514

value: Calf


title: trich-00099: A357

value: Dead

value: Forearm

value: Stage 4


title: topal-00242: TCGA-13-1510-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IIIC


title: trich-00099: A388

value: Alive

value: Paraspinal

value: primary tumor


title: trich-00099: B655

value: Infratemporal Fossa

value: male

value: III

value: Stage 3


title: topal-00242: TCGA-29-1783-01A


title: vince-00013: DCIS16

value: Breast Carcinoma

value: Ductal carcinoma in situ

value: Breast

tag: nuclear grade

value: HG

tag: ihc_her2 (%)

tag: her2 status (acgh)

value: NAMP

value: POS


title: trich-00099: RD2

value: Embryonal

value: UNKNOWN

value: tumor cell line

value: Muscle


title: topal-00242: TCGA-29-1762-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IV


title: trich-00099: A381

value: Dead

value: Alveolar

value: Uterus

value: female

value: Stage 4

value: primary tumor


title: trich-00099: A337

value: Alive

value: Retroperitoneum

value: Stage 3


title: topal-00242: TCGA-13-0897-01A

value: IIIC


title: topal-00242: TCGA-36-2540-01A

value: NOT SPECIFIED

value: UNKNOWN


title: topal-00242: TCGA-20-1687-01A


title: trich-00099: A418

value: Spindle

value: Testis-Paratestis

value: male

value: Stage 1

value: Muscle


title: trich-00099: JR2

value: tumor cell line


title: trich-00099: B739

value: Alveolar

value: Forearm

value: IIA


title: topal-00242: TCGA-24-1548-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: topal-00242: TCGA-24-1464-01A


title: topal-00242: TCGA-23-1121-01A


title: trich-00099: BIRCH2

value: Embryonal


title: topal-00242: TCGA-04-1371-01A


title: topal-00242: TCGA-13-0804-01A


title: trich-00099: C340

value: Alive

value: primary tumor


title: topal-00242: TCGA-24-2038-01A

value: IIIA

value: GB


title: trich-00099: A426

value: Dead

value: Other


title: topal-00242: TCGA-24-2260-01A

value: IIIB


title: topal-00242: TCGA-24-1563-01A

value: IIIC


title: trich-00099: B666

value: Uterus

value: female

value: IV

value: Stage 4

value: Muscle


title: topal-00242: TCGA-09-1664-01A

value: Serous Cystadenocarcinoma


title: trich-00099: A542

value: Buttock

value: male


title: topal-00242: TCGA-23-2072-01A

value: Ovary

value: Female


title: trich-00099: A383

value: Alive

value: Embryonal

value: Testis-Paratestis

value: IA

value: Stage 1

value: primary tumor


title: topal-00242: TCGA-42-2582-01A

value: NOT SPECIFIED

value: UNKNOWN


title: trich-00099: B760

value: Alveolar

value: Pelvis, Site Indeterminate

value: female

value: III

value: Stage 3


title: trich-00099: A339

value: Undifferentiated Sarcoma

value: Bladder

value: Muscle


title: topal-00242: TCGA-30-1859-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: trich-00099: B648

value: Dead

value: Pterygopalatine

value: IV

value: Stage 4


title: topal-00242: TCGA-13-1495-01A

value: IIIC


title: topal-00242: TCGA-04-1517-01A


title: trich-00099: B766

value: Alive

value: Embryonal

value: Testis-Paratestis

value: male

value: IA

value: Stage 1

value: primary tumor


title: topal-00242: TCGA-25-2400-01A


title: trich-00099: A466

value: Prostate

value: III

value: Stage 3


title: trich-00099: A379

value: Testis

value: Muscle


title: topal-00242: TCGA-61-2096-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IC


title: trich-00099: A520

value: Dead

value: Alveolar

value: Lung


title: topal-00242: TCGA-24-0966-01A

value: IIIC


title: topal-00242: TCGA-13-0899-01A


title: topal-00242: TCGA-09-0367-01A


title: trich-00099: RH28-2

value: UNKNOWN

value: tumor cell line


title: topal-00242: TCGA-24-1564-01A


title: trich-00099: RH30-1


title: topal-00242: TCGA-61-1916-01A


title: trich-00099: A384

value: Alive

value: Embryonal

value: Uterus

value: female

value: IV

value: Stage 4


title: trich-00099: A342

value: Buttock

value: IA

value: Stage 2

value: primary tumor

value: Muscle


title: topal-00242: TCGA-61-1916-02A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: trich-00099: HR1

value: Alveolar


title: trich-00099: B665

value: Dead

value: Forearm

value: male


title: topal-00242: TCGA-04-1337-01A

value: IIIC


title: topal-00242: TCGA-24-1424-01A


title: trich-00099: A403

value: Alive

value: Embryonal

value: Retroperitoneum

value: Stage 3


title: trich-00099: A409

value: Testis-Paratestis

value: IV

value: Stage 4


title: trich-00099: P3F4

value: UNKNOWN

value: tumor cell line


title: trich-00099: A355

value: Prostate

value: III

value: primary tumor

value: Muscle


title: topal-00242: TCGA-24-1105-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: topal-00242: TCGA-24-1434-01A

value: IIIC


title: topal-00242: TCGA-29-2428-01A


title: trich-00099: A524

value: Alive

value: Pharyngeal

value: male


title: topal-00242: TCGA-30-1856-01A


title: trich-00099: A341

value: Spindle

value: IA

value: Stage 1


title: topal-00242: TCGA-24-2297-01A


title: topal-00242: TCGA-24-1418-01A


title: trich-00099: A449

value: Other

value: Vagina

value: female


title: trich-00099: B660

value: Embryonal

value: Testis-Paratestis

value: IIB


title: topal-00242: TCGA-24-2262-01A


title: trich-00099: A442

value: Alveolar

value: Pelvis, Site Indeterminate

value: III

value: Stage 2

value: primary tumor

value: Muscle


title: trich-00099: A537

value: Dead

value: Ischiorectal fossa

value: UNKNOWN


title: topal-00242: TCGA-23-1107-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IV


title: topal-00242: TCGA-29-2414-02A

value: IIIC


title: trich-00099: A371

value: Alive

value: Thigh

value: male

value: IA


title: topal-00242: TCGA-25-1329-01A


title: trich-00099: TTC516-2

value: Embryonal

value: tumor cell line


title: trich-00099: A374

value: Paranasal Sinus

value: III

value: Stage 2


title: topal-00242: TCGA-29-2414-01A


title: trich-00099: P3F2

value: Muscle


title: trich-00099: P7F1


title: trich-00099: A385

value: Dead

value: Alveolar

value: Retroperitoneum

value: female

value: Stage 3

value: primary tumor


title: topal-00242: TCGA-24-2033-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IIIC


title: topal-00242: TCGA-24-1436-01A


title: trich-00099: B638

value: Alive

value: Bladder

value: male


title: topal-00242: TCGA-23-1113-01A

value: IV


title: topal-00242: TCGA-29-2427-01A


title: topal-00242: TCGA-30-1861-01A


title: topal-00242: TCGA-36-1581-01A

value: IIC


title: trich-00099: C339

value: UNKNOWN


title: trich-00099: A363

value: Embryonal

value: Cheek

value: III

value: Stage 1

value: Muscle


title: trich-00099: B767

value: Alveolar

value: female

value: Stage 4


title: trich-00099: A402

value: Infratemporal Fossa

value: Stage 3

value: primary tumor


title: topal-00242: TCGA-29-1690-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IIIC


title: topal-00242: TCGA-13-1484-01A


title: trich-00099: A427

value: Alive

value: Undifferentiated Sarcoma

value: Buttock


title: topal-00242: TCGA-24-0975-01A


title: trich-00099: A349

value: Embryonal

value: Orbit & PM Extension

value: male

value: IIA

value: Stage 2


title: topal-00242: TCGA-61-1721-01A

value: IV


title: trich-00099: A464

value: Alveolar

value: Thigh

value: IA

value: Muscle


title: trich-00099: A390

value: female

value: IB

value: primary tumor


title: topal-00242: TCGA-59-2349-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: trich-00099: A360

value: Alive

value: Bladder

value: Stage 3


title: topal-00242: TCGA-29-1698-01A

value: IIIC


title: topal-00242: TCGA-29-2432-01A

value: NOT SPECIFIED

value: UNKNOWN


title: topal-00242: TCGA-61-1900-01A

value: IIIB


title: trich-00099: A396

value: Embryonal

value: Stage 2


title: trich-00099: A400

value: Dead

value: Alveolar

value: Nasopharynx

value: male

value: III


title: topal-00242: TCGA-13-1498-01A

value: Serous Cystadenocarcinoma


title: trich-00099: A419

value: Leg

value: IIB

value: primary tumor

value: Muscle


title: trich-00099: A338

value: Alive

value: Other

value: Buttock

value: female

value: Stage 3


title: trich-00099: A446

value: Forearm


title: trich-00099: JR1

value: UNKNOWN

value: tumor cell line


title: topal-00242: TCGA-29-1710-02A

value: Ovary

value: Female

value: IIIC


title: topal-00242: TCGA-36-2538-01A

value: NOT SPECIFIED


title: topal-00242: TCGA-29-1696-01A

value: Serous Cystadenocarcinoma


title: trich-00099: V4

value: Embryonal


title: topal-00242: TCGA-23-1028-01A


title: trich-00099: A404

value: Alveolar

value: male

value: IV

value: Stage 4


title: trich-00099: A518

value: Dead

value: Chest Wall met

value: primary tumor

value: Muscle


title: trich-00099: A467

value: Bladder

value: Stage 3


title: topal-00242: TCGA-13-0765-01A


title: topal-00242: TCGA-30-1892-01A


title: topal-00242: TCGA-61-2002-01A


title: topal-00242: TCGA-61-2610-02A

value: UNKNOWN


title: trich-00099: ge 371

value: Alive

value: Leg

value: III


title: topal-00242: TCGA-13-1512-01A

value: Ovary

value: Female

value: IIIC


title: trich-00099: A412

value: Embryonal

value: Prostate


title: topal-00242: TCGA-24-0981-01A

value: NOT SPECIFIED


title: topal-00242: TCGA-23-1109-01A

value: Serous Cystadenocarcinoma


title: trich-00099: RH18-2

value: Alveolar

value: tumor cell line


title: topal-00242: TCGA-29-1710-01A


title: trich-00099: B743

value: Testis-Paratestis

value: male

value: IA

value: Stage 1

value: primary tumor


title: trich-00099: A531

value: Dead

value: Thigh

value: Muscle


title: topal-00242: TCGA-25-1312-01A

value: Ovary

value: IV


title: topal-00242: TCGA-29-2431-01A

value: UNKNOWN


title: topal-00242: TCGA-13-1507-01A

value: Female

value: IIIC


title: topal-00242: TCGA-24-1567-01A

value: IIIB


title: trich-00099: A377

value: Stage 3


title: topal-00242: TCGA-13-0894-01B

value: Serous Cystadenocarcinoma


title: trich-00099: A346

value: Alive

value: Embryonal

value: Chest Wall

value: Stage 2


title: trich-00099: A382

value: Other


title: trich-00099: A470

value: Uterus

value: female

value: IA

value: Stage 1

value: primary tumor


title: topal-00242: TCGA-13-0799-01A

value: Ovary


title: topal-00242: TCGA-36-2544-01A

value: NOT SPECIFIED

value: UNKNOWN


title: trich-00099: A455

value: Testis-Paratestis

value: male

value: Muscle


title: trich-00099: A405

value: Alveolar

value: Leg


title: topal-00242: TCGA-23-1119-01A

value: Serous Cystadenocarcinoma

value: Female

value: IIIC


title: trich-00099: A519

value: Dead

value: Renal

value: IV

value: Stage 4


title: trich-00099: C341

value: Alive


title: topal-00242: TCGA-36-1578-01A


title: topal-00242: TCGA-13-1500-01A


title: trich-00099: A387

value: Chest Wall

value: IIA

value: Stage 2

value: primary tumor


title: trich-00099: B776

value: Embryonal

value: Testis-Paratestis

value: IA

value: Stage 1


title: topal-00242: TCGA-09-2055-01B

value: Ovary

value: IC


title: topal-00242: TCGA-09-1673-01A

value: Serous Cystadenocarcinoma

value: Female


title: topal-00242: TCGA-36-1571-01A

value: IIIB


title: trich-00099: A522

value: Alveolar

value: Leg

value: male

value: Muscle


title: topal-00242: TCGA-61-1724-01A

value: IIIC


title: trich-00099: B765

value: Alive


title: topal-00242: TCGA-61-1738-01A


title: trich-00099: C342

value: UNKNOWN

value: IV

value: Stage 4


title: topal-00242: TCGA-13-0921-01A


title: topal-00242: TCGA-13-1409-01A


title: trich-00099: C338

value: Dead

value: Stage 3

value: primary tumor


title: trich-00099: A350

value: Embryonal

value: Shoulder Girdle

value: female

value: IA

value: Stage 2


title: topal-00242: TCGA-13-0762-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: topal-00242: TCGA-42-2589-01A

value: NOT SPECIFIED


title: trich-00099: A429

value: Oral Cavity

value: male

value: Stage 1

value: Muscle


title: trich-00099: RD1

value: UNKNOWN

value: tumor cell line


title: trich-00099: A368

value: Alive

value: Nasopharynx

value: III

value: Stage 3


title: trich-00099: A468

value: Dead

value: Alveolar

value: Retroperitoneum

value: primary tumor


title: topal-00242: TCGA-13-0726-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: IIIC

value: GX


title: topal-00242: TCGA-61-2009-01A

value: Female


title: trich-00099: A335

value: Other

value: Lung

value: male

value: IV

value: Stage 4


title: topal-00242: TCGA-13-0758-01A


title: trich-00099: A424

value: Alive

value: Embryonal

value: Bladder

value: IIA

value: Muscle


title: trich-00099: BIRCH1

value: UNKNOWN

value: tumor cell line


title: topal-00242: TCGA-61-1737-01A

value: Serous Cystadenocarcinoma


title: topal-00242: TCGA-24-2036-01A

value: Ovary

value: IIIA


title: topal-00242: TCGA-13-0766-01A

value: IIIC


title: topal-00242: TCGA-61-2088-01A

value: Female


title: trich-00099: A352

value: Other

value: Stage 3

value: primary tumor


title: trich-00099: HR2

value: Alveolar


title: trich-00099: A373

value: Spindle

value: Testis-Paratestis

value: male

value: IA

value: Stage 1


title: topal-00242: TCGA-13-0802-01A


title: trich-00099: A395

value: Dead

value: Foot

value: female

value: III

value: Muscle


title: topal-00242: TCGA-13-0911-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: IV


title: trich-00099: B780

value: Chest Wall

value: Stage 4


title: trich-00099: B645

value: primary tumor


title: topal-00242: TCGA-13-1505-01A

value: Female

value: IIIC


title: topal-00242: TCGA-13-0924-01A


title: topal-00242: TCGA-25-1878-01A


title: topal-00242: TCGA-04-1362-01A

value: IIC


title: trich-00099: A530

value: Embryonal

value: Abdominal mass

value: male


title: trich-00099: A369

value: Alive

value: Alveolar

value: Neck


title: topal-00242: TCGA-09-1668-01B


title: topal-00242: TCGA-04-1348-01A

value: IIIB


title: topal-00242: TCGA-36-1577-01A


title: trich-00099: TTC516-1

value: UNKNOWN

value: tumor cell line

value: Muscle


title: trich-00099: P7F2


title: topal-00242: TCGA-13-0905-01B

value: Serous Cystadenocarcinoma

value: Ovary


title: trich-00099: A431

value: Dead

value: Pelvis

value: Stage 3


title: topal-00242: TCGA-36-2533-01A

value: NOT SPECIFIED


title: topal-00242: TCGA-61-1734-01B

value: Female

value: IC


title: trich-00099: RH30-2


title: topal-00242: TCGA-13-0888-01A

value: IIIC


title: trich-00099: B642

value: Undifferentiated Sarcoma

value: Chest Wall

value: male

value: primary tumor


title: trich-00099: RH18-1

value: Alveolar


title: trich-00099: A345

value: Embryonal

value: Parapharyngeal Area

value: female

value: IV

value: Stage 4


title: topal-00242: TCGA-13-0755-01A

value: Serous Cystadenocarcinoma

value: Ovary


title: trich-00099: B738

value: Dead

value: Retroperitoneum

value: Muscle


title: topal-00242: TCGA-57-1993-01A

value: Female


title: trich-00099: A539

value: Alive

value: Mixed Alv/Emb

value: Thigh


title: topal-00242: TCGA-04-1365-01A

value: IIIB


title: trich-00099: A348

value: Perineum

value: male

value: III

value: Stage 3

value: primary tumor


title: trich-00099: A366

value: Embryonal

value: Bladder

value: IV


title: trich-00099: B768

value: Nasopharynx

value: Stage 2


title: trich-00099: A416

value: Botryoid

value: Cervix

value: female

value: Stage 1


title: topal-00242: TCGA-24-2254-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female

value: IIIC


title: topal-00242: TCGA-30-1891-01A


title: topal-00242: TCGA-13-0795-01A


title: trich-00099: A413

value: Alive

value: Nasal Cavity & Sinus

value: male

value: Muscle


title: trich-00099: B771

value: Embryonal

value: III

value: Stage 3

value: primary tumor


title: trich-00099: A440

value: Dead

value: Infratemporal Fossa


title: topal-00242: TCGA-10-0934-01A


title: topal-00242: TCGA-09-1670-01A

value: IIIA


title: topal-00242: TCGA-13-0757-01A


title: topal-00242: TCGA-24-1565-01A


title: trich-00099: A392

value: Pelvis, Site Indeterminate

value: female


title: topal-00242: TCGA-24-1560-01A

value: Serous Cystadenocarcinoma


title: trich-00099: B740

value: Alveolar

value: Leg

value: IA

value: Stage 2


title: trich-00099: A441

value: IV

value: Stage 4


title: topal-00242: TCGA-23-2077-01A

value: Ovary

value: Female

value: IIIC


title: trich-00099: B746

value: Alive

value: Perineum

value: III

value: Stage 3

value: Muscle


title: trich-00099: V1

value: Embryonal

value: UNKNOWN

value: tumor cell line


title: trich-00099: B759

value: Parapharyngeal Area

value: male

value: primary tumor


title: topal-00242: TCGA-04-1357-01A

value: Serous Cystadenocarcinoma

value: IIIB


title: topal-00242: TCGA-23-1024-01A

value: IV


title: topal-00242: TCGA-09-2053-01C

value: Ovary


title: trich-00099: P3F3


title: topal-00242: TCGA-25-1324-01A

value: Female


title: topal-00242: TCGA-31-1956-01A


title: trich-00099: A344

value: Dead

value: Alveolar

value: Pelvis, Site Indeterminate


title: trich-00099: A439

value: Alive

value: Botryoid

value: Gall Bladder & Biliary Tree

value: III


title: trich-00099: A460

value: Cheek

value: IIA

value: Stage 1

value: Muscle


title: trich-00099: A513

value: Embryonal

value: Buttock

value: female

value: primary tumor


title: topal-00242: TCGA-61-1725-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: IIIC


title: topal-00242: TCGA-13-0723-01A

value: Female


title: topal-00242: TCGA-23-1118-01A


title: trich-00099: A521

value: Dead

value: Alveolar

value: Submand (primary thigh)

value: male

value: IV

value: Stage 4


title: topal-00242: TCGA-13-0717-01A


title: topal-00242: TCGA-01-0639-11A

source_name: Solid normal tissue

value: NOT SPECIFIED

value: UNKNOWN

value: many


title: trich-00099: A545

value: Embryonal

value: Chest Wall

value: Muscle


title: topal-00242: TCGA-25-1630-01A


title: trich-00099: A867

value: Liver

value: Stage 2

value: primary tumor


title: topal-00242: TCGA-30-1714-01A

value: Serous Cystadenocarcinoma

value: Ovary


title: topal-00242: TCGA-61-1728-01A

value: Female


title: topal-00242: TCGA-23-1027-01A

value: IIIC


title: trich-00099: P7F4

value: tumor cell line


title: topal-00242: TCGA-10-0926-01A


title: topal-00242: TCGA-61-1741-01A

value: IIIB


title: topal-00242: TCGA-25-2392-01A

value: IV


title: topal-00242: TCGA-25-1322-01A


title: trich-00099: A860


title: siESR1 I

city: Urbana

first: Milan

middle: K

last: Bagchi

state: IL

address: 407 S. Goodwin Ave

department: MIP

institute: UIUC

description: Human endometrial stromal cell culture sample 1, transfected with siRNA targeting ESR1 mRNA

hyb_protocol: 10 micrograms of labeled aRNA of sample 1 and sample 2 were hybridized to Affymetrix Human Genome HG-U133 A2.0 Array, cRNA of samples 3,4,5 and 6 were hybridized to Affymetrix GeneChip Human Gene 1.0 ST Arrays.  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing:
To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix Expression Console with default analysis settings.
affymetrix-algorithm-name = rma (for HG-U133A_2)
affymetrix-algorithm-name = rma-gene-default (HuGene-1_0-st-v1)
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: endometrial stromal cell_siRNA targeting ESR1

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample 1 and sample 2 total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions. Total RNA from sample 3, 4, 5 and 6 were prepared using Affymetrix

growth_protocol: growth in 5%FBS containing DMEM:F12 medium

extract_protocol: Total RNA was performed using TRIzol® according to the manufacturer's instructions. Total RNA was cleaned up using RNeasy Mini Kit (Qiagen)  following manufacturer's instructions

treatment_protocol: treatment in 2% charcoal stripped serum sontaining DMEM:F12 medium, 48h siRNA transfection, 24h differentiation cocktail treatment composed of E, P and 8-Br-cAMP

tag: cell type

value: Human endometrial stromal cell

tag: transfected with

value: siRNA targeting ESR1 for 48hrs

tag: treated with

value: differentiation cocktail for 24hrs


title: topal-00242: TCGA-23-2079-01A

tag: age

tag: Sex


title: topal-00242: TCGA-01-0636-11A

value: NOT SPECIFIED

value: UNKNOWN

value: many


title: topal-00242: TCGA-01-0629-11A


title: topal-00242: TCGA-29-1774-01A


title: topal-00242: TCGA-29-1699-01A


title: topal-00242: TCGA-24-1430-01A


title: topal-00242: TCGA-13-2057-01A


title: willm-00090: ALL_253

source_name: Pre-treatment leukemia diagnostic sample

tag: agevalue

value: male

value: Peripheral Blood/Bone Marrow

tag: histology

value: B Precursor ALL


title: willm-00090: ALL_254

tag: diseasestate

value: Pre-treatment leukemia diagnostic sample


title: willm-00090: ALL_252

value: T-Cell lineage ALL


title: topal-00242: TCGA-10-0933-01A

value: Serous Cystadenocarcinoma

value: Ovary

tag: individual


title: willm-00090: ALL_251


title: topal-00242: TCGA-29-1778-01A

value: Female

tag: diseasestaging

value: IIIC


title: willm-00090: ALL_250


title: topal-00242: TCGA-13-0916-01A

tag: external id


title: willm-00090: ALL_249


title: siControl I

description: Human endometrial stromal cell culture sample 1, transfected with nontargeting control siRNA

source_name: endometrial stromal cell_nontargeting control siRNA

value: nontargeting control siRNA for 48hrs


title: siESR1 III

description: Human endometrial stromal cell culture sample 3, transfected with siRNA targeting ESR1 mRNA


title: topal-00242: TCGA-09-2043-01A

value: IC


title: siESR1 II

description: Human endometrial stromal cell culture sample 2, transfected with siRNA targeting ESR1 mRNA

value: Human endometrial stromal cell


title: siControl II

description: Human endometrial stromal cell culture sample 2, transfected with nontargeting control siRNA


title: topal-00242: TCGA-61-1727-01A


title: willm-00090: ALL_247


title: topal-00242: TCGA-13-1494-01A

value: IV


title: topal-00242: TCGA-13-0923-01A


title: topal-00242: TCGA-57-1582-01A


title: willm-00090: ALL_245


title: willm-00090: ALL_246


title: siControl III

description: Human endometrial stromal cell culture sample 3, transfected with nontargeting control siRNA

value: differentiation cocktail for 24hrs


title: BoneMarrow_Resistant_2

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

hyb_protocol: Gene 1.0 ST Array (Affymetrix) standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Raw data were processed with aroma.affymetrix (Bengtsson et al., 2008) and background corrected with RMA followed by quantile normalization and summarization using the RMA probe-level model (PLM) to obtain gene-level summaries. Statistically significant differential expression between sensitive and resistant cells was determined with a moderated empirical Bayes approach (Smyth, 2004) and multiple hypothesis correction was performed. Significant genes were those with a False Discovery Rate (FDR) of <1%.

source_name: Flushed bone marrow

label_protocol: Affymetrix standard protocol

growth_protocol: Transplanted into sublethally mouse recipients

extract_protocol: Rneasy Mini Kit (Qiagen)

treatment_protocol: Not applicable

tag: strain

value: C57BL/6 x 129Sv/Jae

tag: specimen

value: Resistant

tag: tissue

value: total bone marrow


title: BoneMarrow_Sensitive_3

value: Sensitive


title: BoneMarrow_Resistant_3


title: BoneMarrow_Sensitive_2


title: BoneMarrow_Resistant_1


title: BoneMarrow_Sensitive_1


title: willm-00090: ALL_244

value: female

tag: organismpart

value: Peripheral Blood/Bone Marrow


title: topal-00242: TCGA-13-1487-01A

tag: tumorgrading

value: GX


title: topal-00242: TCGA-61-1995-01A


title: willm-00090: ALL_243

value: Pre-treatment leukemia diagnostic sample

value: male

value: B Precursor ALL


title: topal-00242: TCGA-25-1321-01A

value: Serous Cystadenocarcinoma

value: Ovary

value: Female


title: willm-00090: ALL_242


title: topal-00242: TCGA-04-1651-01A

value: IIIC


title: willm-00090: ALL_241


title: willm-00090: ALL_240


title: willm-00090: ALL_248


title: topal-00242: TCGA-23-1031-01A


title: willm-00090: ALL_239

value: T-Cell lineage ALL


title: topal-00242: TCGA-13-0794-01A


title: willm-00090: ALL_237


title: topal-00242: TCGA-25-1871-01A


title: willm-00090: ALL_235


title: topal-00242: TCGA-61-2092-01A


title: topal-00242: TCGA-24-1844-01A


title: topal-00242: TCGA-04-1361-01A

value: IIIB


title: topal-00242: TCGA-25-2393-01A


title: willm-00090: ALL_231


title: willm-00090: ALL_233


title: topal-00242: TCGA-25-1633-01A


title: topal-00242: TCGA-13-0904-01A


title: willm-00090: ALL_232


title: topal-00242: TCGA-13-1504-01A


title: topal-00242: TCGA-01-0630-11A

value: NOT SPECIFIED

value: UNKNOWN

value: many


title: willm-00090: ALL_229


title: willm-00090: ALL_234


title: topal-00242: TCGA-25-2401-01A


title: topal-00242: TCGA-04-1519-01A