title: STB-6, biological rep1

city: Wuhan

first: hongbo

last: Cao

address: No.1,Shizishan Street · Hongshan District

department: Key Laboratory of Horticultural Plant Biology

country: China

institute: Huazhong Agricultural University

description: Gene expression data from the representative transgenic callus line SBT-6 with twenty-day culture

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

data_processing: The scanned images from the GeneChip Citrus Arrays were analyzed by GeneChip Operating Software (GCOS 1.4; Affymetrix) using default settings to generate raw data, which were saved as CEL files. The raw data were normalized by a robust multichip analysis approach implemented in the Affy package.

organism: Citrus x tangelo

source_name: SBT-6, a representative transgenic calli of SBT genotype

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

growth_protocol: The calli were propagated on MT medium in dark and kept at 25 ± 1˚C. MT medium, which is typically used for citrus culture in vitro, was prepared according to Murashige and Tucker. Twenty-day-old calli were harvested and stored at -80˚C for later RNA extraction and hybridization on Affymetrix microarrays.

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

treatment_protocol: The transgenic callus lines were established by over-expressing 35S::CrtB (tp–rbcS–CrtB) [CrtB protein, phytoene synthase from Erwinia herbicola (now known as Pantoea agglomerans), containing a Pea rbcS transit peptide] in citrus embryogenic calli.

tag: tissue

value: embryogenic calli

tag: age

value: Twenty-day-old calli on new medium

tag: genotype

value: 35S::CrtB insertion

tag: common name

value: Sunburst mandarin


title: SBT-WT, biological rep2

status: Public on Sep 23 2014

type: RNA

description: Gene expression data from wild-type SBT calli with twenty-day culture

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

label: biotin

molecule: total RNA

source_name: Wild type calli of SBT genotype

value: Wild type


title: LCS-405A

type: genomic

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MD

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

country: USA

institute: National Cancer Institute

description: No additional information.

hyb_protocol: Illumina Hybridization Protocol Hybridization was performed following the manufacturer's protocol for Illumina's Infinium Human Methylation27 BeadChip microarrays.

scan_protocol: Illumina Scanning Protocol Illumina's Infinium Human Methylation27 BeadChip microarrays were scanned using a HiScan (Illumina). Images were analyzed using BeadStudio software (Illumina).

data_processing:
Data Processing Protocol
Calculation Method: Raw data from the Infinium Human Methylation27 BeadChip microarrays were extracted using BeadStudio software (Illumina). Thereafter, the SSN method in the R lumi package was used to normalize the data. Further analysis was carried out using the lumi package in R. IlluminaHumanMethylation27k.db_1.4.7 package (http://www.bioconductor.org) was used for annotation. Only probes which did not have any NAs were included which resulted in 23,972 probes.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol:
Zymo EZ DNA Methylation
Used 1 ug of high quality DNA and completed the bisulfite conversion according to the manufacturer's protocol (Zymo Research Corporation, Irvine, CA).

extract_protocol:
Phenol/Chloroform Extraction Protocol
Other: DNA was extracted using Phenol/Chloroform/Isoamyl Alcohol (Invitrogen, Carlsbad, CA) according to the manufacturer's protocol.

tag: gender

value: male

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: AVR-CC

tag: alt

value: low

tag: main tumor size

value: large

tag: multinodular

value: No

tag: cirrhosis

value: Yes

tag: tnm staging

value: I

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status

value: Alive

tag: survival months

tag: recurr status

value: True

tag: recurr months


title: LCS-401A

description: No additional information.

tag: age

tag: tissue

tag: hbv viral status:

value: small

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

value: False


title: RB-WT, biological rep2

description: Gene expression data from wild-type RB calli with twenty-day culture

organism: Citrus x paradisi

source_name: Wild type calli of RB genotype

value: embryogenic calli

value: Twenty-day-old calli on new medium

tag: genotype

tag: common name

value: Star Ruby grapefruit


title: STB-6, biological rep2

value: 35S::CrtB insertion

value: Sunburst mandarin


title: RB-WT, biological rep1

value: Wild type


title: Rep-MEFs express OKSM+ascorbic acid and GSK3i for 4 days

city: Boston

first: Ori

last: Bar-Nur

state: MA

address: 185 Cambridge st.

department: Center of Regenerative medicine

institute: Harvard University

description: Rep-MEFs+OKSM+AGi 4days

hyb_protocol: Hybridization was done by the Partners Center for Personalized Genetic Medicine.

scan_protocol: Scanning was done by the Partners Center for Personalized Genetic Medicine.

data_processing: Data was processed using Expression Console software, the processing algorithm was RMA

organism: Mus musculus

source_name: Rep-MEFs+OKSM+AGi 4days

label_protocol: Labeling was done by the Partners Center for Personalized Genetic Medicine.

growth_protocol: Cells were grown in ESC media or MEFs mefia depencing on the cell type as described in the materials section

extract_protocol: RNA (Dnase treated) was islolated and extracted using the Rneasy Mini Kit (Qiagen).

treatment_protocol: Cells were treated with ascorbic acid and GSK3i, control cells did not.

tag: strain

tag: cell type

value: Bulk Rep-MEF population

tag: genotype/variation

value: expressing OKSM

tag: treatment protocol

value: AGi

tag: time

value: 4 days


title: RB-4, biological rep1

description: Gene expression data from the representative transgenic callus line RB-4 with twenty-day culture

source_name: RB-4, a representative transgenic calli of RB genotype


title: SBT-WT, biological rep1


title: M-WT, biological rep1

description: Gene expression data from wild-type M calli with twenty-day culture

source_name: Wild type calli of M genotype

value: Marsh grapefruit


title: Rep-MEFs express OKSM for 6 days

description: Rep-MEFs+OKSM 6days

source_name: Rep-MEFs+OKSM 6days

value: 6 days


title: LCS-406A

description: No additional information.

tag: gender

value: male

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: alt

value: high

tag: main tumor size

tag: multinodular

value: Yes

tag: cirrhosis

tag: afp

tag: survival status

value: Dead


title: Rep-MEFs express OKSM+ascorbic acid and GSK3i for 2 days

description: Rep-MEFs+OKSM+AGi 2days

source_name: Rep-MEFs+OKSM+AGi 2days

value: 2 days


title: M-WT, biological rep2

tag: tissue

value: embryogenic calli

tag: age

value: Twenty-day-old calli on new medium


title: Rep-MEFs express OKSM for 4 days

description: Rep-MEFs+OKSM 4days

source_name: Rep-MEFs+OKSM 4days


title: M-33, biological rep2

description: Gene expression data from the representative transgenic callus line M-33 with twenty-day culture

source_name: M-33, a representative transgenic calli of M genotype

tag: genotype

value: 35S::CrtB insertion


title: M-33, biological rep1

tag: common name


title: MEFs derived from Reprogrammable-mouse

description: Rep-MEFs no dox

source_name: Rep-MEFs no dox

tag: strain

value: MEFs


title: Rep-MEFs express OKSM for 2 days

description: Rep-MEFs+OKSM 2days

source_name: Rep-MEFs+OKSM 2days

tag: cell type

value: Bulk Rep-MEF population


title: RB-4, biological rep2

value: Star Ruby grapefruit


title: GMPs

description: GMPs

source_name: GMPs

value: GMPs


title: IBF+T3, L5

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: Microarray slides were hydrated by inversion in coplin jars with 0.1X SSC then incubated for 45 min at 48 °C in a filtered (0.22 μm) pre-hybridization buffer containing; 5X SSC (ThermoFisher Scientific), 0.1% SDS (ThermoFisher Scientific), and 0.2% BSA fraction V (ThermoFisher Scientific). Slides were then washed twice with room temperature dH2O and immersed in isopropanol (HPLC-grade, ThermoFisher Scientific) followed by centrifugation at 1000 x g for 4 min in sterile 50 mL polypropylene centrifuge tubes (Sarstedt Inc., Montreal, PQ, Canada). Slides were then placed microarray side-up in Corning hybridization chambers (ThermoFisher Scientific) with silanized Lifter-Slips placed over each cDNA microarray and the preheated cDNA/UDR samples added to each slide. MAGEX microarrays were hybridized 17 hrs at 42 °C. All wash solutions were heated to 48 °C prior to use. After overnight hybridization, the slides were soaked in a pre-warmed (48 °C) solution of 1X SSC, 0.1% SDS to remove the LifterSlip. The slides were then washed for 4 min with a warm (48 °C) solution of 1XSSC, 0.1% SDS, followed by a 4 min room temperature wash with 1XSSC, 0.1% SDS and two washes with room temperature 0.1X SSC. The slides were dried by centrifugation at 1000 x g for 4 min in clean 50 mL polypropylene tubes. Dry slides were transferred to dark storage boxes, incubated in a dessicator for an hour, and then scanned using a microarray scanner.

scan_protocol: Hybridized MAGEX microarray slides were scanned on a ProScanArray (PerkinElmer) at 10 µm resolution using dual channels; laser 1 (Cy3 channel) was 543 nm, laser 2 (Cy5 channel) was 633 nm. Laser power was 90% and the PMT gain was 54 for Cy3 and 80 for Cy5.

data_processing:
Data was acquired from raw scanned MAGEX microarray images using ImaGene v5.6.1.
ImaGene V5.6.1 computed signals were normalized using correction factors derived for each array from spot signals greater than 187 and representing genes displaying low standard deviation of the crossing point value (Pfaffl et al., Biotechnology Letters 26: 509-515, 2004).

organism: Aquarana catesbeiana

source_name: liver, iBF+T3

label_protocol: Liver total RNA (25 µg) was labeled with Cy5 using the Superscript Direct cDNA Labeling System (Life Technologies) according to the manufacturer's instructions. Cy5-labelled cDNA was isolated using the Cyscribe GFX Purification kit (GE Healthcare Life Sciences Ltd., Baie d’Urfe PQ, Canada) as per the manufacturer's protocol with cDNA eluted in two consecutive 60 µL aliquots from the column with 5 min ambient temperature incubations for each elution. Isolated cDNA samples were stored at -20 °C in 1.5 mL amber tubes. To aid in microarray data collection, a universal DNA reference (UDR) containing amplicons representative of all gene sequences present on the MAGEX microarray was prepared using a Qiagen PCR Purification kit as described previously (Veldhoen etal 2006; Johanssen etal 2013) with a final stock of 91 ng/µL in dH2O. For each MAGEX microarray, a labelled UDR was prepared from 455 ng of UDR stock, 1 nmol of Cy3-dCTP (GE Healthcare), and Ready-To-Go beads (GE Healthcare) as per the manufacturer's protocol with an increased 2-hr incubation at 37 °C included to maximize yield. The reaction was terminated by addition of 2 µL of 0.5 M EDTA (pH 8.0) and labeled UDR purified using the Cyscribe GFX Purification kit as described above. Each labelled UDR was combined with Cy5-labelled hepatic cDNA sample derived from an individual exposed tadpole (240 μL total volume) and precipitated with sequential addition of 20 μg glycogen (ThermoFisher Scientific), 0.1 vol of 3 M sodium acetate (pH 5.2), and 2.5 volumes of chilled 98% ethanol. Samples were incubated at -80 °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 500 µL 70% ethanol and air dried for 10 min prior to addition of 30 μL of hybridization solution containing; 15 µL formamide (ThermoFisher Scientific), 7 µL of 20X SSC (ThermoFisher Scientific), 0.3 µL 10% SDS (ThermoFisher Scientific), 2.4 µL of 5 mg/ml polyA (Life Technologies), 2.4 µL of 2 mg/mL BSA fraction V (BioLynx), and 2.4 µL of 10 mg/mL yeast tRNA (Life Technologies). Complete resuspension was ensured by heating at 95 °C for 3 min with gentle vortexing.

growth_protocol: The care and treatment of Rana catesbeiana tadpoles used in this study were in compliance with the Canadian Council on Animal Care. All animal exposures were conducted at the Pacific Environmental Science Centre (PESC; North Vancouver, B.C) of Environment Canada by the Environmental Toxicology Section (ETOX). Premetamorphic Gosner stages 31-33 tadpoles (Gosner 1960) were collected locally and maintained at 15±1 °C in a fiberglass aquarium containing 1300 L of on-site well water circulated in a flow-through system. Tadpoles were fed Nutra Plus trout chow (Skretting, Vancouver, BC) and algae wafers (Hikari Sales USA Inc., Hayward, CA, USA) daily with the exception of during the acute and non-lethal chemical exposure periods, when they were not fed. Tadpoles were transferred to aquaria containing 90 L water and acclimated for two weeks prior to the chemical exposures to 22±1 °C and a light:dark photoperiod of 16:8 hours with morning and evening transition times of 15 min.

extract_protocol: Approximately 30 mg of RNAlater preserved liver from each tadpole was homogenized in 1 mL of Qiazol buffer (Qiagen Inc., Mississauga, ON, Canada) using a 3 mm tungsten-carbide bead and a Mixer Mill 300 (Qiagen) at 20 Hz for 4 min (or until homogenization was complete, a maximum of 8 min). Total RNA was isolated from the homogenate using the RNeasy Mini kit (Qiagen) with inclusion of on-column DNaseI digestion. Total RNA was obtained from the column in two sequential 35 µL eluates that were combined. RNA concentration was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Products, Wilmington, DE, USA) while RNA integrity was evaluated using an Experion Automated Electrophoresis System (Bio-Rad Laboratories Inc., Hercules, CA, USA) with the Experion RNA StdSens Analysis Kit as described by the manufacturer. Isolated total RNA was stored at -80 °C.

treatment_protocol: A 6-day exposure regimen was performed with no water exchange. Tadpoles per were exposed for four days in triplicate 50 L tanks (5 animals/tank) to dechlorinated municipal drinking water alone or with the addition of 15 μg/L IBF. On exposure day 4, animals were injected into the peritoneal cavity via the tail muscle with either 10e-5 M T3 dissolved in 100 μM NaOH (1 μL of T3 stock/g body weight) or the equivalent volume of 100 μM NaOH vehicle. The resultant in vivo T3 concentration of 10 pmol/g body weight induces coordinated metamorphosis in tadpoles (White and Nicoll 1981). On exposure day 6, tadpoles were euthanized in 0.1% (w/v) MS-222 and liver tissue collected and preserved in RNAlater RNA stabilization solution as described by the manufacturer (Life Technologies Corp., Carlsbad, CA, USA). The preserved tissue was stored at -20 °C until isolation of total RNA.

value: liver

tag: developmental stage

value: Gosner stage 31-33 tadpole

tag: treatment


title: LCS-400A

description: No additional information.

tag: hbv viral status:

value: large

value: No

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

tag: survival months

tag: recurr status

value: True

tag: recurr months


title: LCS-396A

description: No additional information.

tag: gender

value: female

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: N

tag: alt

value: low

tag: main tumor size

tag: multinodular

tag: cirrhosis

tag: tnm staging

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: shKAP1-4, replicate1

city: Morgantown

first: Alexey

middle: Virginia

last: Ivanov

state: West Virginia

address: 64 Medical Center Drive

department: Department of Biochemistry and Molecular Medicine and WVU Cancer Institute

institute: West Virginia University

description: Gene expression data from human breast cancer cells.

hyb_protocol: The hybridization was done as per GeneChip WT Terminal Labeling and Hybridization User Manual (Affymetrix). Briefly, the entire reaction of fragmented and biotin-labeled cDNA (50 mL) with added hybridization controls was hybridized to the human GeneChip 1.0 ST Exon Arrays (Affymetrix) at 45'C for 17 hours in GeneChip Hybridization Oven 640 (Affymetrix). Human GeneChip 1.0 ST Exon Arrays were stained with FS 450_0001 protocol in Affymetrix GeneChip Fluidics Station 450. Biotin-labeled cDNA was reacted using 2 rounds of washes with a solution containing a streptavidin-phycoerythrin complex, with an intermediate treatment of biotin-labeled anti-streptadvidin antibody to amplify the signal.

scan_protocol: Scanning was done according to GeneChip Expression Wash, Stain and Scan User Manual (Affymetrix, P/N 702731 ). Briefly, phycoerythrin labeling was detected by the Affymetrix GeneChip Scanner 3000 7G Plus using 532nm light.

data_processing: Expression Console software (Affymetrix) was used to check quality controls of hybridized chips. All chips that passed quality controls were RMA normalized with Expression Console software.

source_name: KAP1 knockdown, replicate1

label_protocol: The labeling of the RNA was done as per GeneChip WT Terminal Labeling and Hybridization User Manual (Affymetrix). Briefly, 250 nanograms of each RNA sample with an RNA integrity number (RIN) value greater than 9 was processed by the Ambion WT Expression Kit according to the manufacturer's instructions. The typical yield from the reaction was 6 to 9 micrograms of cDNA. The required amount of cDNA (5.5 mg) was processed for fragmentation and biotin labeling by the GeneChip WT Terminal Labeling Kit. The efficiency of fragmentation reaction was checked via Agilent Bioanalyzer.

growth_protocol: MDA-MB-231LN cells were cultured in Alpha Modification of Eagle's Medium (AMEM) (Fisher Scientific, cat. MT15012CV) supplemented with Penicillin-Streptomycin-L-Glutamine (Fisher Scientific, cat. MT30009CI) and 10% heat-inactivated fetal bovine serum (FBS)

extract_protocol: Total RNA was isolated using mirVana miRNA isolation kit (Ambion) according to the manufacturer's instructions. Purity and integrity of the isolated RNA was confirmed by BioAnalyzer (Agilent).

treatment_protocol: 0.5ug/ml doxycycline was added to all samples for 7 days to induce shRNA expression

tag: cell line

tag: breast cancer subtype

value: claudin-low

tag: expressing

value: KAP1 knockdown


title: MCC

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was renered using Genome Studio, normalization: rank invariant, background substracted

label: Biotin

source_name: 4T1 cells purified from metastatic loci in lung

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

extract_protocol: RNA was extracted with RNeasy Plus Mini Kit (Qiagen) with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: Sex

tag: age

value: 10-12 weeks old

tag: strain

value: Balb/C


title: GBM PL TIMs

first: Amy

middle: B

last: Heimberger

address: 1400 Holcombe Blvd., FC7.2000

department: Neurosurgery

institute: The University of Texas MD Anderson Cancer Center

description:
PI
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0691. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.

hyb_protocol: Hybridization amount started from 2.5 μg total RNA and followed the Phalanx Human miRNA OneArray Pre-Hybridization/Hybridization protocol.

scan_protocol: The arrays were scanned with a GenePix 4000B (Molecular Devices) according to the manufacturer's instruction. The Gal file HmiOA 3.0.gal was used for GenePix Pro software.

data_processing: Foreground values of target probes were imported from GPR files and the flagged probes were deleted. Intensities were normalized with 75% Scaling Normalized method. The log ratio value was then calculated for each gene.

source_name: tumor-infiltrating macrophages, GBM donor

label_protocol: The RNA samples were labeled with Cy5 using the Kreatech ULS miRNA labeling kit, according to the manufacturer's protocol. Labeling efficiency was calculated by the concentration of CyDye and RNA measured by NanoDrop ND-1000. All labeling efficiencies were above 15.

extract_protocol:
Tumors were washed in RPMI medium and dissected to remove blood products and surrounding non-tumor brain tissue. The total tissue was broken down into smaller pieces and digested for 2 hours using a cancer cell isolation kit (Panomics). We have further refined our glioma-infiltrating macrophage isolation protocol by performing CD11b+ MACS positive selection after Percoll gradient centrifugation to achieve over 90% purity (Hussain SF et al. Neuro Oncol. 2006).
The cells were suspended in RNAlater solution (Ambion, Austin, TX) in RNase-free tubes and stored at 4ºC overnight; after 24 hours, they were transferred to -20ºC until needed for total RNA extraction. Extraction was performed using the mirVana kit (Ambion), according to the manufacturer's instructions. Once extracted, RNA levels were analyzed for concentrations and purity using NanoDrop 2000 at 230, 260, and 280 nm.

tag: diagnosis

value: glioblastoma multiforme

tag: who grade

value: IV

tag: tissue

value: tumor

tag: cell type

value: tumor-infiltrating macrophages

tag: donor

value: GBM patient PL


title: shKAP1-4, replicate2

source_name: KAP1 knockdown, replicate2


title: control shRNA, replicate2

source_name: control, replicate2

value: control


title: IBF+T3, L2

value: liver

tag: developmental stage

value: Gosner stage 31-33 tadpole

tag: treatment


title: IBF+T3, L3


title: PCC

source_name: 4T1 cells purified from breast primary tumor

value: female


title: LCS-385A

description: No additional information.

tag: gender

value: male

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

value: small

tag: multinodular

value: No

tag: cirrhosis

value: Yes

tag: tnm staging

value: I

tag: bclc staging

tag: clip staging

tag: afp

tag: survival status

value: Alive

tag: survival months

tag: recurr status

value: False

tag: recurr months


title: GBM BT TIMs

description:
BI
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0691. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.

tag: diagnosis

value: glioblastoma multiforme

tag: who grade

value: IV

tag: tissue

value: tumor

tag: cell type

tag: donor

value: GBM patient BT


title: GMP-iPS, biological rep1

description: GMP-iPS (2 days AGi derived)

source_name: GMP-iPS (2 days AGi derived)

tag: strain

value: GMPt-derived iPSC


title: LCS-379A

description: No additional information.

tag: gender

tag: age

tag: disease state

tag: hbv viral status

value: H

tag: alt

value: low

tag: main tumor size

value: A

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-382A

description: No additional information.

value: male

value: Liver Tumor Tissue

value: N

tag: multinodular

tag: cirrhosis

tag: tnm staging

tag: bclc staging

tag: clip staging

tag: afp

tag: survival status

tag: survival months

tag: recurr status

value: True

tag: recurr months


title: IBF+T3, K2

tag: tissue

value: liver

tag: developmental stage

value: Gosner stage 31-33 tadpole

tag: treatment


title: control shRNA, replicate3

source_name: control, replicate3

tag: cell line

tag: breast cancer subtype

value: claudin-low

tag: expressing

value: control


title: CCC

source_name: 4T1 cells purified from systemic circulation

tag: Sex

value: female

tag: age

value: 10-12 weeks old

tag: strain

value: Balb/C


title: control shRNA, replicate1

source_name: control, replicate1


title: LCS-387A

description: No additional information.

tag: gender

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

value: large

tag: multinodular

value: No

tag: cirrhosis

tag: tnm staging

value: C

value: high

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: shKAP1-3, replicate1

tag: cell line

tag: breast cancer subtype

value: KAP1 knockdown


title: IBF+T3, J4

tag: tissue

tag: developmental stage

tag: treatment


title: LCS-395A

description: No additional information.

tag: gender

value: male

tag: age

value: Liver Tumor Tissue

value: low

value: Yes

value: I

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status

value: Alive

tag: survival months

tag: recurr status

tag: recurr months


title: LCS-376A

description: No additional information.

tag: disease state

tag: hbv viral status

value: AVR-CC

tag: alt

tag: main tumor size

tag: multinodular

tag: cirrhosis

tag: tnm staging

value: Dead

value: True


title: shKAP1-3, replicate2

tag: cell line

tag: breast cancer subtype

value: claudin-low

tag: expressing


title: Fibroblasts-iPS, biological rep1

description: Fibroblasts-iPS(4 days AGi derived)

source_name: Fibroblasts-iPS(4 days AGi derived)

tag: strain

tag: cell type

value: Fibroblast-derived iPSC


title: WT ESCs

description: WT ESCs

source_name: WT ESCs

value: WT ESCs


title: IBF+T3, J1

tag: tissue

value: liver

tag: developmental stage

value: Gosner stage 31-33 tadpole

tag: treatment


title: GBM CD TIMs

description:
CI
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0691. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.

tag: diagnosis

value: glioblastoma multiforme

tag: who grade

value: IV

value: tumor

value: tumor-infiltrating macrophages

tag: donor

value: GBM patient CD


title: T3, F5

source_name: liver, T3


title: GBM MW TIMs

description:
MI
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0691. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.

value: GBM patient MW


title: T3, E3


title: T3, D5


title: T3, D1


title: T3, D4


title: T3, D2


title: GBM BT monocytes

description:
BO
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.

source_name: monocytes, GBM donor

extract_protocol:
The peripheral monocytes from GBM patients were purified based on the same Ficoll-Hypaque density gradient and anti-CD14 microbeads protocol as from the healthy donors. The purity and viability of cells were >90%.
The cells were suspended in RNAlater solution (Ambion, Austin, TX) in RNase-free tubes and stored at 4ºC overnight; after 24 hours, they were transferred to -20ºC until needed for total RNA extraction. Extraction was performed using the mirVana kit (Ambion), according to the manufacturer's instructions. Once extracted, RNA levels were analyzed for concentrations and purity using NanoDrop 2000 at 230, 260, and 280 nm.

value: peripheral blood

value: peripheral monocytes

value: GBM patient BT


title: GBM PL monocytes

description:
PO
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.

value: GBM patient PL


title: Ibuprofen, I1

source_name: liver, ibuprofen

value: ibuprofen


title: Ibuprofen, I2


title: GBM CD monocytes

description:
CO
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.


title: Ibuprofen, H3


title: GBM MW monocytes

description:
MO
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687. Tumors were pathologically confirmed as GBM (World Health Organization grade IV) by a board-certified neuropathologist.


title: LCS-372A

description: No additional information.

tag: gender

value: male

tag: age

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: N

value: low

value: large

value: No

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: Healthy donor monocytes 3

description:
H3
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687.

source_name: monocytes, healthy donor

extract_protocol:
Human PBMCs were prepared from healthy donor blood (Gulf Coast Blood Center, Houston, TX) by centrifugation on a Ficoll-Hypaque density gradient (Sigma-Aldrich, St. Louis, MO). Human CD14+ monocytes were purified from PBMC by anti-CD14 microbeads magnetic cell sorting, according to the manufacturer's instructions (Miltenyi Biotec). The purity and viability of cells were >90%.
The cells were suspended in RNAlater solution (Ambion, Austin, TX) in RNase-free tubes and stored at 4ºC overnight; after 24 hours, they were transferred to -20ºC until needed for total RNA extraction. Extraction was performed using the mirVana kit (Ambion), according to the manufacturer's instructions. Once extracted, RNA levels were analyzed for concentrations and purity using NanoDrop 2000 at 230, 260, and 280 nm.

tag: tissue

tag: cell type

value: healthy donor #3


title: Healthy donor monocytes 4

description:
H4
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687.

value: healthy donor #4


title: Ibuprofen, H2

value: liver

tag: developmental stage

value: Gosner stage 31-33 tadpole

tag: treatment


title: LCS-360A

description: No additional information.

value: CC

tag: alt

value: high

tag: main tumor size

tag: multinodular

tag: cirrhosis

value: Yes

tag: tnm staging

value: IIIB

value: C

tag: survival status

value: Dead

tag: survival months

tag: recurr status

value: True

tag: recurr months


title: LCS-347A

description: No additional information.

tag: gender

value: male

tag: age

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status:

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

tag: afp


title: Healthy donor monocytes 2

description:
H2
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687.

tag: diagnosis

tag: who grade

tag: tissue

value: peripheral blood

tag: cell type

value: peripheral monocytes

tag: donor

value: healthy donor #2


title: Healthy donor monocytes 1

description:
H1
This study was approved by the institutional review board of MD Anderson and conducted under protocol #LAB03-0687.

value: healthy donor #1


title: second Transfection, replicate 2

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description: Stable shSOX2#2 transfected HNO223 cells of transfection 2, compared with shLuci transfected control cells of transfection 2.

hyb_protocol: Hybridization was performed according to the Two-Color Microarrays-based Gene Expression Analysis (Quick Amp Labeling) protocol. Briefly, 2x GEx Hybridization Buffer HI-RPM was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: After hybridization, slides were washed and immediately scanned with an Agilent DNA  Microarray Scanner G 2505 C

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Normalization and data processing was performed in R statistical environment and LIMMA package. For within array normalization, background was substracted by normexp method and then normalized by loess method. Then  quantile method was used to normalize between arrays. The normalized data was used as input to LIMMA for differential analysis.

source_name: HNSCC patient derived cell line

label_protocol: 1µg of RNA was used for cDNA synthesis according to the Two-Color Microarrays-based Gene Expression Analysis (Quick Amp Labeling) protocol. Samples were either Cy5- or Cy3-labeled.

growth_protocol: HNSCC cells (HNO223) were cultured as monolayer with Dulbecco's Modified Eagle Medium (DMEM; PAA, Germany) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich, Germany), 100 U/ml penicillin (Sigma-Aldrich, Germany), 100 mg/ml streptomycin (Sigma-Aldrich, Germany) and 2 mM L-glutamine (PAA, Austria) at 37°C and 5% CO2  in a humidified incubator.

extract_protocol: Total RNA was extracted from stable HNO223-shLuci and HNO223-shSOX2 cell lines from two independent experiments using Qiagen RNeasy Mini kit (Qiagen)

treatment_protocol: Plasmids for stable SOX2 silencing in HNO223 cells were generated by cloning shRNA sequences into the pSUPER-dL_Zeo vector following digestion with BglΙΙ and HindΙΙΙ restriction enzymes.  Successful cloning was confirmed by Sanger sequencing. HNO223 cells were transfected with Effectene Transfection Reagent (Qiagen, Germany), and selection for stable integration was done using 60 mg/ml of Zeocin (Invitrogen, Germany).

tag: cell line

tag: shRNA

value: shLuci


title: LCS-357A

description: No additional information.

tag: hbv viral status

tag: alt

value: low

tag: main tumor size

value: small

tag: multinodular

value: No

tag: cirrhosis

tag: tnm staging

value: I

tag: bclc staging

tag: clip staging

tag: survival status

tag: survival months

tag: recurr status


title: LCS-345A

description: No additional information.

tag: gender

tag: age

tag: disease state

value: AVR-CC

value: large

value: Yes

value: A

tag: afp

tag: recurr months


title: Ibuprofen, G1

tag: tissue

value: liver

tag: developmental stage

value: Gosner stage 31-33 tadpole

tag: treatment

value: ibuprofen


title: Control, C5

source_name: liver, control

value: control


title: Ibuprofen, G2


title: Control, C4


title: LCS-339A

description: No additional information.

value: male

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status:

tag: alt

tag: main tumor size

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

value: Alive

value: False


title: first Transfection, replicate 2

description: Stable shSOX2#2 transfected HNO223 cells of transfection 1, compared with shLuci transfected control cells of transfection 1.

tag: cell line

tag: shRNA

value: shLuci


title: first Transfection, replicate 1

description: Stable shSOX2#1 transfected HNO223 cells of transfection 1, compared with shLuci transfected control cells of transfection 1.


title: LCS-342A

description: No additional information.

tag: hbv viral status

value: CC

value: low

tag: multinodular

tag: cirrhosis

tag: tnm staging

value: IIIB

tag: bclc staging

value: C

tag: clip staging

value: high

tag: survival status

value: Dead

tag: survival months

tag: recurr status

value: True


title: LCS-332A

description: No additional information.

tag: gender

tag: age

tag: tissue

tag: disease state

value: N

value: small

value: No

value: A

tag: afp

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: LCS-340A

description: No additional information.

value: male

tag: hbv viral status

value: AVR-CC

tag: alt

tag: main tumor size

value: large

tag: multinodular

value: Yes

value: IIIC

value: B


title: second Transfection, replicate 1

description: Stable shSOX2#1 transfected HNO223 cells of transfection 2, compared with shLuci transfected control cells of transfection 2.

tag: cell line

tag: shRNA

value: shLuci


title: anti-CD3, biological rep4

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

description:
CD3_4
Gene expression data from CD4+ T-cells restimulated with anti-CD3 for 8 hours.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE).

scan_protocol: Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

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

source_name: CD4+ T-cells restimulated with anti-CD3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

extract_protocol: RNA was prepared with the RNeasy Plus micro kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: Naïve CD4+ T-cells were purified from single cell suspensions of B6 spleen and stimulated with anti-CD3 and anti-CD28 for 2d followed by resting overnight before 20 min of incubation with anti-CD3 and/or anti-ICOS and cross-linking with goat anti-hamster Ab for 8h.

tag: strain/background

tag: cell type

value: CD4+ T-cells

tag: restimulation


title: LCS-343A

description: No additional information.

tag: gender

tag: age

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status:

value: low

tag: cirrhosis

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

tag: survival status

tag: survival months

tag: recurr status

tag: recurr months


title: anti-CD3 and anti-ICOS, biological rep1

description:
ICOS_1
Gene expression data from CD4+ T-cells restimulated with anti-CD3 and anti-ICOS for 8 hours.

value: anti-CD3 and anti-ICOS


title: LCS-330A

description: No additional information.

tag: tissue

tag: disease state

tag: hbv viral status

tag: alt

tag: main tumor size

tag: multinodular

tag: tnm staging

value: IIIA

tag: bclc staging

tag: clip staging

tag: afp

value: high

value: Dead

tag: recurr status:

tag: recurr months:


title: anti-CD3 and anti-ICOS, biological rep2

description:
ICOS_2
Gene expression data from CD4+ T-cells restimulated with anti-CD3 and anti-ICOS for 8 hours.

tag: strain/background

tag: cell type

tag: restimulation


title: Control, B1

value: liver

tag: developmental stage

value: Gosner stage 31-33 tadpole

tag: treatment

value: control


title: Control, A4

tag: tissue


title: Hipp-29M-4

city: Cork

first: Roman

middle: M

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

hyb_protocol: Hybridization was done according to SOPs of the Transcriptomics core facility of the Univeristy Medical Center Goettingen

scan_protocol: Scanning was done according to SOPs of the Transcriptomics core facility of the Univeristy Medical Center Goettingen

data_processing: Data processing was done using standard routines on R and Bioconductor

molecule: polyA RNA

source_name: hand dissected full hippocampus

label_protocol: Labeling was done according to SOPs of the Transcriptomics core facility of the Univeristy Medical Center Goettingen

extract_protocol: Total RNA was extracted using TRI reagent (Sigma-Aldrich) according to the suppliers manual. Following DNase1 (life Technologies) treatment for 20min at 37deg C, RNA was again purified using phenol-chloroform extraction.

treatment_protocol: mice were aged in their home cage

tag: strain

value: Hippocampus

tag: genotype

value: Wild type

tag: age

value: 29 months


title: anti-CD3, biological rep2

description:
CD3_2
Gene expression data from CD4+ T-cells restimulated with anti-CD3 for 8 hours.


title: Hipp-29M-2


title: anti-CD3, biological rep1

description:
CD3_1
Gene expression data from CD4+ T-cells restimulated with anti-CD3 for 8 hours.


title: anti-CD3, biological rep3

description:
CD3_3
Gene expression data from CD4+ T-cells restimulated with anti-CD3 for 8 hours.


title: Hipp-29M-3


title: LCS-329A

description: No additional information.

tag: gender

value: male

tag: disease state

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

value: small

value: No

tag: cirrhosis

value: Yes

value: I

value: A

tag: survival status

tag: survival months

tag: recurr status

value: True

tag: recurr months


title: Control, A3


title: Control, A2


title: LCS-346A

description: No additional information.

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status:

tag: multinodular

tag: tnm staging:

tag: bclc staging:

tag: clip staging:

tag: afp


title: sfp1delta_4

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

description: US10463851_251632210574_S01_GE1_1010_Sep10_2_3

hyb_protocol: Probes were hybridized following the One-Color Microarray-Based Gene Expression Analysis Protocol.

scan_protocol: The slides were scanned on Agilent Scanner G2505C

data_processing: Analyzed by Feature Extraction V.10.10.1.1; data import, log2 transformation and remove controls probes, normalization with limma package version 3.10.3; quality controls before normalization with with limma package version 3.10.3 and geneplotter version 1.32.

organism: Saccharomyces cerevisiae

source_name: sfp1delta strain

label_protocol: Samples were labeled with Cy3 with Low Input Quick Amp Labeling kit

growth_protocol: Yeast strains were grown in liquid YPD (2% glucose, 1% yeast extract, 2% peptone) until OD595 (iMark spectrophotometer) reached 0.4, then frozen

extract_protocol: RNA extraction was performed with E.Z.N.A. Plant RNA extraction kit (Omega bio-tech)

treatment_protocol: No treatment was applied. All strains were grown in full medium

tag: strain background

value: 25-25-2V-P3982 in Peterhoff genetic collection

tag: genotype/variation

tag: clone id

value: clone 4

tag: bears sfp1

tag: bears the [isp+] prion


title: ISP+_4

description: US10463851_251632210574_S01_GE1_1010_Sep10_2_4

source_name: [ISP+] strain

value: [ISP+]


title: Hipp-3M-4

tag: strain

tag: tissue

tag: genotype

tag: treatment

tag: age

value: 3 months


title: KELLY cells transfected with vector

first: Timur

last: Yusufzai

address: 450 Brookline Ave

institute: DFCI

hyb_protocol: Following fragmentation, the cRNA is hybridized overnight at 45C to Human Gene 1.0 ST arrays

scan_protocol: The arrays were scanned at the DFCI Microarray Core Facility using

data_processing: The data were analyzed using dCHIP with the 'Average' modelling method and '5th percentile of region (PM-only)' as background subtraction

label_protocol: Biotinylated cRNA were prepared at the DFCI Microarray Core Facility according to the Affymetrix protocol

growth_protocol: KELLY cells were maintained in complete RPMI media at 37C

extract_protocol: Total RNA was purified using RNeasy columns according to the manufacturer's protocol.

treatment_protocol: The cells were transiently transfected for two days with pOZ-N or pOZ-N-CHD5 with Lipofectamine 2000

tag: cell line

value: KELLY

tag: cell type

value: human neuroblastoma cells

tag: transfected with

value: empty vector


title: LCS-294A

description: No additional information.

tag: gender

value: male

tag: disease state

tag: hbv viral status

value: H

tag: alt

value: high

tag: main tumor size

value: large

tag: multinodular

tag: cirrhosis

tag: tnm staging

value: II

tag: bclc staging

value: C

tag: clip staging

value: low

tag: survival status

value: Alive

tag: survival months

tag: recurr status

tag: recurr months


title: Hipp-29M-1

tag: strain

tag: tissue

value: Hippocampus

tag: genotype

value: Wild type

tag: treatment

tag: age

value: 29 months


title: KELLY cells transfected with CHD5 cDNA

source_name: KELLY_CHD5 cDNA

tag: cell line

tag: cell type

tag: transfected with

value: CHD5 cDNA


title: sfp1delta_1

description: US10463851_251632210574_S01_GE1_1010_Sep10_1_4

tag: strain background

value: 25-25-2V-P3982 in Peterhoff genetic collection

tag: genotype/variation

tag: clone id

value: clone 1

tag: bears sfp1

tag: bears the [isp+] prion


title: LCS-295A

description: No additional information.

tag: gender

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

value: small

tag: multinodular

value: No

tag: cirrhosis

value: Yes

tag: tnm staging

value: I

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status

value: True


title: isp-_2

description: US10463851_251632210573_S01_GE1_1010_Sep10_2_4

source_name: [isp-] strain

tag: strain background

value: [isp-]

value: clone 2


title: LCS-067A

description: No additional information.

value: male

tag: age

tag: tissue

value: AVR-CC

value: high

value: II

value: B

value: Alive

tag: survival months

tag: recurr status

tag: recurr months


title: isp-_1

description: US10463851_251632210574_S01_GE1_1010_Sep10_1_3

value: 25-25-2V-P3982 in Peterhoff genetic collection

tag: genotype/variation

tag: clone id

value: clone 1

tag: bears sfp1

tag: bears the [isp+] prion


title: LCS-069A

description: No additional information.

tag: gender

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: CC

tag: alt

value: low

tag: main tumor size

value: large

tag: multinodular

value: IIIB

value: C

value: Dead


title: Hipp-3M-1

tag: strain

value: Hippocampus

tag: genotype

value: Wild type

tag: treatment

value: 3 months


title: Hipp-3M-2

tag: tissue

tag: age


title: XST_3

city: Hangzhou

first: Xiaohui

last: Fan

state: Zhejiang

address: Yuhangtang 866

institute: Zhejiang Univ.

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 (Affymetrix) and Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000.

data_processing: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings. Spike-in control transcripts were monitored to verify hybridization integrity.

organism: Rattus norvegicus

source_name: tissue samples on the right hemispheres in XST treatment rats

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

growth_protocol: The rats were maintained in air-conditioned rooms (temperature, 22-26 ºC) with a 12-h light-dark cycle,

extract_protocol: Total RNA was extracted using TRIZol Reagent (Invitrogen) and purified using RNeasy Mini kit (QIAGEN), following manufacturers’ protocols.

treatment_protocol: All surgery was performed under isoflurane anesthesia, and all efforts were made to minimize suffering.The right middle cerebral artery were occluded with a 0.25 mm nylon monofilament by inserting it through right external carotid artery to produce the cerebral focal ischemia. Two hours after occlusion, the inserted filament was slowly withdrawn to allow reperfusion. The incision on the neck was closed. Sham-operated rats underwent the same surgical procedures but without the insertion of the nylon filament into the inner carotid. The tissue samples were stored at -80℃ refrigerator.

value: Sprague-Dawley

value: male

value: right hemisphere in brain


title: LCS-063A

description: No additional information.

value: high

value: small

value: Yes

tag: cirrhosis

tag: tnm staging

value: II

tag: bclc staging

value: B

tag: clip staging

tag: afp

tag: survival status

tag: survival months

tag: recurr status

value: True


title: XST_4

tag: gender


title: Hipp-3M-3


title: ISP+_2

description: US10463851_251632210573_S01_GE1_1010_Sep10_2_3

tag: strain background

value: 25-25-2V-P3982 in Peterhoff genetic collection

tag: genotype/variation

value: [ISP+]

tag: clone id

value: clone 2

tag: bears sfp1

tag: bears the [isp+] prion


title: XST_1

tag: strain


title: H358 Brg1i.2 technical replicate #3

city: Chapel Hill

first: Vonn

last: Walter

state: NC

address: CB#7295, School of Medicine

institute: Lineberger Comprehensive Cancer Center

description: technical replicate

hyb_protocol: Hybridization was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

scan_protocol: Scanned on an Agilent High Resolution Model B scanner that has been upgraded to Model C.

data_processing: Images were quantified using Agilent Feature Extraction software.

source_name: H358 Brg1i.2 cells

label_protocol: Labeling was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

growth_protocol: H358 cells were maintained in RPMI1640 plus 10% fetal bovine serum. H358 Control and Brg1i.1 were maintained in RPMI1640 + 10% fetal bovine serum and 400 micrograms/ml G418. H358 Brg1i.2 cells were maintained in RPMI1640 + 10% fetal bovine serum and 1 microgram/ml puromycin

extract_protocol: Total RNA was extracted as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.

tag: shRNA

tag: cell line

source_name: H358 parental cells


title: H358 Brg1i.2 technical replicate #4

description: technical replicate


title: XST_2

tag: tissue


title: LCS-196A

description: No additional information.

tag: age

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: CC

tag: alt

tag: main tumor size

tag: multinodular

value: No

tag: cirrhosis

tag: tnm staging

value: A

tag: recurr months


title: XST_5

value: Sprague-Dawley

tag: gender


title: isp-_4

description: US10463851_251632210573_S01_GE1_1010_Sep10_2_1

tag: strain background

tag: genotype/variation

value: [isp-]

tag: clone id

value: clone 4


title: LCS-049A

description: No additional information.

value: male

value: high

value: large

value: IIIA

tag: bclc staging

value: C

tag: clip staging

tag: afp

value: low

tag: survival status

value: Alive

tag: survival months

tag: recurr status

value: False


title: sfp1delta_3

description: US10463851_251632210573_S01_GE1_1010_Sep10_2_2

value: 25-25-2V-P3982 in Peterhoff genetic collection

value: clone 3

tag: bears sfp1

tag: bears the [isp+] prion


title: H358 Brg1i.2 technical replicate #2

description: technical replicate

tag: shRNA

tag: cell line


title: Model_5

source_name: tissue samples on the right hemispheres in model rats

tag: strain

tag: tissue

value: right hemisphere in brain


title: LCS-056A

description: No additional information.

value: female

tag: age

value: Liver Tumor Tissue

tag: disease state

value: Hepatocellular carcinoma (HCC)

tag: hbv viral status

value: AVR-CC

tag: alt

tag: main tumor size

value: small

tag: multinodular

tag: cirrhosis

value: Yes

tag: tnm staging

value: I

tag: recurr months


title: H358 Brg1i.1 technical replicate #4

description: technical replicate

source_name: H358 Brg1i.1 cells


title: LCS-045A

description: No additional information.

tag: gender

value: male

value: CC

value: No

value: II

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status

tag: survival months


title: Model_4

tag: strain

value: Sprague-Dawley


title: Model_2

tag: tissue


title: sfp1delta_2

description: US10463851_251632210573_S01_GE1_1010_Sep10_1_3

tag: strain background

tag: genotype/variation

tag: clone id

value: clone 2

tag: bears sfp1

tag: bears the [isp+] prion


title: ISP+_1

description: US10463851_251632210573_S01_GE1_1010_Sep10_1_4

value: 25-25-2V-P3982 in Peterhoff genetic collection

value: [ISP+]

value: clone 1


title: H358 Brg1i.2 technical replicate #1

description: technical replicate

tag: shRNA

tag: cell line


title: H358 Brg1i.1 technical replicate #3

description: technical replicate


title: LCS-038A

description: No additional information.

tag: age

tag: disease state

tag: hbv viral status

tag: alt

value: high

tag: main tumor size

value: large

tag: multinodular

tag: cirrhosis

tag: tnm staging

value: IIIA

value: C

value: Alive

tag: recurr status

value: False


title: Model_1

tag: strain

tag: gender

tag: tissue

value: right hemisphere in brain


title: Sham_5

source_name: tissue samples on the right hemispheres in sham rats

value: male


title: Model_3


title: H358 Brg1i.1 technical replicate #1

description: technical replicate


title: LCS-043A

description: No additional information.

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

value: CC

value: small

value: Yes

value: I

tag: bclc staging

tag: clip staging

tag: afp

value: low

tag: survival status

tag: survival months

value: True

tag: recurr months


title: H358 Brg1i.1 technical replicate #2

description: technical replicate

tag: shRNA

tag: cell line


title: isp-_3

description: US10463851_251632210573_S01_GE1_1010_Sep10_1_2

tag: strain background

value: 25-25-2V-P3982 in Peterhoff genetic collection

tag: genotype/variation

value: [isp-]

tag: clone id

value: clone 3

tag: bears sfp1

tag: bears the [isp+] prion


title: H358 Control technical replicate #4

description: technical replicate

source_name: H358 Control cells

value: Control


title: LCS-042A

description: No additional information.

tag: age

tag: disease state

tag: hbv viral status

tag: alt

value: high

tag: main tumor size

tag: multinodular

value: No

tag: cirrhosis

tag: tnm staging

value: II

value: A

tag: recurr status


title: LCS-036A

description: No additional information.

tag: gender

value: male

tag: tissue

value: large

tag: bclc staging

tag: clip staging

tag: afp

tag: survival status

value: Alive

tag: survival months

tag: recurr months


title: LCS-033A

description: No additional information.

tag: age

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

value: CC

value: III

value: B

value: Dead


title: H358 Control technical replicate #3

description: technical replicate

tag: shRNA

tag: cell line


title: Sham_4

tag: strain

value: Sprague-Dawley

value: right hemisphere in brain


title: ISP+_3

description: US10463851_251632210573_S01_GE1_1010_Sep10_1_1

tag: strain background

value: 25-25-2V-P3982 in Peterhoff genetic collection

tag: genotype/variation

value: [ISP+]

tag: clone id

value: clone 3

tag: bears sfp1

tag: bears the [isp+] prion


title: LCS-009A

description: No additional information.

tag: gender

tag: disease state

tag: hbv viral status

value: AVR-CC

tag: alt

value: high

tag: main tumor size

value: small

tag: multinodular

value: No

tag: cirrhosis

value: Yes

tag: tnm staging

value: low

tag: recurr status

value: True


title: Sham_2

value: male

tag: tissue


title: H358 Control technical replicate #1

description: technical replicate

tag: shRNA

value: Control

tag: cell line


title: Sham_1

tag: strain


title: LCS-007A

description: No additional information.

tag: age

value: Liver Tumor Tissue

value: Hepatocellular carcinoma (HCC)

value: II

tag: bclc staging

value: A

tag: clip staging

tag: afp

tag: survival status

value: Alive

tag: survival months

tag: recurr months


title: RA treated SH-SY5Y CSB-KD cells for 3 days, biological rep 1

status: Public on Sep 22 2014

city: London

first: Yuming

address: South Mimms

department: Mechanisms of Transcription Laboratory

country: United Kingdom

institute: Cancer Research UK

hyb_protocol: Following labelling, 4ug of Cy3-cDNA were hybridized for 16 hr at 42ºC on Nimblegen 12 x 125K human expression array by using Nimblegen hybridization kit. The array was washed using Nimblegen washing buffers followed by drying on a microarray dryer.

scan_protocol: The array was scanned using NimbleGen MS 200 Microarray scanner.

data_processing: Data was analysed using Biocondutor 2.12 running on R3.0.0. Probe set expression measures were calculated using quantile normalisation of log2 transformed data.

label: Cyanine 3

label_protocol: Double-stranded cDNA was synthesized using Nimblegen cDNA synthesis kit from 10-20 μg total RNA, up to 1 μg cDNA was labelled with Cy3 according to the standard Nimblegen protocol by using Nimblegen labeling kit.

growth_protocol: human neuroblastoma cell line SH-SY5Y was maintained in 1:1 E4/F12 + 10% FBS medium at 37ºC with 5% CO2.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) as per the manufacturer's instructions.

treatment_protocol: 104/ml cells were seeded onto poly-L-lysine coated dishes one day before treatment, medium was replaced by 1:1 E4/F12 + 1% FBS + 5 μM RA and cells were cultured for the indicated time as described in the study.

tag: cell type

value: human neuroblastoma cells

tag: genotype/variation

value: expressing shCSB; SCB-KD

tag: treated with

value: 5 μM RA for 3 days


title: RA treated SH-SY5Y CSB-KD cells for 3 days, biological rep 2


title: Sham_3

value: Sprague-Dawley

tag: gender

value: right hemisphere in brain


title: H358 Control technical replicate #2

description: technical replicate


title: RA treated SH-SY5Y CSB-KD cells for 9 days, biological rep 2

value: 5 μM RA for 9 days


title: RA treated SH-SY5Y CSB-KD cells for 6 days, biological rep 1

value: 5 μM RA for 6 days


title: RA treated SH-SY5Y CSB-KD cells for 1 day, biological rep 1

value: 5 μM RA for 1 day


title: RA treated SH-SY5Y CSB-KD cells for 30 min, biological rep 1

value: 5 μM RA for 30 min


title: RA treated SH-SY5Y CSB-KD cells for 9 days, biological rep 1


title: untreated SH-SY5Y CSB-KD cells, biological rep 2

source_name: untreated SH-SY5Y CSB-KD cells


title: RA treated SH-SY5Y CSB-KD cells for 1 day, biological rep 2


title: RA treated SH-SY5Y CSB-KD cells for 30 min, biological rep 2


title: LCS-328A

description: No additional information.

value: female

tag: disease state

tag: hbv viral status

value: AVR-CC

tag: alt

value: low

tag: main tumor size

value: large

tag: multinodular

value: Yes

tag: cirrhosis

value: No

tag: tnm staging

value: B

tag: survival status:

tag: survival months:

tag: recurr status:

tag: recurr months:


title: RA treated SH-SY5Y WT cells for 6 days, biological rep 2

source_name: RA treated SH-SY5Y WT cells for 6 days

tag: cell line

value: expressing shGFP; WT


title: RA treated SH-SY5Y WT cells for 3 days, biological rep 2

source_name: RA treated SH-SY5Y WT cells for 3 days

value: human neuroblastoma cells


title: RA treated SH-SY5Y CSB-KD cells for 6 days, biological rep 2

value: expressing shCSB; SCB-KD


title: RA treated SH-SY5Y WT cells for 30 min, biological rep 2

source_name: RA treated SH-SY5Y WT cells for 30 min


title: RA treated SH-SY5Y WT cells for 9 days, biological rep 2

source_name: RA treated SH-SY5Y WT cells for 9 days


title: untreated SH-SY5Y CSB-KD cells, biological rep 1


title: RA treated SH-SY5Y WT cells for 6 days, biological rep 1


title: untreated SH-SY5Y WT cells, biological rep 2

source_name: untreated SH-SY5Y WT cells


title: RA treated SH-SY5Y WT cells for 30 min, biological rep 1


title: RA treated SH-SY5Y WT cells for 9 days, biological rep 1


title: RA treated SH-SY5Y WT cells for 1 day, biological rep 1

source_name: RA treated SH-SY5Y WT cells for 1 day


title: CSB BAC reconstituted cell line, biological rep 2

source_name: CSB BAC reconstituted cell line

growth_protocol: Transformed fibroblast cells were maintained in DMEM + 10% FBS.

treatment_protocol: Cells were transduced with either shCtrl- or shPTB-expressing lentiviruses, grew in fibroblast medium containing 0.2 μg ml-1 puromycin for three days before total RNA isolation.

value: SV40 T-antigen transformed CS fibroblasts expressing CSB BAC

tag: transduced with

value: control shRNA


title: CSB deficient cell line, biological rep 2

source_name: CSB deficient cell line

value: SV40 T-antigen transformed human fibroblasts derived from CS patient


title: CSB BAC reconstituted cell line, biological rep 1


title: untreated SH-SY5Y WT cells, biological rep 1

tag: cell type


title: PTB-depleted CSB BAC reconstituted cell line, biological rep 1

value: shPTB-expressing lentiviruses


title: CSB TetON reconstituted cell line, biological rep 1

hyb_protocol: Following labelling, 4ug of Cy3-cDNA were hybridized for 16 hr at 42ºC on Nimblegen 12 x 135K human expression array by using Nimblegen hybridization kit. The array was washed using Nimblegen washing buffers followed by drying on a microarray dryer.

source_name: CSB TetON reconstituted cell line

growth_protocol: Transformed fibroblast cells were maintained in DMEM + 10% FBS. Cell lines for the tetracycline-inducible systems (CS1AN_Vector and CSB TetON) were cultured in DMEM + 10% Tet-free FBS, 2 ng ml-1 doxycycline was added to the cells 48 hr before total RNA isolation.

value: human fibroblast derived from CS patient and transformed with SV40 T-antigen, expressing CSB TetON


title: CSB BAC reconstituted cell line_B, biological rep 2

value: human fibroblast derived from CS patient and transformed with SV40 T-antigen, expressing CSB BAC


title: PTB-depleted CSB BAC reconstituted cell line, biological rep 2


title: CSB deficient cell line_B, biological rep 2

value: human fibroblast derived from CS patient and transformed with SV40 T-antigen


title: CSB BAC reconstituted cell line_A, biological rep 1


title: CSB deficient cell line_A, biological rep 1


title: CSB deficient cell line, biological rep 1


title: CSB TetON reconstituted cell line, biological rep 2


title: RA treated SH-SY5Y WT cells for 1 day, biological rep 2

tag: genotype/variation

value: 5 μM RA for 1 day


title: PTB-depleted CSB deficient cell line, biological rep 1

source_name: PTB-depleted CSB deficient cell line


title: PTB-depleted CSB deficient cell line, biological rep 2


title: CSB deficient cell line expressing empty vector, biological rep 1

value: human fibroblast derived from CS patient and transformed with SV40 T-antigen, expressing pTRE3G vector


title: patient 3, biological rep 1

source_name: CS_frozen cerebellum

growth_protocol: cerebellum tissues were frozen at -80ºC

extract_protocol: Total RNA was extracted using the RNeasy lipid tissue minikit (Qiagen) as per the manufacturer's instructions.

tag: subject condition

value: Cockayne Syndrome (CS) patient

tag: age

tag: tissue

value: frozen cerebellum

tag: pmi (post-mortem interval, hr)

tag: tissue section number

tag: rin (rna integrity number)


title: patient 3, biological rep 2


title: CSB deficient cell line expressing empty vector, biological rep 2


title: control 2, biological rep 2

source_name: control_frozen cerebellum

value: age-matched control


title: control 1, biological rep 2


title: control 2, biological rep 1


title: control 3, biological rep 2


title: patient 2, biological rep 2


title: c-Myc-Max_L heterodimer at 10nM concentration

type: protein

city: Durham

first: Raluca

last: Gordan

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Protein was diluted to 10 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated mouse IgG antibody to His-tag (Qiagen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 7.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: The raw PBM data was processed using the Universal Protein Binding Microarray (PBM) Analysis Suite, available at http://the_brain.bwh.harvard.edu/PBMAnalysisSuite/index.html. Briefly, to correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. The adjusted Alexa 488 signals are available in the column Alexa488Adjusted. Next, the Seed-and-wobble algorithm was applied on the adjusted signals to compute enrichment scores (E-score) and median intensities for all possible 8-mers (in 4x44k_MycMax_Max_8mer_data.txt).

label: Alexa 488

molecule: protein

source_name: Human c-Myc and Max

label_protocol: Proteins were tagged with C-terminal His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated mouse IgG antibody to His tag (Qiagen).

growth_protocol: Coding sequences of Myc (gi:29839758) and Max(L) (gi:21704261) were amplified from HeLa cDNA and individually cloned into pET21a (C-term His-tag). All proteins were expressed in BL21 star E. coli after overnight induction of Max(L) at 18oC or four-hour induction of Myc at 37oC.

extract_protocol: Soluble Max protein was purified over Ni-NTA and Mono S. Yields were ~20 mg per liter. Myc was purified over Ni-NTA and Mono Q in the presence of 7 M urea yielding 7 mg of Myc per liter. Myc-Max heterodimers were prepared by mixing equal moles of Myc and Max in 6 M urea followed by step dialysis against 4 M, 2 M, 1 M and 0.5 M urea with 500 mM HGKEDP (25 mM HEPES, pH 7.6, 15% glycerol, indicated KCl, 0.1 mM EDTA, 1 mM DTT, and 0.1% of a solution of saturated PMSF in isopropanol) for 1.5 hour each, then against 100 mM HGKEDP overnight. The renatured Myc-Max proteins were finally purified over Mono Q in HGKEDP. All protein samples were aliquoted and kept at -80oC. In the absence of urea, Myc was prone to aggregation, but Max and Myc-Max chromatographed cleanly and behaved well. Myc-Max heterodimers partially dissociated over time generating a small amount (<10%) of Max homodimers.

tag: transcription factor

value: c-Myc, Max

tag: protein concentration

value: Protein concentration:10nM


title: patient 1, biological rep 2


title: control 3, biological rep 1


title: patient 1, biological rep 1


title: patient 2, biological rep 1


title: control 1, biological rep 1


title: Max_L homodimer at 10nM concentration

source_name: Human Max

value: Max


title: RA treated SH-SY5Y WT cells for 3 days, biological rep 1

value: human neuroblastoma cells

value: expressing shGFP; WT

tag: treated with

value: 5 μM RA for 3 days


title: Normal_adjacent_tissue_002

city: Guangzhou

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

institute: Sun Yat-sen Memorial Hospital

description:
Gene expression without treatment
NAT002

hyb_protocol: Each Slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent) in Hybridization Oven (Agilent), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon) with Gene Expression Wash Buffer Kit (Agilent), following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent) with default settings, Dye channel: Green, Scan resolution=3 μm, 20 bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent).

source_name: Normal adjacent tissue patient002

label_protocol: Total RNA was then amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN).

extract_protocol: Total RNA from cells was isolated using Trizol reagent (Life technologies). RNA purity and integrity was analyzed by Agilent Bioanalyzer 2100 (Agilent). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN) and RNase-free DNase set (QIAGEN).

treatment_protocol: Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were used directly for total RNA extraction.

tag: individual

value: patient 002

tag: disease state

value: Bladder cancer

value: Normal adjacent tissue

tag: gender

value: male


title: HVSMCs incubated with RANKL rep3

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Gene expression data from cells incubated with RANKL

hyb_protocol: Fragmented aRNA was hybridized to Affymetrix HG-U133A 2.0 chips

scan_protocol: standard Affymetrix protocol

data_processing:
Data were analyzed in R
Qspline and expression index was calculated using liwong. No background correction of data was performed.

source_name: Human vascular smooth muscle cells

label_protocol: total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

growth_protocol: HVSMCs were grown in DMEM supplemented with 10% FBS

extract_protocol: Total RNA was extracted from cells using Trizol

treatment_protocol: 100 nmol/l neg. ctrl. or OPG siRNA. 10 ng/ml recombinant RANKL or TRAIL for six hours.

value: Cells before passage number 8

value: Human vascular smooth muscle cells

tag: treatment

value: recombinant RANKL


title: Bladder_cancer_tissue_002

description:
Gene expression without treatment
BCa002

source_name: Bladder cancer tissue patient002

value: Bladder cancer tissue


title: HVSMCs incubated with TRAIL rep3

description: Gene expression data from cells incubated with TRAIL

value: recombinant TRAIL


title: control cell TRAIL rep1

description: Gene expression data from control cells

value: control


title: control cell TRAIL rep2

description: Gene expression data from control cells


title: control HVSMCs RANKL rep1

description: Gene expression data from control cells


title: HVSMCs with siRNA-mediated knockdown of OPG rep3

description: Gene expression data from cells with siRNA-mediated knockdown of OPG

tag: knockdown

value: siRNA-mediated knockdown of OPG


title: control HVSMCs RANKL rep3

description: Gene expression data from control cells


title: control HVSMCs RANKL rep2

description: Gene expression data from control cells


title: HVSMCs incubated with TRAIL rep1


title: control cell TRAIL rep3

description: Gene expression data from control cells


title: Normal_adjacent_tissue_001

description:
Gene expression without treatment
NAT001

source_name: Normal adjacent tissue patient001

value: patient 001

value: female


title: HVSMCs incubated with RANKL rep1


title: brain_hom_rep2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

description: replicate 2

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

tag: genotype

value: homozygous

tag: allele

value: ko

value: 21 weeks

tag: mouse id

tag: Sex


title: brain_hom_rep1

description: replicate 1

tag: age


title: control HVSMCs siRNA rep2

description: Gene expression data from control cells

tag: cell type


title: HVSMCs incubated with TRAIL rep2


title: brain_hom_rep3

description: replicate 3


title: control HVSMCs siRNA rep3

description: Gene expression data from control cells


title: Bladder_cancer_tissue_001

description:
Gene expression without treatment
BCa001

source_name: Bladder cancer tissue patient001

tag: tissue


title: HVSMCs with siRNA-mediated knockdown of OPG rep2


title: 5355441026_D

city: Dallas

first: Kimberly

last: Batten

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

description: G12D mutant K-ras

data_processing: Data was processed using tools in Bioconductor/R. Quality control and outlier dection with lumi;  background correction, quantile normalization, and log2 transformation with MBCB. One outlier (5355441026_D) was removed during quality control procedures.

source_name: 0.2Gy x 5 56Fe Irradiated

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep Kit for Illumina arrays

growth_protocol: Animals were bred and housed in ventilated microisolator cages within a specific pathogen free facility at UT Southwestern Medical Center at Dallas.

extract_protocol: Whole left lung of euthanized animals were flash frozen.  RNA was extracted from frozen tissue using Qiagen Rneasy Plus Kit.

treatment_protocol: Animals were transported to Brookhaven National Laboratory and either left unirradiated or irradiated with a fractionated or acute dose of 1.0 GeV/nucleon 56Fe- particles.

value: 129S2 K-rasLA1

value: F

value: lung; left lobe


title: HVSMCs incubated with RANKL rep2


title: brain_wildtype_rep4

description: replicate 4

value: wild type


title: brain_wildtype_rep2

description: replicate 2

value: male


title: 5355441026_C

description: G12D mutant K-ras

source_name: 1.0Gy x 1 56Fe Irradiated

value: M


title: 5355441026_F

description: G12D mutant K-ras

source_name: Unirradiated Control


title: control HVSMCs siRNA rep1

description: Gene expression data from control cells

value: Cells before passage number 8

value: Human vascular smooth muscle cells


title: Embryonic Drosophila cells, Kc167 cells, CSN7 DamID, replicate 2

city: Tel Aviv

first: Danny

last: Chamovitz

address: Ramat aviv

country: Israel

institute: Tel Aviv University

description: CSN7 bound DNA regions in Drosphila Kc167 cells

hyb_protocol: Hybridization was done according to manufacturer's protocol (ftp://ftp.buckinstitute.org/BuckMelov/Fisher/CD%20Files/Application%20Guides/NG_ChIP_Guide_v4p1.pdf).

scan_protocol: Scanning was done according to manufacturer's protocol (ftp://ftp.buckinstitute.org/BuckMelov/Fisher/CD%20Files/Application%20Guides/NG_ChIP_Guide_v4p1.pdf).

data_processing:
Scans were processed using NimbleScan software. The Csn7 DamID data analyses were based on quantile normalization of the four samples and average of the results.
We used the NimbleScan software to generate scaled Log2-Ratios. Replicates were then quantile normalized.

organism: Drosophila melanogaster

source_name: CSN7-Dam DamID DNA from Kc167 cells

label_protocol: DamID DNA was labeled by Klenow random priming with Cy5/Cy3 nonamers according to manufacturer's protocol (http://www.nimblegen.com/downloads/support/05434505001_NG_Expression_UGuide_v6p0.pdf).

growth_protocol: cells were cutlured in SFX medium at 25°C

extract_protocol: Sample extraction was performed as described (Orian A. et al., DamID: a methylation-based chromatin profiling approach. Methods Mol. Biol. 2009;567:155-169)

tag: cell line

value: Kc167 cells

source_name: Control-Dam DamID DNA from Kc167 cells


title: Embryonic Drosophila cells, Kc167 cells, CSN7 DamID, replicate 1


title: Embryonic Drosophila cells, Kc167 cells, CSN7 DamID, replicate 3


title: Myriocin_rep2

city: Lexington

first: Jun

last: Liu

state: KY

address: 741 S. Limestone BBSRB B0136

department: Molecular and Cellular Biochemistry

institute: University of Kentucky

hyb_protocol: Following fragmentation was done by the microarray core facility at the University of kentucky according to the GeneChip® 3’ IVT Express Kit user mannual

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 by the microarray core facility at the University of kentucky according to the GeneChip® 3’ IVT Express Kit user mannual

data_processing: Raw data files (CEL files) were processed by using the Partek® Genomics Suite™ (Partek Incorporated., USA) (2010). S. pombe probesets were excluded from the analysis.

source_name: DBY746 yeast cells at A600=2.0,  treated with 300 ng/ml myriocin

label_protocol: Biotinylated cRNA were prepared by the microarray core facility at the University of kentucky according to the GeneChip® 3’ IVT Express Kit user mannual

growth_protocol: Yeast cells were incubated in a shaker at 30°C, 220rpm. DBY746 cells were grown from 0.002 to 2 A600 units/ml in SDC medium (pH 6) with and without myriocin (300ng/ml).

extract_protocol: Rneasy(Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For control cells, 0.3% 95% ethanol was added at the beginning of culture; for myriocin treated cells, first adding a calculated volume of 95% ethanol to the medium followed by diluting a stock solution of myriocin (200 µg/ml in 95% ethanol, Sigma #M1177) to give a final concentration of 300 ng/ml and the ethanol final conc. is 0.3%.

tag: genotype/variation

value: wild-type


title: 5355492017_F

description: G12D mutant K-ras


title: Myriocin_rep1


title: 5355441026_E

description: G12D mutant K-ras


title: 5355441025_F

description: G12D mutant K-ras


title: 5355441026_A

description: G12D mutant K-ras


title: 5355441025_D

description: G12D mutant K-ras


title: 5355441026_B

description: G12D mutant K-ras


title: brain_wildtype_rep3

description: replicate 3


title: 5355441025_B

description: G12D mutant K-ras


title: HVSMCs with siRNA-mediated knockdown of OPG rep1


title: 5355441025_E

description: G12D mutant K-ras


title: No-myriocin_rep3

source_name: DBY746 yeast cells at A600=2.0, no treatment


title: Embryonic Drosophila cells, Kc167 cells, CSN7 DamID, replicate 4


title: No-myriocin_rep2


title: No-myriocin_rep1


title: 5355441025_A

description: G12D mutant K-ras


title: 5355441012_F

description: G12D mutant K-ras


title: brain_wildtype_rep1

description: replicate 1


title: 5355441012_E

description: G12D mutant K-ras


title: Myriocin_rep3


title: 5355441025_C

description: G12D mutant K-ras


title: 5355441012_D

description: G12D mutant K-ras


title: miR34a thymus_rep8

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597.Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro6.1 image processing software (Axon Instruments, USA). Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500. Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

label_protocol: For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye. HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

value: 17 wk

tag: genetic background

value: thymus

value: mir-34a minus

source_name: Wt RNA pool thymus

value: control


title: miR34a brain_rep4

value: brain

source_name: Wt RNA pool brain


title: miR34a brain_rep6


title: miR34a thymus_rep5


title: miR34a thymus_rep6


title: miR34a thymus_rep3


title: miR34a thymus_rep4


title: miR34a brain_rep2


title: miR34a brain_rep5


title: 5355441012_A

description: G12D mutant K-ras

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol


title: miR34a thymus_rep7


title: miR34a thymus_rep2


title: 5355441011_D

description: G12D mutant K-ras


title: miR34a thymus_rep1


title: 5355441011_B

description: G12D mutant K-ras


title: 5355441011_E

description: G12D mutant K-ras


title: 5355441012_C

description: G12D mutant K-ras


title: 5355441011_F

description: G12D mutant K-ras


title: miR34a brain_rep1


title: miR34a brain_rep3


title: 5355441011_A

description: G12D mutant K-ras


title: 5355441011_C

description: G12D mutant K-ras


title: 5355441010_E

description: G12D mutant K-ras


title: 5355441003_E

description: G12D mutant K-ras


title: 5355441010_F

description: G12D mutant K-ras


title: 5355441010_C

description: G12D mutant K-ras


title: 5355441010_A

description: G12D mutant K-ras


title: 5355441010_B

description: G12D mutant K-ras


title: 5355441003_D

description: G12D mutant K-ras


title: gct-2 mutant 9-day-old seedlings, above-ground portions, biological replicate 2

city: Ithaca

first: Matthew

middle: R

last: Willmann

state: NY

address: B18 Weill Hall, 237 Tower Road

department: School of Integrative Plant Science

institute: Cornell University

description: Gene expression data from above-ground parts of 9-day-old gct-2 seedlings

hyb_protocol: Affymetrix ATH1 GeneChips were hybridized with 3.75 ug of biotin-labeled cDNA at a concentration of 17 ng/ul in the hybridization coctail.  Hybridization was carried out for 16-18 hours at 45oC.  Washing and staining were done using a GeneChip Fluidics Station 450.

scan_protocol: The GeneChips were scanned using a 7G Affymetrix GeneChip Scanner.

data_processing: The data were gcRMA-normalized in R using the gcrma package and filtered to remove all probesets that did not have a MAS5.0 present call in at least three of the arrays.

organism: Arabidopsis thaliana

source_name: Above-ground parts of 9-day-old Arabidopsis thaliana gct-2 seedlings

label_protocol: Biotin-labeled cDNA targets were made from 50 ng starting RNA that was reverse-transcribed and amplified using the OvationTM RNA Amplification SystemV2 and fragmented and labeled using the FL-OvationTM cDNA Biotin Module V2 (NuGEN Technologies, San Carlos, CA) per the manufacturer’s instructions.

growth_protocol: Seeds of wild-type Col-0, cct-1, and gct-2 were sown in Fafard #2 soil.  The flats were placed at 4oC for three days before being put in a Conviron growth chamber at a constant 23oC under a one-to-one ratio of T8 Sylvania Octron 4100K Ecologic and GroLite WS fluorescent lamps (Interlectric) at ~125 μmol m-2 s-1.  Plants were grown under long day conditions—16 hr light (100-125 μmol m-2 s-1):8 hr dark.  Above-ground portions of seedlings were harvested when the first two leaf primordia were 1 mm in length, which was at day 7 for wild-type seedlings and day 9 for the two mutants. Only seedlings that produced cotyledons and leaf primordia were used. 75-100 seedlings were used per biological replicate.

extract_protocol: The seedlings were ground in liquid nitrogen and then Trizol (Invitrogen, Carlsbad, CA) with a mortar and pestle.  After extraction with chloroform (1/5th volume of the Trizol), per the manufacturer’s instructions, the aqueous phase was combined with ½ volume of 100% ethanol, mixed and passed over an RNeasy Mini (Qiagen, Valencia, CA) column.  The RNA was further purified according to the RNeasy Mini directions, including an on-column DNA digestion with Qiagen’s RNase-Free DNase Set.  The final RNA was eluted in the provided RNase-free water, and 1 ul of RNasin was added to increase stability.

treatment_protocol: Above-ground portions of seedlings were collected using forceps and immediately placed in conical tubes in liquid nitrogen, one tube per replicate. To minimize the effect of collection time, small batches of seedlings were collected for a given tube before moving onto the next one, cycling between all nine tubes until the desired total number of seedlings was achieved in each tube.

value: seedling


title: 5355441003_F

description: G12D mutant K-ras


title: 5355441003_B

description: G12D mutant K-ras


title: 5355441003_A

description: G12D mutant K-ras


title: 5355441003_C

description: G12D mutant K-ras


title: gct-2 mutant 9-day-old seedlings, above-ground portions, biological replicate 1


title: 5355441010_D

description: G12D mutant K-ras


title: cct-1 mutant 9-day-old seedlings, above-ground portions, biological replicate 3

description: Gene expression data from above-ground parts of 9-day-old cct-1 seedlings

source_name: Above-ground parts of 9-day-old Arabidopsis thaliana cct-1 seedlings


title: cct-1 mutant 9-day-old seedlings, above-ground portions, biological replicate 1


title: 5355441001_D

description: G12D mutant K-ras


title: 5355441001_E

description: G12D mutant K-ras


title: Outer interzone, replicate 2

city: Vienna

first: Florien

last: Jenner

address: Veterinärplatz 1

department: Equine Surgery

country: Austria

institute: University of Veterinary Medicine Vienna

description: outer interzone, murine embryo 15.5 days gestation

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System.

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. FES derived output data files were further analysed using Partek Genomics Suite software (version 6.11.0321, Partek Inc., Chesterfield, USA). The raw data was quantile normalized and log2 transformed

source_name: outer interzone

label_protocol: Each RNA sample was amplified and labelled using the Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies) following the manufacturer’s protocol, to produce Cyanine 3-CTP (Cy-3) labelled cRNA. Yields of cRNA and dye incorporation rate were measured with a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA).

extract_protocol: Total RNA was extracted from cell lysates using RNeasy Micro Kits (Qiagen Sciences Inc.) according to manufacturer's protocols. RNA integrity, purity and quantity was determined and expressed as RNA integrity number (RIN) with an Agilent Bioanalyzer 2100 (RNA 6000 Pico LabChip® Kit, Agilent Technologies, Waldbronn, Germany). RNA was stored at −80°C.

value: embryo

value: 15.5 days gestation


title: wild-type 7-day-old seedlings, above-ground portions, biological replicate 3

description: Gene expression data from above-ground parts of 7-day-old wild-type Col-0  seedlings

source_name: Above-ground parts of 7-day-old Arabidopsis thaliana wild-type Col-0 seedlings


title: 5355441001_C

description: G12D mutant K-ras

value: 129S2 K-rasLA1


title: Outer interzone, replicate 1


title: Outer interzone, replicate 3


title: 5355441001_F

description: G12D mutant K-ras

value: lung; left lobe


title: Intermediate interzone, replicate 3

description: intermediate interzone, murine embryo 15.5 days gestation

source_name: Intermediate interzone


title: cct-1 mutant 9-day-old seedlings, above-ground portions, biological replicate 2


title: wild-type 7-day-old seedlings, above-ground portions, biological replicate 2

value: wild type


title: 5355441001_B

description: G12D mutant K-ras

value: F


title: Intermediate interzone, replicate 2


title: wild-type 7-day-old seedlings, above-ground portions, biological replicate 1


title: Intermediate interzone, replicate 1


title: M2

status: Public on Sep 21 2014

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

country: Japan

institute: Kumamoto University

description: Gene expression data from M2 treated with vehicle.

hyb_protocol: 2 ug of labeled DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA data was generated by Expression Console (Affymetrix).

source_name: vehicle-treated M2

label_protocol: Amplified sense-strand DNA products were synthesized by the Ambion WT Expression Kit, and were fragmented and labeled by the WT Terminal Labeling and Controls Kit.

growth_protocol: For macrophages differentiation, bone marrow cells from the tibias and fibulas were cultured in cRPMI medium (RPMI medium supplemented with 1% L-glutamine, 1% Hepes, 0.1% mercaptoethanol and 10% fetal bovine serum) containing 10 ng/mL M-CSF. Medium was replaced on days 3 and 6 and cells were harvested on day 9. To induce M1 or M2 phenotypes, cells were stimulated for 48 h with IFN-γ (10 ng/mL) or with IL-4 (20 ng/mL), respectively.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Macrophage cells were incubated with or without interleukin-1alpha (10 ng/ml) for 24 h.

tag: strain/background

value: macrophages

tag: phenotype

value: vehicle


title: M1_IL-1

description: Gene expression data from M1 treated with interleukin-1alpha.

source_name: interleukin-1alpha-treated M1


title: M1

description: Gene expression data from M1 treated with vehicle.

source_name: vehicle-treated M1


title: 5355441001_A

description: G12D mutant K-ras

source_name: 0.2Gy x 5 56Fe Irradiated


title: M2_IL-1

description: Gene expression data from M2 treated with interleukin-1alpha.

source_name: interleukin-1alpha-treated M2


title: gct-2 mutant 9-day-old seedlings, above-ground portions, biological replicate 3


title: Pheochromocytoma VCB-PH-06T

city: Melbourne

first: Aidan

last: Flynn

state: Victoria

address: St Andrews Place, Melbourne East

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

description: Hybridized to CytoScan HD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Raw CEL files were processed using Affymetrix Chromosome Analysis Suite (ChAS) Software
CYCHP files generated by Affymetrix Chromosome Analysis Suite

source_name: Right adrenal phaeochromocytoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from fresh frozen tumour samples using DNeasy Blood and Tissue kit from Qiagen

value: Right adrenal phaeochromocytoma

tag: Stage

value: Metastatic

tag: ageatdiagnosis

tag: origin

value: Familial

tag: drivergene

value: RET


title: Pheochromocytoma VCB-PH-11T

description: Hybridized to CytoScan HD

value: Benign


title: Pheochromocytoma VCB-PH-04T

description: Hybridized to CytoScan HD

source_name: Bilateral phaeochromocytoma

value: Bilateral phaeochromocytoma

value: M

value: VHL


title: Paraganglioma VCB-PH-02T

description: Hybridized to CytoScan HD

source_name: Left supra adrenal paraganglioma

value: Left supra adrenal paraganglioma

value: Unknown


title: Pheochromocytoma VCB-PH-08T

description: Hybridized to CytoScan HD


title: Paraganglioma V-PH-23T

description: Hybridized to CytoScan HD

source_name: Infra renal paraortic paraganglioma

value: Infra renal paraortic paraganglioma

value: SDHB


title: Pheochromocytoma VCB-PH-07T

description: Hybridized to CytoScan HD

value: Sporadic

value: H-RAS


title: Pheochromocytoma V-PH-20T

description: Hybridized to CytoScan HD

value: F


title: Pheochromocytoma VCB-PH-03T

description: Hybridized to CytoScan HD


title: Pheochromocytoma V-PH-29T

description: Hybridized to CytoScan HD

source_name: Adrenal phaeochromocytoma

value: Adrenal phaeochromocytoma


title: Pheochromocytoma VCB-PH-12T

description: Hybridized to CytoScan HD


title: Pheochromocytoma V-PH-17T

description: Hybridized to CytoScan HD

source_name: Right adrenal pheochromocytoma

value: Right adrenal pheochromocytoma


title: Rbfox3 shRNA for T2-P19 cells with neuronal differentiation, biological rep3

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

hyb_protocol: Hybridization of the affymetrix microRNA arrays was done overnight at 45C for 16 hours in a hybridization oven.

scan_protocol: Scanning of the washed, stained arrays was done using Affymetrix 3000 7G scanner

data_processing: the image data was analyzed using the miRNA QC tool software for quality control. The raw data was preprocessed by Affymetrix miRNA QC Tool (Version 1.1.1.0) with the workflow of global background correction, quantile normalization and median polish summarization (miRNA-2_0.cdf).

source_name: Rbfox3 shRNA_T2-P19 cells_with neuronal differentiation

label_protocol: microRNAs were labeled using the flashtag  biotin assay as per the manufacturer's (Genisphere)directions. In brief,  the process begins with a brief tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample.

growth_protocol: P19 mouse embryonal carcinoma cells were purchased from ATCC and maintained in MEMa containing 7.5% calf serum and 2.5% fetal bovine serum.

extract_protocol: Trizol (Invitrogen)

treatment_protocol: Neuronal differentiation by retinoic acid treatment

value: embryonal carcinoma cells

tag: transfected with

value: Rbfox3 shRNA

tag: treated with

value: retinoic acid


title: Pheochromocytoma V-PH-26T

description: Hybridized to CytoScan HD

value: Right adrenal phaeochromocytoma

value: Metastatic

value: Familial


title: Pheochromocytoma VCB-PH-10T

description: Hybridized to CytoScan HD

value: Benign