title: plasma, pre-infection (SIV) PWf2_PB

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

description:
Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards (2 per sample). Quantitative real-time PCR was performed for 768 features, 754 of which represent primate miRNAs.
For each of two cards per sample (A and B), nine ul of pre-amplified, diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into miRNA TLDA cards (Applied Biosystems) by centrifugation. Cards were sealed, and qRT-PCR was performed with a real-time thermocycler (ABI-7900, Applied Biosystems) per manufacturer's recommendations.

data_processing:
SDS software (Applied Biosystems) was used to collect data.
Threshold intensities were set, visually and individually confirmed, and standardized with RQ Manager (Applied Biosystems). Data were processed using DataAssist (Applied Biosystems) and HTqPCR (R/Bioconductor). In HTqPCR, quantile normalization was employed.

label: FAM

organism: Macaca nemestrina

source_name: plasma, pre-infection (SIV)

label_protocol: Five ul total RNA per sample was reverse-transcribed using Megaplex primers, sets A and B (Applied Biosystems). cDNA was pre-amplified for twelve cycles with Mexaplex Pre-Amp primers, sets A and B (Applied Biosystems), then diluted to 100 ul. Manufacturer's protocol was followed throughout.

extract_protocol: Total RNA was extracted from 100 ul plasma with a miRvana isolation kit (Ambion) per the manufacturer's protocol. 5 nM synthetic ath-miR159a was spiked into each sample to correct for technical differences. RNA was eluted in 100 ul nuclease-free water.

tag: sample type

value: plasma

tag: Sex

value: Male

tag: degree of encephalitis at necropsy

value: < 5 years

tag: necropsy, days post inoculation

tag: time

value: pre-infection (SIV)

tag: infection

tag: disease state


title: CHOP0260

status: Public on Sep 15 2011

type: genomic

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

country: USA

institute: Childrens Hospital of Philadelphia

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

hyb_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor DNA

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: plasma, 10 days post inoculation (SIV) PWf2_10dpi

type: RNA

state: MD

molecule: total RNA

source_name: plasma, 10 days post inoculation (SIV)

value: 10 days post inoculation (SIV)

value: SIV


title: CHOP0366

scan_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: plasma, pre-infection (SIV) PRd2_PB

value: Severe

value: Severe encephalitis


title: plasma, 10 days post inoculation (SIV) PRd2_10dpi


title: CHOP0222

data_processing: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: CHOP0298

label_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: CHOP0237


title: CHOP0266


title: plasma, pre-infection (SIV) PLc2_PB


title: CHOP0215


title: CHOP0309


title: CHOP0198


title: CHOP0241


title: plasma, 10 days post inoculation (SIV) PLc2_10dpi


title: CHOP0230


title: CHOP0205


title: plasma, pre-infection (SIV) PLb2_PB


title: CHOP0220


title: CHOP0232


title: plasma, 10 days post inoculation (SIV) PLb2_10dpi


title: CHOP0129


title: CHOP0158


title: CHOP0141


title: CHOP0160


title: CHOP0153


title: CHOP0154


title: CHOP0157


title: CHOP0128


title: plasma, 10 days post inoculation (SIV) CT64_10dpi

value: Female


title: CHOP0108


title: CHOP0122


title: CHOP0121


title: plasma, pre-infection (SIV) 01P006_PB


title: CHOP0091


title: CHOP0083


title: plasma, 10 days post inoculation (SIV) 01P006_10dpi


title: CHOP0193


title: CHOP0076


title: Wild-type iPSCs, rep1

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

description: Genomic DNA extracted from blood, fibroblasts, iPS and neuralised iPS cell lines was genotyped using HumanOmni1-Quad BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: Beadchips were scanned using an iSscan(Illumina) with an AutoLoader (Illumina).

data_processing: Genomic DNA extracted from blood, fibroblasts, iPS and neuralised iPS cell lines was genotyped using and processed in GenomeStudio v1.8.X (Illumina) to generate SNP calls.

source_name: NAS2 iPSCs

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

growth_protocol: Fibroblasts: grown in DMEM/FCS, brought to equivalent passage; iPSCs: grown in mTESR1 media on BD Matrigel; Neurons: differentiated according to the dual SMAD/ floor plate protocol, then enriched for dopaminergic neurons.

extract_protocol: Genomic DNA was was extracted from blood, fibroblasts, iPS and neuralised iPS cell lines using the DNeasy Blood and Tissue Kit (Qiagen).

tag: cell type

value: iPSCs


title: CHOP0081


title: CHOP0068


title: CHOP0072


title: CHOP0060


title: plasma, pre-infection (SIV) CT64_PB


title: 14178714 - mad2 2 vs GFP171 2

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: What gene sets are differentially expressed in mad mutants?

hyb_protocol: GFP171 2 Cy5 / mad2 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media: MS-agar medium  hygrometry: saturated  Temperature: 21°C  Light: 16h

extract_protocol: GFP171 2:20ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (mad1)

tag: dev.stage (boyes et al. plant cell 2001)

source_name: mad2 2

extract_protocol: mad2 2:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (mad2)


title: Wild-type iPSCs, rep2

source_name: NAS9 iPSCs


title: CHOP0192


title: 14178713 - GFP171 2 vs mad2 2

hyb_protocol: mad2 2 Cy5 / GFP171 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)


title: CHOP0073


title: CHOP0054


title: CHOP0037


title: SNCA triplication neurons, rep2

source_name: AST18 neurons

value: Neurons


title: CHOP0035


title: CHOP0238


title: 14178712 - mad1 2 vs GFP171 2

hyb_protocol: GFP171 2 Cy5 / mad1 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: mad1 2

extract_protocol: mad1 2:5ug. (Qiagen_RNeasy.pdf)


title: CHOP0015


title: CHOP0236


title: 14178711 - GFP171 2 vs mad1 2

hyb_protocol: mad1 2 Cy5 / GFP171 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178718 - mad6 2 vs GFP171 2

hyb_protocol: GFP171 2 Cy5 / mad6 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: mad6 2

extract_protocol: mad6 2:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (mad6)


title: CHOP0053


title: 14178717 - GFP171 2 vs mad6 2

hyb_protocol: mad6 2 Cy5 / GFP171 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178710 - dcl1-12 1 vs GFP171 1

hyb_protocol: GFP171 1 Cy5 / dcl1-12 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: GFP171 1:20ug. (Qiagen_RNeasy.pdf)

extract_protocol: dcl1-12 1:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (dcl1-12)


title: SNCA triplication iPSCs, rep1

source_name: AST13 iPSCs


title: CHOP2103


title: CHOP2102


title: Wild-type neurons, rep1

source_name: NAS2 neurons


title: CHOP0061


title: CHOP2101


title: 14178709 - GFP171 1 vs dcl1-12 1

hyb_protocol: dcl1-12 1 Cy5 / GFP171 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178708 - mad6 1 vs GFP171 1

hyb_protocol: GFP171 1 Cy5 / mad6 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: mad6 1

extract_protocol: mad6 1:5ug. (Qiagen_RNeasy.pdf)


title: CHOP0012


title: CHOP2104


title: 14178707 - GFP171 1 vs mad6 1

hyb_protocol: mad6 1 Cy5 / GFP171 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CHOP2100


title: Wild-type fibroblasts

source_name: NAS fibroblasts

value: Fibroblasts


title: Human embryonic stem cells

source_name: Shef4 hESCs

value: hESCs


title: SNCA triplication fibroblasts

source_name: AST fibroblasts


title: 14178706 - mad3 1 vs GFP171 1

hyb_protocol: GFP171 1 Cy5 / mad3 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: mad3 1

extract_protocol: mad3 1:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (mad3)


title: SNCA triplication iPSCs, rep2

source_name: AST18 iPSCs


title: 14178704 - GFP171 1 vs mad3 1

hyb_protocol: mad3 1 Cy5 / GFP171 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HC_50_1wk_19-5

city: RTP

first: Harvey

last: Clewell

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: HC_50_1wk_19-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.0

label: biotin

organism: Mus musculus

source_name: urinary bladder

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 1, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 50, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ug

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNA later

tag: pooled from multiple samples

value: no pool

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Carbon Dioxide Euthanasia

tag: Sex

tag: units of age

value: days

tag: tissue

value: Urinary Bladder

tag: tissue harvest methods

tag: units of harvest time point

value: week


title: Unaffected (wild-type) subject

source_name: NAS control subject

tag: cell type

value: Blood


title: CHOP0011

source_name: Tumor DNA

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP2095


title: HC_50_1wk_19-4

description: HC_50_1wk_19-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id


title: CHOP0058

tag: stage

tag: risk


title: 14178703 - mad2 1 vs GFP171 1

hyb_protocol: GFP171 1 Cy5 / mad2 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)  mutant (mad1)

tag: age

tag: dev.stage (boyes et al. plant cell 2001)

source_name: mad2 1

extract_protocol: mad2 1:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (mad2)


title: CHOP0136

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP2096


title: HC_50_1wk_19-3

description: HC_50_1wk_19-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP2088

tag: stage

tag: risk

tag: mycn

tag: age


title: 14178701 - mad1 1 vs GFP171 1

hyb_protocol: GFP171 1 Cy5 / mad1 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)  mutant (mad1)

tag: dev.stage (boyes et al. plant cell 2001)

source_name: mad1 1

extract_protocol: mad1 1:5ug. (Qiagen_RNeasy.pdf)


title: HC_50_1wk_19-2

description: HC_50_1wk_19-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id


title: CHOP2093

hyb_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

tag: shimada

tag: sex

tag: ploidy


title: CHOP2097

tag: stage

tag: risk


title: HC_50_1wk_19-1

description: HC_50_1wk_19-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: ratio

tag: dilution

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP2099

tag: mycn


title: CHOP2086

tag: shimada


title: 14178720 - dcl1-12 2 vs GFP171 2

hyb_protocol: GFP171 2 Cy5 / dcl1-12 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)  mutant (mad1)

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: dcl1-12 2:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (dcl1-12)


title: 14178700 - GFP171 1 vs mad1 1

hyb_protocol: mad1 1 Cy5 / GFP171 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)


title: CHOP3109

tag: stage

tag: risk

tag: sex

tag: ploidy


title: HC_50_12wk_20-5

description: HC_50_12wk_20-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 12, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 50, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: harvest time point


title: HC_50_12wk_20-4

description: HC_50_12wk_20-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP2085

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP2059


title: 14178702 - GFP171 1 vs mad2 1

hyb_protocol: mad2 1 Cy5 / GFP171 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)  mutant (mad2)

tag: dev.stage (boyes et al. plant cell 2001)

tag: arabidopsis thaliana (c24)


title: CHOP2074


title: CHOP2087


title: SNCA triplication subject

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

source_name: AST affected subject

tag: cell type


title: HC_50_12wk_20-3

description: HC_50_12wk_20-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: harvest time point


title: CHOP2079

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP2058


title: CHOP0022


title: 14178332 - GFP171 2 vs dcl1-12 2

hyb_protocol: dcl1-12 2 Cy5 / GFP171 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)  mutant (dcl1-12)

tag: dev.stage (boyes et al. plant cell 2001)

tag: arabidopsis thaliana (c24)


title: CHOP3087


title: CHOP2050


title: 14178715 - GFP171 2 vs mad3 2

hyb_protocol: mad3 2 Cy5 / GFP171 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: mad3 2

extract_protocol: mad3 2:5ug. (Qiagen_RNeasy.pdf)

tag: arabidopsis thaliana (c24)  mutant (mad3)


title: Human embryonic stem cells

description: Wild-type hESCs

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Partek Genomics Suite v6.5. Arrays were preprocessed using RMA quantile normalization with GC background correction. Gene level summary signals were generated by calculating the median expression value of all probe sets annotated to a transcript.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na30.hg19.probeset_core.mps

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted using the RNeasy Plus kit (Qiagen). cDNA synthesis and amplification was performed using the Ambion®WT Expression Kit (Ambion).

tag: cell type

tag: genotype

value: wild-type


title: CHOP2098


title: CHOP2028


title: HC_50_12wk_20-1

description: HC_50_12wk_20-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: Wild-type fibroblasts

description: Wild-type fibroblasts

tag: cell type

tag: genotype


title: CHOP2027

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: HC_2_1wk_11-4

description: HC_2_1wk_11-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 1, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 2, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: developmental state

tag: sacrifice method


title: HC_2_1wk_11-5

description: HC_2_1wk_11-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: ncbi taxonomy id

tag: individual

tag: Sex

value: Female

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: SNCA triplication fibroblasts

description: SNCA triplication fibroblasts

tag: cell type

tag: genotype

value: SNCA triplication


title: CHOP2090

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP2013


title: HC_2_1wk_11-3

description: HC_2_1wk_11-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: developmental state

tag: sacrifice method


title: CHOP2006

tag: stage

tag: risk

tag: mycn


title: CHOP2023

tag: age

tag: shimada

tag: sex


title: CHOP2001

tag: ploidy


title: SNCA triplication iPSCs, rep2

description: SNCA triplication iPSCs

tag: cell type

value: iPSCs

tag: genotype


title: SNCA triplication iPSCs, rep1

description: SNCA triplication iPSCs


title: CHOP1992


title: HC_50_12wk_20-2

description: HC_50_12wk_20-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: ncbi taxonomy id

tag: individual

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: harvest time point

tag: units of harvest time point


title: CHOP2094

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex


title: CHOP1977

tag: ploidy


title: CHOP1987


title: Wild-type iPSCs, rep2

description: Wild-type iPSCs

source_name: NAS9 iPSCs

tag: cell type

tag: genotype


title: 14178308 - mad3 2 vs GFP171 2

hyb_protocol: GFP171 2 Cy5 / mad3 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: arabidopsis thaliana (c24)  mutant (mad1)

tag: dev.stage (boyes et al. plant cell 2001)

tag: arabidopsis thaliana (c24)  mutant (mad3)


title: HC_2_1wk_11-2

description: HC_2_1wk_11-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age


title: HC_2_1wk_11-1

description: HC_2_1wk_11-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: ratio

tag: age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: Wild-type iPSCs, rep1

description: Wild-type iPSCs

source_name: NAS2 iPSCs

tag: cell type

tag: genotype


title: HC_2_12wk_12-5

description: HC_2_12wk_12-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 12, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 2, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: harvest time point


title: CHOP1973

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP1982

tag: age


title: CHOP1979


title: CHOP2091


title: HC_2_12wk_12-4

description: HC_2_12wk_12-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: ratio

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1955

tag: stage

tag: risk

tag: mycn

tag: shimada


title: SNCA triplication neurons day 31, rep1

description: SNCA triplication neurons day 31

source_name: AST13 neurons day 31

tag: cell type

value: Neurons

tag: genotype


title: Wild-type neurons day 31, rep1

description: Wild-type neurons day 31

source_name: NAS2 neurons day 31


title: CHOP1986

tag: age

tag: sex

tag: ploidy


title: CHOP1956


title: HC_2_12wk_12-3

description: HC_2_12wk_12-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: harvest time point


title: Wild-type neurons day 31, rep2

description: Wild-type neurons day 31

source_name: NAS9 neurons day 31

tag: cell type

tag: genotype


title: CHOP1944

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex


title: CHOP1953

tag: ploidy


title: Wild-type neurons day 22, rep2

description: Wild-type neurons day 22

source_name: NAS9 neurons day 22


title: CHOP2014


title: CHOP1942


title: HC_2_12wk_12-1

description: HC_2_12wk_12-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: HC_10_1wk_16-4

description: HC_10_1wk_16-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 1, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 10, Units of Dose or Concentration: ppm

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: age


title: Wild-type neurons day 22, rep1

description: Wild-type neurons day 22

source_name: NAS2 neurons day 22

tag: cell type

tag: genotype


title: HC_10_1wk_16-5

description: HC_10_1wk_16-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number


title: CHOP1964

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP1972


title: CHOP1918


title: CHOP1872


title: SNCA triplication neurons day 31, rep2

description: SNCA triplication neurons day 31

source_name: AST18 neurons day 31


title: CHOP1866


title: HC_10_1wk_16-2

description: HC_10_1wk_16-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1896

tag: stage

tag: risk

tag: age


title: CHOP2033

tag: mycn

tag: shimada

tag: sex


title: CHOP1830

tag: ploidy


title: HC_10_1wk_16-1

description: HC_10_1wk_16-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: individual


title: SNCA triplication neurons day 22, rep2

description: SNCA triplication neurons day 22

source_name: AST18 neurons day 22

tag: cell type

tag: genotype


title: HC_10_1wk_16-3

description: HC_10_1wk_16-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: rna integrity number

tag: strain or line

tag: ncbi taxonomy id

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1723

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP1800


title: induced pluripotent stem cells

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

description:
IP_CD34_2
healthy sample

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

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

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: cell type

value: induced pluripotent stem cells from CD34+ HSCs


title: CD34+ differentiation

description:
CD34_HSC_DIFF
healthy sample

source_name: CD34+ differentiation

value: CD34+ HSCs differentiated


title: CD34+

description:
CD34_HSC
healthy sample

source_name: pool CD34+ cord blood

value: CD34+ HSCs


title: HC_10_12wk_15-5

description: HC_10_12wk_15-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

source_name: urinary bladder

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 12, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 10, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ug

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNA later

tag: pooled from multiple samples

tag: strain or line

tag: individual

tag: harvest time point


title: HC_10_12wk_15-4

description: HC_10_12wk_15-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

value: no pool

tag: ncbi taxonomy id

tag: developmental state

value: adult

tag: sacrifice method

value: Carbon Dioxide Euthanasia

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1714

source_name: Tumor DNA

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP1743


title: SNCA triplication neurons day 22, rep1

description: SNCA triplication neurons day 22

source_name: AST13 neurons day 22

tag: cell type

tag: genotype


title: NK cells

description:
NK
healthy sample

source_name: pool natural killers

value: NK cells


title: CHOP1587


title: HC_2_12wk_12-2

description: HC_2_12wk_12-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

value: days

value: Urinary Bladder

tag: harvest time point

value: week


title: HC_10_12wk_15-3

description: HC_10_12wk_15-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: developmental state

tag: sacrifice method

tag: Sex

value: Female

tag: age

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1479

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP1903


title: HC_10_12wk_15-2

description: HC_10_12wk_15-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id


title: CHOP1585

tag: stage

tag: age


title: CHOP1579

tag: risk

tag: mycn


title: CHOP1792

tag: shimada

tag: sex


title: HC_10_12wk_15-1

description: HC_10_12wk_15-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: harvest time point

tag: units of harvest time point


title: HC_0_1wk_-3-5

description: HC_0_1wk_3-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Water, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 1, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id


title: CD4+ cells

description:
CD4
healthy sample

source_name: pool CD4 cells

tag: cell type

value: CD4+ cells


title: CHOP1688

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP1280


title: Neutrophils

description:
Neutrophils
healthy sample

source_name: pool neutrophils

value: Neutrophils


title: CD8+ cells

description:
CD8
healthy sample

source_name: pool CD8 cells

value: CD8+ cells


title: HC_0_1wk_3-3

description: HC_0_1wk_3-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

value: good

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1418

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

tag: stage

tag: risk


title: blood2

description:
blood-2
healthy sample

source_name: peripheral blood

tag: primary tissue

value: blood


title: B-cells

description:
B-cells
healthy sample

source_name: pool B cells

tag: cell type

value: B-cells


title: HC_0_1wk_3-4

description: HC_0_1wk_3-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

value: ug

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: age


title: CHOP1270

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP1411

tag: stage


title: CHOP1438

tag: risk


title: CHOP1258


title: HC_0_1wk_3-2

description: HC_0_1wk_3-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

value: excellent

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1461

tag: mycn

tag: age


title: HC_0_1wk_3-1

description: HC_0_1wk_3-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

value: RNA later

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id


title: CHOP1245

tag: stage

tag: risk

tag: shimada

tag: sex

tag: ploidy


title: CHOP1257


title: CHOP1244


title: brain1

description:
brain-1
healthy sample

source_name: brain primary tissue

tag: primary tissue

value: brain


title: HC_0_12wk_4-5

description: HC_0_12wk_4-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Water, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 12, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: no pool

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue

tag: tissue harvest methods

tag: harvest time point

tag: units of harvest time point


title: CHOP1194

tag: stage

tag: risk

tag: mycn

tag: age


title: CHOP1213

tag: shimada

tag: sex

tag: ploidy


title: blood1

description:
blood-1
healthy sample

tag: primary tissue


title: HC_0_12wk_4-4

description: HC_0_12wk_4-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

value: Carbon Dioxide Euthanasia


title: CHOP1183

tag: stage

tag: risk

tag: mycn

tag: age


title: brain2

description:
brain-2
healthy sample

tag: primary tissue


title: CHOP1556

tag: shimada

tag: sex

tag: ploidy


title: thyroid_N82

description:
Tir_N82
healthy sample

source_name: thyroid primary tissue

value: thyroid


title: thyroid_N81

description:
Tir_N81
healthy sample


title: CHOP1158


title: CHOP1132


title: CHOP1109


title: HC_0_12wk_4-1

description: HC_0_12wk_4-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

value: days

tag: tissue

value: Urinary Bladder

tag: tissue harvest methods

tag: harvest time point

tag: units of harvest time point


title: CHOP1166

tag: stage

tag: risk

tag: mycn

tag: age


title: HC_0_12wk_4-3

description: HC_0_12wk_4-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

value: Female

value: week


title: HC_0_12wk_4-2

description: HC_0_12wk_4-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age


title: liver_N91

description:
Liver_N91
healthy sample

source_name: liver primary tissue

tag: primary tissue

value: liver


title: CHOP1126

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP1033


title: HC_05_1wkk_8-5

description: HC_05_1wk_8-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 1, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 0.5, Units of Dose or Concentration: ppm

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP1154

tag: stage

tag: risk


title: muscle2

description:
muscle-2
healthy sample

source_name: muscle primary tissue

tag: primary tissue

value: muscle


title: muscle1

description:
muscle-1
healthy sample


title: HC_05_1wkk_8-4

description: HC_05_1wk_8-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age


title: CHOP0974

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: CHOP1004


title: CHOP0562


title: CHOP0557


title: liver_N93

description:
Liver_N93
healthy sample


title: fat2

description:
Fat-2
healthy sample

source_name: fat primary tissue

value: fat


title: fat1

description:
Fat-1
healthy sample


title: CHOP0981


title: HC_05_12wk_7-5

description: HC_05_12wk_7-5_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

treatment_protocol: in vivo Treatment: Arsenate, Treatment Repeat: 1, Units of Treatment Repeat: day, Treatment Duration: 12, Units of Duration: week, Treatment Time: 24, Units of Treatment Time: hr, Vehicle for Chemical: water, Amount of Vehicle: ad lib, Route of Exposure: drinking water, Units of Amount of Vehicle: ad lib, Dose or Concentration: 0.5, Units of Dose or Concentration: ppm

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: tissue

tag: tissue harvest methods

tag: harvest time point

tag: units of harvest time point


title: HC_05_1wkk_8-2

description: HC_05_1wk_8-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

value: good

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age


title: CHOP1169

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: bone2

description:
bone-2
healthy sample

source_name: bone normal tissue

tag: primary tissue

value: bone


title: CHOP0441


title: CHOP0444


title: CHOP0419


title: HC_05_1wkk_8-3

description: HC_05_1wk_8-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

value: ug

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: CHOP0499

tag: stage

tag: risk

tag: age


title: CHOP0440

tag: mycn

tag: shimada

tag: sex


title: HC_05_12wk_7-3

description: HC_05_12wk_7-3_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

value: excellent

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: harvest time point


title: HC_05_12wk_7-4

description: HC_05_12wk_7-4_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: rna integrity number

tag: bioanalyzer results

tag: sample preservation

value: RNA later

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: tissue

tag: tissue harvest methods

tag: units of harvest time point


title: bone1

description:
bone-1
healthy sample

tag: primary tissue


title: CHOP0868

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP0478


title: colon3

description:
Ncolon3
healthy sample

source_name: colon normal tissue

value: colon


title: HC_05_12wk_7-2

description: HC_05_12wk_7-2_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: no pool

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: harvest time point


title: CHOP0396

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

tag: stage

tag: risk

tag: mycn


title: CHOP0418

tag: age

tag: shimada

tag: sex


title: CHOP0402

tag: ploidy


title: colon1

description:
Ncolon1
healthy sample

tag: primary tissue


title: CHOP0258


title: KrasTgfbr2-/-  mouse with lung tumor no.4

city: New York

first: Charles

middle: A

last: Powell

state: NY

address: One Gustave Levy Place, Box 1232

department: MEDICINE/PULMONARY

institute: Mount Sinai School of Medicine

description: Gene expression data from KrasTgfbr2-/- lung tumor, 7 weeks

hyb_protocol: cRNA was hybridized to the Affymetrix(Santa Clara,CA) 430 2.0 arrays

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

data_processing: Array data were normalized using the RMA algorithm with R/Bioconductor as implemented in BRB-Array Tools V4.1. To exclude genes with minimal variation across the specimens, the data were filtered to remove genes with variance of log ratios for each gene < 75 percentile, thus leaving 11,275 genes for analysis.

source_name: KrasTgfbr2-/- lung tumor, 7 weeks

label_protocol: Biotinylated cRNA was generated by the modified Eberwine protocol

extract_protocol: Total RNA was extracted using Rneasy minikit ; Qiagen, Valencia, CA

tag: tissue

value: lung tumor

tag: genotype/variation


title: CHOP0539


title: CHOP1000


title: HC_05_12wk_7-1

description: HC_05_12wk_7-1_AsDW_MusBladder_Mouse430_2_HJCENV601_2: Urinary Bladder_Knocked out via CO2, bled out by cardiac puncture and all organs and tissues harvested.

source_name: urinary bladder

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: sample preservation

tag: pooled from multiple samples

tag: strain or line

tag: ncbi taxonomy id

tag: individual

value: adult

value: Carbon Dioxide Euthanasia

tag: tissue harvest methods

tag: units of harvest time point


title: 9-hESC

description:
SHEF7
healthy sample

source_name: human embryonic stem cell

tag: cell line

value: human embryonic stem cell SHEF7


title: 10-hESC

description:
SHEF1
healthy sample

value: human embryonic stem cell SHEF1


title: CHOP1062

source_name: Tumor DNA

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: CHOP1435


title: CHOP0273


title: 7-hESC

description:
SHEF4
healthy sample

value: human embryonic stem cell SHEF4


title: 8-hESC

description:
SHEF5
healthy sample

value: human embryonic stem cell SHEF5


title: CHOP0229


title: KrasTgfbr2-/-  mouse with lung tumor no.2

tag: tissue

tag: genotype/variation


title: KrasTgfbr2-/-  mouse with lung tumor no.5


title: KrasTgfbr2-/-  mouse with lung tumor no.3


title: CHOP0961


title: 6-hESC

description:
I3
healthy sample

value: human embryonic stem cell I3


title: CHOP0166


title: CHOP0120


title: 5-hESC

description:
H181
healthy sample

value: human embryonic stem cell H181


title: CHOP0088


title: CHOP0130


title: KrasTgfbr2  wt mouse with lung tumor no.13

description: Gene expression data from KrasTgfbr2 wt lung tumor, 7 weeks

source_name: KrasTgfbr2 wt lung tumor,7weeks

value: KrasTgfbr2 wt


title: 4-hESC

description:
H14
healthy sample

value: human embryonic stem cell H14


title: KrasTgfbr2  wt mouse with lung tumor no.12


title: 3-hESC

description:
H7
healthy sample

value: human embryonic stem cell H7


title: CHOP0055


title: KrasTgfbr2  wt mouse with lung tumor no.11


title: KrasTgfbr2  wt mouse with lung tumor no.15

source_name: KrasTgfbr2 wt lung  tumor,7weeks


title: CHOP0234


title: KrasTgfbr2  wt mouse with lung tumor no.14


title: 1-hESC

description:
H14S9
healthy sample

value: human embryonic stem cell H14S9


title: CHOP0038


title: CHOP2619


title: 2-hESC

description:
H7S14
healthy sample

value: human embryonic stem cell H7S14


title: CHOP0028


title: CHOP0370


title: CHOP0008


title: CHOP0036


title: CHOP2618


title: KrasTgfbr2  wt mouse with lung tumor no.10


title: CHOP2613


title: CHOP2617


title: KrasTgfbr2-/-  mouse with lung tumor no.1


title: Against CDK19-2 rep2

city: Toyama

first: Taiki

last: Tsutsui

country: Japan

institute: Univ. Toyama

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using GeneSpring software. Base line was created as median of all sample.

source_name: Against CDK19-2 transfected HeLa S3 cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: HeLa S3 cells were seeded on 6-well plate at 4 x 104 cells per well in 2ml antibiotic free DMEM medium before 24hr transfection.

extract_protocol: RNA was prepared using RNeazy column (QIAGEN).

treatment_protocol: We transfect siRNA using Lipofectamine 2000 (invitrogen) according to its manual and siRNA final concentration in the medium was 20nM. After culturing for 48hr, transfection medium was changed to fresh antibiotic containing medium. Then the cells were incubated for additional 12hr

tag: transfection

value: HeLa S3


title: CHOP2615


title: CHOP2610


title: CHOP2601


title: CHOP2609


title: Against CDK19-2 rep3


title: CHOP0087


title: Against CDK19-2 rep1


title: KrasTgfbr2-/- lung tumor specimen 114

description: Gene expression data from KrasTgfbr2-/- lung tumor

data_processing: Array data were normalized using the RMA algorithm with R/Bioconductor as implemented in BRB-Array Tools V4.1.

source_name: KrasTgfbr2-/- lung tumor, 5 weeks

extract_protocol: Total RNA was extracted using Rneasy minikit;Qiagen,Valencia,CA

tag: strain background

value: LSL-KrasG12D x C57/Bl6 x Tgfbr2 flox/flox


title: Against CDK19-1 rep3

source_name: Against CDK19-1 transfected HeLa S3 cell


title: CHOP2596


title: KrasTgfbr2-/- lung tumor specimen 113


title: CHOP2597


title: Against CDK19-1 rep2


title: CHOP2604


title: Against CDK19-1 rep1


title: CHOP2605


title: CHOP2594


title: KrasTgfbr2wt  lung tumor specimen 103

description: Gene expression data from KrasTgfbr2wt lung tumor

source_name: KrasTgfbr2wt lung tumor, 9 weeks

value: LSL-KrasG12D x C57/Bl6


title: KrasTgfbr2-/- lung tumor specimen 112

value: lung tumor


title: KrasTgfbr2-/- lung tumor specimen 111


title: KrasTgfbr2wt  lung tumor specimen 102


title: CHOP2600


title: CHOP2593


title: Against CDK8-2 rep2

source_name: Against CDK8-2 transfected HeLa S3 cell


title: Against CDK8-2 rep1


title: CHOP2589


title: KrasTgfbr2-/-  stroma specimen 114

description: Gene expression data from KrasTgfbr2-/- lung tumor stroma

source_name: KrasTgfbr2-/-  stroma of lung tumor , 5 weeks

value: stroma


title: CHOP2595


title: CHOP2587


title: KrasTgfbr2-/-  stroma specimen 113


title: Against CDK8-1 rep3

source_name: Against CDK8-1 transfected HeLa S3 cell


title: CHOP2582


title: KrasTgfbr2wt  lung tumor specimen 101


title: KrasTgfbr2-/-  stroma specimen 112


title: CHOP2584


title: CHOP2581


title: KrasTgfbr2-/-  stroma specimen 111


title: CHOP2579


title: Against CDK8-2 rep3


title: CHOP2591


title: Control siRNA rep3

source_name: Control siRNA transfected HeLa S3 cell

value: Control siRNA


title: CHOP2585


title: KrasTgfbr2wt  stroma specimen 103

description: Gene expression data from KrasTgfbr2wt lung tumor stroma

source_name: KrasTgfbr2wt  stroma of lung tumor , 9 weeks


title: CHOP2578


title: Control siRNA rep2


title: CHOP2575


title: CHOP2576


title: CHOP2573


title: Control siRNA rep1


title: KrasTgfbr2wt  stroma specimen 102


title: CHOP2577


title: Against CDK8-1 rep2


title: CHOP2592


title: cDNA of MG1614 vs MG1614(pBL1) exp 1 rep2

city: Villaviciosa

first: Beatriz

last: Martinez

address: Paseo Río Linares s/n

institute: IPLA-CSIC

description:
869-b
raw data file = 869.txt

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner.  Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (ref. van Hijum, S. A., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244.).  Duplicate spots on each array were not combined during normalization, therefore there are 6 Samples for 3 raw data files.  The raw data files are therefore provided in the TAR archive on the Series record to avoid duplication.

organism: Lactococcus lactis

source_name: Net intensity (tr.mean) {A}

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dCTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

growth_protocol: L. lactis strains were incubated in M17 containing 0.5% glucose (GM17) at 30 ºC without shaking

extract_protocol: RNA was isolated from 50 ml of cells grown to midexponential phase of growth (A600 = 0.4). Cells were harvested by centrifugation for 1 min at 10,000 rpm at room temperature. Cell pellets were immediately frozen in liquid nitrogen and stored at –80 °C. Pellets were resuspended in 500 µl of 10 mM Tris-HCl, 1 mM EDTA (T10E1), pH 8.0, after which 50 µl of 10% SDS, 500 µl of phenol/chloroform, 500 mg of glass beads (75–150 µm), and 175 µl of Macaloid suspension (Bentone) were added. Further purification was done using the High Pure RNA isolation (Roche), using the suppliers protocol.

tag: subspecies

tag: plasmid

source_name: Net intensity (tr.mean) {B}


title: Gsk-3b-/- ESCs Rep3

city: Columbus

first: Christopher

last: Phiel

state: OH

address: 700 Children's Drive W432

institute: The Research Institute at Nationwide Children's Hospital

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.

source_name: Total RNA from Gsk-3b-/- ESCs

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.

extract_protocol: Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).

tag: cell type

value: embryonic stem cells


title: Sample Preparation Nugen V2

city: Stockholm

first: Therese

last: Hogfeldt

address: Cancer Centre Karolinska, R:8

country: Sweden

institute: Karolinska Institutet

scan_protocol: The arrays were washed and stained with Streptavidin-Phycoerythrin (SAPE) (Molecular Probes Inc., Eugene, OR, USA) in an Affymetrix fluidics station. The arrays were then scanned in an Affymetrix scanner and the expression values for each probe set were estimated using the Affymetrix Microarray Suite Software (MAS v5.0).

data_processing: MAS 5.0

label: Biotin

source_name: Lung Cancer

label_protocol: Fragmentation, labelling and hybridization of cDNA from Nugen FFPE, Nugen V2 FF and Nugen Pico FF were performed using Nugen Technologies, Inc FL-Ovation cDNA Biotin Module V2 according to the manufacturer’s recommendations. Fragmented and labelled cDNA was hybridized onto Affymetrix human U133 plus 2.0 gene chips, followed by washing and scanning.

extract_protocol: RNA extraction methods from Ambion (Austin, TX, USA) designed for FFPE material was used as well as Qiagen kit designed for fresh frozen material. The RNA further analyzed by qPCR and Affymetrix microarray. Amplification of RNA prior to microarray analysis was performed using Nugen technologies (San Carlos, CA, USA). Nugen has developed amplification kits both for FFPE and FF materials: WT- ovation FFPE RNA amplification System V2 (Nugen FFPE), Ovation FF RNA Amplification System V2 (Nugen V2 FF) and Ovation FF Pico RNA Amplification System (Nugen PICO FF). The Nugen FFPE kit, designed for FFPE material was only used for FFPE tissue. The Nugen Pico FF kit, designed to target small amounts of FF RNA (>500 pg) and the Nugen V2 FF kit designed to target total FF RNA, were only used for FF tissue. Affymetrix standard amplification protocol (Affy FF) designed for FF RNA was also included as the standard method for amplification.

tag: disease state

value: Lung Cancer

tag: sample type

value: formalin fixed and paraffin embedded (ffpe) material and fresh (ff) material was used. age of blocks:more than 20 years.

tag: sample preparation

value: Nugen V2 FF

value: lung cancer tumor


title: Against CDK8-1 rep1

tag: cell line


title: CHOP2574

tag: stage

tag: risk


title: CHOP2559

tag: mycn

tag: age


title: Gsk-3b-/- ESCs Rep2


title: Sample Preparation Nugen Pico

hyb_protocol: Fragmented and labelled cDNA was hybridized onto Affymetrix human U133 plus 2.0 gene chips, followed by washing and scanning.

value: Nugen Pico FF


title: CHOP2555

tag: shimada

tag: sex


title: CHOP2556

tag: ploidy


title: CHOP2572


title: Sample Preparation Nugen FFPE

value: Nugen FFPE

tag: tissue


title: cDNA of MG1614(pBL1) vs MG1614 exp 2 (dyeswap) rep2

description:
868-b
raw data file = 868.txt


title: CHOP2554


title: CHOP2567


title: cDNA of MG1614 vs MG1614(pBL1) exp 1 rep1

description:
869-a
raw data file = 869.txt


title: Gsk-3b-/- ESCs Rep1

tag: genotype/variation


title: CHOP2552


title: cDNA of MG1614(pBL1) vs MG1614 exp 2 (dyeswap) rep1

description:
868-a
raw data file = 868.txt


title: Sample Preparation AFFY

value: standard Affymetrix amplification for FF


title: CHOP2580


title: cDNA of MG1614 vs MG1614(pBL1) exp 3 rep2

description:
886-b
raw data file = 886.txt


title: CHOP2553


title: Gsk-3a-/- ESCs Rep2

source_name: Total RNA from Gsk-3a-/- ESCs


title: Gsk-3a-/- ESCs Rep3


title: CHOP2550

source_name: Tumor DNA


title: cDNA of MG1614 vs MG1614(pBL1) exp 3 rep1

description:
886-a
raw data file = 886.txt


title: CHOP2557


title: Human embryonic stem cells, SHEF4

description: total RNA

data_processing: Data were processed using Partek Genomics Suite v6.5. Arrays were preprocessed together with publicly available array data (GSE16190, GSE19902, GSE22499, GSE26451, GSE7179, GSE7879, GSE8590 and GSE9440) using RMA quantile normalization with GC background correction.

source_name: Wild-type hESCs

growth_protocol: iPSCs: grown in mTESR1 media on BD Matrigel;

treatment_protocol: not applicable

value: human embryonic stem cells (hESCs)

value: wild-type


title: SNCA triplication iPSCs, AST18

description: total RNA

source_name: SNCA triplication iPSCs

value: induced pluripotent stem cells (iPSCs)

value: SNCA triplication


title: KrasTgfbr2wt  stroma specimen 101

tag: strain background


title: SNCA triplication iPSCs, AST13

description: total RNA


title: Patient 2-73AN

city: Shanghai

first: Wei-Wen

last: Jiang

address: Room 305, Building #1,639 Zhi Zao Ju Road

country: China

institute: Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

hyb_protocol: 1) Prepare the hybridization mix in a PCR tube.2) Incubate at 95℃ for 2 min. During the incubation the target preparation should be protected from light. 3) Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after ice incubation. 4) Take cover slide out of the package. 5) Carefully laid the miRCURYTM Array on top of the assembly of cover slide and spacer, where the printed side of array should be facing toward the cover slide, to form a hybridization assembly. The printed side of array is on the side of the label. 6) Insert the hybridization assembly into a (3.1 x 9cm) heat-shrank hybridization (hyb.) bag. Sample loading side of the hybridization assembly should face the opening side of film bag. Lower the assembly to the end of the bag (Assembly viewed from the other side). 7) Clip the bag with a clipper “securely” from the opening end. Immerse the assembly to the rim of the slide in 95℃ hot water swiftly (approximately 2~5 sec). Do not dip the assembly too far into the water to avoid water leaking into the assembly. The hyb. bag will shrink and tightly wrap around the assembly. 8) Remove the assembly from water and wipe off the water from the assembly. Trim off the excess film from the top of the assembly. Keep the assembly in a 50℃ oven for at least 10 minutes. 9) Load the180ul target hybridization mix into the assembly through the sample loading opening. Fill up the hybridization space with 1X Hybridization buffer till the liquid level reaches to approximately 5 mm (0.5cm) away from the top rim.10) Cut the second Hyb. Bag to approximately one-half of its original length.11) Keep the assembly vertical and slip on the shortened hyb. bag from step 11 all the way until the assembly reaches the end of the hyb. bag.12) Use a pair of forceps to hold onto the top of the assembly. Immerse the entire assembly into 95℃ hot water with the assembly in upright position.13) Place the hybridization assembly into a 56℃ oven and set it on a rotator. Remember to rotate the assembly at 2 rotations per minute (RPM) for overnight.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: The intensity of green signal is calculated after background subtraction and three Replicated spots of each probe on the same slide have been averaged. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data=(Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

source_name: head and neck squamous cell carcinoma

label_protocol: miRCURYTM Array  Power Labeling kit (Cat #208032-A, Exiqon) was used. 1) Thaw all kit components  Place all kit components on ice and thaw for 15- 20 min. Mix thoroughly by vortexing followed by brief centrifugation. Don’t thaw or vortex the enzymes. Flick these tubes followed by brief centrifugation. 2) Combine reagents. Mix on ice:Reagent should be combined in an RNase-free microcentrifuge tube and should be mixed by pipetting up and down to ensure that all reagents are mixed thoroughly. 3) Incubate 30 min.at 37℃, using a PCR cycler with heated lid. 4) Stop the enzyme reaction and denaturate the RNA by incubation at 95℃ followed by snap cooling on ice. 5) Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after incubation on ice.  6) Combine reagents. Mix on ice: Add the reagents listed in the table to the 4ul CIP reaction from step5. In order to minimize variation between slides, master mixes is prepared for the labeling reaction. 7) Mix the reagents by gentle vortexing or by pipetting up and down to ensure that all reagents are mixed thoroughly. 8) Incubate at 16℃ for 1hour, using a PCR cycler with heated lid. Protect the reaction from light. 9) Incubate for 15 min. at 65℃. After stopping the labeling procedure, briefly spin the reaction and leave it at 4℃. The labeled sample is now ready for hybridization on the array. Hybridization on the array. Hybridization should preferably occur within 1-2h.

extract_protocol: TRIzol® Reagent (Invitrogen life technologies)was used. 1) HOMOGENIZATION, a) Cryopulverization of tissue using the Biopulverizer, b)homogenization using the Mini-Bead-Beater-16. 2) PHASE SEPARATION, Incubate the homogenized samples for 5 minutes at 15 to 30℃ to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIZOL Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30℃ for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4℃. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. 3) RNA PRECIPITATION,transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30℃ for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4℃. The RNA precipitate, often invisible before centrifugation, forms a gel-like pellet on the side and bottom of the tube. 4) RNA WASH,remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4℃.5) REDISSOLVING THE RNA, at the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Do not dry the RNA by centrifugation under vacuum. It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility. Partially dissolved RNA samples have an A260/280 ratio < 1.6. Dissolve RNA in RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60℃. RNA can be stored at -70℃.

value: adjacent normal mucosa


title: Patient 1-24AN


title: Patient 2-73C

value: head and neck squamous cell carcinoma


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U36

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Lipodystrophic patient

hyb_protocol: The slides were scanned with GenePix 4200 AL (Axon Instruments, Molecular Devices, Silicon Valley, CA) at the resolution of 5 µm/pixel and at 16 bit depth.

scan_protocol: GPR files were imported in R v. 2.10 and preprocessed by the BioConductor package limma.

data_processing: quantile normalized log ratios (base2) from the median foregraound intensities with no background correction.

source_name: Dorsocervical adipose tissue

label_protocol: Labelled aRNAs was hybridized onto Whole Human Genome 4x44K microarrays (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions. The slides were then washed according to the instructions with buffers from Agilent.

extract_protocol: The amplified RNA (aRNA, 5 µg/sample) was labelled using monoreactive Cy3 or Cy5 dyes (GE Healthcare, GE Life Sciences, Uppsala, Sweden) followed by purification according the manufacturer’s instructions.

treatment_protocol: Adipose tissue was homogenised using the Geneclean kit (Bio101 systems, Obiogene Inc., Carlsbad, CA). RNA was extracted with the RNeasy Lipid Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Quantity and integrity of RNA were verified using RNA 6000 nanochips (Agilent 2100 Bioanalyser, Palo Alto, CA). Part of the isolated RNA was stored at -80°C until quantification of the target mRNAs by microarray.

value: Dorsocervical adipose tissue

value: HIV+

tag: treatment result

value: developed lipodystrophy

source_name: Abdominal subcutaneous adipose tissue

value: Abdominal subcutaneous adipose tissue


title: CHOP2549

hyb_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: Wild-type iPSCs, NAS9

description: total RNA

source_name: Wild-type iPSCs


title: Patient 1-24C


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U34

description: Lipodystrophic patient


title: CHOP2547


title: CHOP1350


title: noninvasive lung adenocarcinoma specimen AC0125

description: Gene expression data from human noninvasive lung adenocarinoma tumor (BAC)

hyb_protocol: cRNA was hybridized to the Affymetrix(Santa Clara,CA) Human Genome U133 Plus 2.0 Array

source_name: Microdissected noninvasive lung tumor

extract_protocol: Total RNA was extracted from laser capture microdissected cells using Rneasy minikit;Qiagen,Valencia,CA

value: lung tumor

tag: pathological type

value: BronchioloAlveolar Carcinoma

tag: gender

value: female

tag: age at dx

tag: stage grouping

value: Ia

tag: t stage

tag: n stage


title: CHOP1306

tag: stage


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U33

description: Lipodystrophic patient

tag: disease state


title: CHOP1007

tag: risk

tag: mycn


title: Wild-type iPSCs, NAS2

description: total RNA

tag: cell line

tag: cell type


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U32

description: Lipodystrophic patient


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U28

description: Lipodystrophic patient