title: RNAseq-lncRNAs_1

status: Public on Jan 30 2017

type: SRA

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

library_source: transcriptomic

data_processing:
AB SOLID data:  Primary alignment with Lifescope software version 2.1
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1
Genome_build: hg19
Supplementary_files_format_and_content: Reads counts based on Ensembl GRCH37 version 75 + lncRNAs from Casero D, Sandoval S, Seet CS, Scholes J, Zhu Y, Ha VL, Luong A, Parekh C, Crooks GM. 2015. Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages. Nat Immunol 16(12): 1282-1291.

source_name: Tumoral biospecimen

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. Following a DNAse I treatment, total or mature RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System.

value: Bone marrow

tag: age diagnosis (month)

tag: Sex

value: F


title: RNAseq-lncRNAs_2

country: Canada

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: M


title: RNAseq-lncRNAs_46


title: RNAseq-lncRNAs_47


title: RNAseq-lncRNAs_4


title: RNA_Seq_d29 iPSC_Clone1

status: Public on Jan 27 2017

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.5, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.11, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Trimmed sequences were mapped to the mouse NCBIM37 genome using Bismark (Krueger and Andrews, 2011) (v0.12.3, parameters --bowtie2); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts. Global methylation comparison was calculated by averaging 1kb window methylation levels of CpGs covered by at least 30 reads.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Bismark coverage report: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are tab delimited and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7) RPKM value

organism: Mus musculus

source_name: RNA Seq P12 iPSC Clone1

extract_protocol:
RNA was DNase treated with the DNA-free kit (Life Technologies). mRNA was purified from 50 ng of total RNA, using a Dynabeads® mRNA Purification Kit (Life Technologies).  Strand-specific libraries were generated as previously described (Wang et al., 2011).
Genomic DNA and RNA were isolated from the same samples using the Allprep DNA/RNA kit (Qiagen).

tag: background strain

tag: time-point in reprogramming

value: late passage iPSC

tag: genotype

value: Wild-type


title: MCF7 (CM shEphA2-2)

status: Public on Feb 28 2017

type: RNA

city: Osaka-shi

first: Masaki

last: Takasugi

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Graduate School of Medicine

country: Japan

institute: Osaka Metropolitan University

hyb_protocol: Cy3-labeled cRNA was hybridized to Agilent Human Genome 8 x 60 K arrays (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Arrays were scanned by a DNA Microarray Scanner (Agilent).

data_processing:
Microarray images were analyzed with Agilent Feature Extraction software.
Data were normalized to 75th percentile for inter-array comparison.

source_name: MCF7 cultured 3 days in the CM prepared from senescent RPE1 expressing shEphA2-2

label_protocol: RNA was reverse transcribed, and Cy3-labeled cRNA was generated by in vitro transcription.

growth_protocol: Cells were cultured under atmospheric oxygen.

extract_protocol: Total RNA was isolated by Trizol Reagent.

treatment_protocol: Cells were cultured in control 10%FBS/DMEM or CM prepared from doxorubicin-treated RPE1 expressing control or two different EphA2 shRNA.

tag: cell line

value: breast cancer cell line MCF7

tag: culture protocol

value: conditioned medium prepared from senescent RPE1 expressing shEphA2-2


title: MCF7 (Control)

source_name: MCF7 cultured in control medium

value: control medium


title: MCF7 (CM shEphA2-1)

source_name: MCF7 cultured 3 days in the CM prepared from senescent RPE1 expressing shEphA2-1

value: conditioned medium prepared from senescent RPE1 expressing shEphA2-1


title: CAF1-Peroxide

status: Public on Mar 01 2017

city: Toronto

first: Ming

last: Tsao

state: Ontario

address: 610 University Avenue

department: Ontario Cancer Institute

institute: University of Toronto

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: biotin

source_name: CAF, Peroxide

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

growth_protocol: Fibroblasts were cultured from collagenase digested primary adult human pancreatic cancer tissue; samples were minced and plated in DMEM/HamF12 media with 10% bovine serum. Control cell lines were passage 5.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Peroxide treated cell lines were exposed to 550 µM hydrogen peroxide for 2 hours to induce cellular senescence; Replication senescence cell lines were continuously passaged until their morphology changed and growth ceased.  Senescent cells stained positively on β-galactosidase assay

tag: cell type

value: pancreatic cancer associated fibroblasts

tag: protocol

value: Peroxide

tag: growth state

value: senescent

tag: gender

value: Male


title: RNAseq-lncRNAs_3


title: strain ITD00185, time point 96h, replicate 1

city: Paterna

first: Roberto

last: Pérez

state: Valencia

address: Av Agustín Escardino 7

country: Spain

institute: Centro Superior de Investigaciones Científicas

description: Biological replicate one of three

hyb_protocol: A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight.  (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution contained 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with different solutions containing different SSC 20X and SDS 10% concentrations (Sol.1: 2X SSC-0.1% SDS; Sol.2: 0.1X SSC-0.1% SDS; Sol.3: 0.1 SSC; Sol4: 0.01X SSC).

scan_protocol: Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.

data_processing:
Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After lowess normalization, data were filtered to remove spots flagged as not found.
Only spots with at least two replicates were considered. Finally, replicates were combined and their medians were calculated.
Genes with a two-fold log2 ratio values were considered to be significantly expressed.

organism: Saccharomyces cerevisiae

label_protocol:
2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA).
The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.

growth_protocol: Fermentations in synthetic agave must at 28 ºC

extract_protocol: RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).

tag: strain

tag: time point

source_name: sample mix

value: mixed


title: WS 45 degree slanted forward 8 days old Rep3

status: Public on Aug 31 2016

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

country: USA

institute: University of Florida

hyb_protocol: The cRNA was purified using magnetic beads and was fragmented. Following fragmentation, cRNA products (12.5 µg) were hybridized with rotation to the Affymetrix GeneChip® Arabidopsis ATH1 Genome Arrays for 16 h at 45°C.  Arrays were washed on a Fluidics Station 450 (Affymetrix) using the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: Primary data analysis was carried out using the MAS5 algorithm within the Affymetrix Expression Console software.

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; grown in Vertical configuration for 3 days and then 45 degree slanted forward for 5 days

label_protocol: 100 ng of total RNA from each sample was reverse transcribed into double-stranded cDNA, from which biotin-labeled cRNA was generated using the 3′ IVT plus Kit (Affymetrix).

growth_protocol: General biology operations  Arabidopsis thaliana plants (wild type cultivars Col-0 and WS) were grown on media plates made from 0.5x MS liquid media, autoclaved with 0.5% Phytagel and poured in square-gridded plates (Fisherbrand, Fisher Scientific, Pittsburgh, PA). Seeds were wet sterilized in 1.7 mL Eppendorf microfuge tubes (Eppendorf, Hamburg, Germany) using a 5-minute 70% ethanol wash, followed by a 5 minute 50% v/v sodium hypochlorate solution wash (8.3%; Clorox, Oakland, CA), followed by 6 washes with sterile ddH2O. Seeds were planted on plates and moved to 4°C for two days, followed by three days of vertical growth (Agp 90°) in 19°C +/- 2°C, and 24-hour fluorescent light at approximately 80 μmol m-2 s-1 PAR. Plates were photographed, moved to their respective experimental condition (Agp 45°, 90°, or 135°), and photographed again on day 8.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: Seeds were planted on plates and moved to 4°C for two days, followed by three days of vertical growth (Agp 90°) in 19°C +/- 2°C, and 24-hour fluorescent light at approximately 80 μmol m-2 s-1 PAR. Plates were photographed, moved to their respective experimental condition (Agp 45°, 90°, or 135°), and photographed again on day 8. Plants were harvested and fixed in RNAlater (Ambion, Grand Island, New York, USA).

tag: cultivar

value: WS

tag: material type

value: Roots

tag: organism part

tag: age

value: 8 days old plants, light grown

tag: biosource type

value: RNAlater fixed_sample


title: Col-0 45 degree slanted backward 8 days old Rep1

source_name: solid 0.5x MS media plates; grown in Vertical configuration for 3 days and then 45 degree slanted backward for 5 days


title: Col-0 45 degree slanted forward 8 days old Rep1


title: MCF7 (CM shNT)

source_name: MCF7 cultured 3 days in the CM prepared from senescent RPE1 expressing non-targeting shRNA

value: conditioned medium prepared from senescent RPE1 expressing non-targeting shRNA


title: Col-0 Vertical 8 days old Rep3

source_name: solid 0.5x MS media plates; grown in Vertical configuration for 8 days


title: Col-0 45 degree slanted backward 8 days old Rep2


title: WS 45 degree slanted forward 8 days old Rep1


title: p120 wild-type pancreas, biological replicate #2

status: Public on Jul 25 2016

city: Baltimore

first: Audrey

middle: Marie

last: Hendley

state: MD

address: 733 North Broadway

department: Human Genetics

institute: Johns Hopkins University

description: FACS GFP+ pancreatic cells

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: p120 wild-type, pancreas

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: Pancreases from mice were digested and sorted 2 weeks post tamoxifen injection.

extract_protocol: Genotypes of animals were identified by PCR.  GFP+ cells were sorted into media and RNA was immediately isolated using Arcterus PicoPure RNA isolation kit

treatment_protocol: Mice were given tamoxifen at 7-9 weeks of age to induce Cre recombination.

value: KCiMist1G; p120wt/wt

value: 2 weeks post tamoxifen injection

tag: tissue

value: pancreas


title: WS 45 degree slanted forward 8 days old Rep2


title: Col-0 45 degree slanted backward 8 days old Rep3


title: WS 45 degree slanted backward 8 days old Rep3


title: Col-0 45 degree slanted forward 8 days old Rep3


title: WS Vertical 8 days old Rep2


title: Col-0 Vertical 8 days old Rep1


title: WS 45 degree slanted backward 8 days old Rep2


title: Col-0 45 degree slanted forward 8 days old Rep2


title: WS Vertical 8 days old Rep3


title: Col-0 Vertical 8 days old Rep2


title: WS 45 degree slanted backward 8 days old Rep1


title: p120 wild-type pancreas, biological replicate #1

description: FACS GFP+ pancreatic cells


title: WS Vertical 8 days old Rep1


title: p120 knockout pancreas, biological replicate #3

description: FACS GFP+ pancreatic cells

source_name: p120 knockout, pancreas

value: KCiMist1G; p120f/f


title: p120 knockout pancreas, biological replicate #2

description: FACS GFP+ pancreatic cells


title: CD56-ve cells subject 8

status: Public on Mar 16 2016

city: Londonderry

first: William

middle: John

last: Duddy

address: C-TRIC building, Altnagelvin Hospital Campus

department: Northern Ireland Centre for Stratified Medicine

institute: Ulster University

description: CD56-ve cells subject 8

hyb_protocol: 750ng of the biotin-labeled IVT product (cRNA) was hybridized to HumanHT-12v4_BeadChip for 16 hours, followed by washing, blocking, and streptavidin-Cy3 staining according to the WholeGenome Gene Expression Direct Hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScanSQ System

data_processing: Raw intensity values (Illumina idat files) of 94 samples were passed to the R lumidat library to create an EListRaw class object compatible with further downstream analyses in R/Bioconductor. Two samples were excluded at this stage due to having zero proportion of expressed probes (all other samples had more than 40% of probes expressed). The limma library was then used to carry out neqc normalization – this involves background correction followed by quantile normalization, using negative control probes for background correction and both negative and positive controls for normalization. Probes were excluded if: (1) they had low bead numbers in at least one sample; (2) they were not expressed (expression p-value < 0.01) in at least 16 arrays; (3) they were annotated as ‘no match’ or ‘bad’ quality according to the Bioconductor illuminaHumanv4.db library. This gave a total of 15,342 probes for further analysis.

source_name: Cultured cells

label_protocol: An aliquot of 150 ng of high-quality total RNA from each sample was used for mRNA expression profiling. Reverse Transcription for synthesis of the cDNA strand, followed by a single in vitro transcription (IVT) amplification, that incorporates biotin-labeled nucleotides, were performed with Illumina® TotalPrep™ -96 RNA Amplification Kit (Ambion, Austin, TX).

extract_protocol: Cells were scraped and collected in PBS (100 uL). Cells were centrifuged at 13,000 rpm for 10 minutes, and PBS supernatant removed. Each pellet was dissolved in TRIzol (1 mL). The RNA was subsequently isolated (PureLink RNA Mini Kit, ‘Using TRIzol® Reagent with the PureLink® RNA Mini Kit’ section of the standard protocol) with the RNA eluted in 30 µL H2O.

value: non-myogenic CD56-negative

tag: differentiation state

tag: clonal state

tag: disease state


title: CD56-ve cells subject 4

description: CD56-ve cells subject 4


title: CD56-ve cells subject 7

description: CD56-ve cells subject 7


title: p120 wild-type pancreas, biological replicate #3

description: FACS GFP+ pancreatic cells

tag: genotype


title: CD56-ve cells subject 6

description: CD56-ve cells subject 6


title: CD56-ve cells subject 1

description: CD56-ve cells subject 1


title: p120 knockout pancreas, biological replicate #1

description: FACS GFP+ pancreatic cells


title: kidney-elevated density-replicate2

status: Public on Jan 06 2016

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

country: Germany

institute: Research Institute for Farm Animal Biology

description: Pool of 7 individual RNAs

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA (0.6 µg) in hybridization buffer was hybridized at 65 °C for 17 h to 8×60 K Whole Salmon Genome Oligo Microarrays (AMADID 049158; Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 10.7.3.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Coregonus maraena

source_name: kidney-elevated density-replicate2

label_protocol: Seven individual RNA samples from the same tissue (liver, spleen, kidney) and treatment (MD, ED, LD, HD) were pooled. 100 ng of each total RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Fish were grown in water recirculation tanks at the Institute for Fisheries in Born, Germany.

extract_protocol: Liver, spleen, kidney were sampled. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations and quantitative real-time PCR (qPCR) assays.

treatment_protocol: Fish (21.6 ± 1.4 cm in length, and 92.0 ± 24.7 g in weight ) were randomly allocated to identical 300-L glass tanks (0.74 m length × 0.58 m width × 0.72 m height; MD, ED, LD or HD conditions), receiving brackish water from the Darss-Zingst Bodden chain (2.5–6 practical salinity units) to the recirculating aquaculture system with an exchange rate of about 0.5 times per hour. Fish were randomly sampled using hand nets. Anaesthetization of fish with was done using phenoxyethanol prior to tissue sampling.

value: kidney

value: 205 days post hatch


title: CD56-ve cells subject 5

description: CD56-ve cells subject 5


title: CD56-ve cells subject 3

description: CD56-ve cells subject 3

value: unknown


title: kidney-low density-replicate2

description: Pool of 7 individual RNAs

source_name: kidney-low density-replicate2


title: liver-low density-replicate1

description: Pool of 7 individual RNAs

source_name: liver-low density-replicate1

value: liver


title: kidney-moderate density-replicate1

description: Pool of 7 individual RNAs

source_name: kidney-moderate density-replicate1


title: kidney-high density-replicate2

description: Pool of 7 individual RNAs

source_name: kidney-high density-replicate2


title: liver-elevated density-replicate2

description: Pool of 7 individual RNAs

source_name: liver-elevated density-replicate2


title: Stomach_tumor_T93

status: Public on Apr 17 2015

type: genomic

city: Indianapolis

first: Jason

middle: C

last: Ting

state: Indiana

address: Lilly Corporate Center

department: Lilly Research Labs - IT

institute: Eli Lilly and Company

description: Affymetrix SNP6 - Stomach tumor tissue T93

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

scan_protocol: The Arrays were scanned using the Affymetrix GeneChip Scanner 3000 G7

data_processing:
The CEL files was processed by PICNIC (Predicting Integer Copy Number In Cancer) analysis package running on Linux cluster. The segmented copy number regions produced from PICNIC was used to map to genes, based on hg19, to generate copy number for each gene. CEL files were also processed by ASCAT (Allele-Specific Copy number Analysis of Tumors) analysis pipeline, to generate tumor purity and ploidy results.
The perGene_CN .tsv files (one for 13 normal samples and one for 271 tumor samples) were generated by mapping PICNIC's segmented CNV regions (listed in the "segments_SAMPLE.feature_intensity.csv" file) into Ensemble's gene locations, downloaded 2014-01-17.
The ASCAT_ploidy.txt file contains ploidy and averrant_cell_fraction generated from ASCAT analysis.
[primary data description] Format of PICNIC segments_sampleID.feature_intensity.csv: segment_number, first_segment_probe, last_segment_probe, chromosome, seg_pos1, seg_pos2, stages.mino_cn,states.total_cn   Total copy number = states.total_cn - 1

label: Biotin

molecule: genomic DNA

source_name: Stomach tumor tissue T93

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from stomach samples obtained from tumor or adjacent normal sites at surgery, using QIAGEN kit, QIAamp DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop ND-1000 Spectrophotometer, and agarose gel electrophoresis.

tag: tissue type

value: tumor

value: M

tag: molecular subtype

value: EMT


title: Stomach_tumor_T88

description: Affymetrix SNP6 - Stomach tumor tissue T88

source_name: Stomach tumor tissue T88


title: Stomach_tumor_T97

description: Affymetrix SNP6 - Stomach tumor tissue T97

source_name: Stomach tumor tissue T97

value: MSI


title: Stomach_tumor_T90

description: Affymetrix SNP6 - Stomach tumor tissue T90

source_name: Stomach tumor tissue T90


title: Stomach_tumor_T89

description: Affymetrix SNP6 - Stomach tumor tissue T89

source_name: Stomach tumor tissue T89


title: Stomach_tumor_T95

description: Affymetrix SNP6 - Stomach tumor tissue T95

source_name: Stomach tumor tissue T95

value: F


title: Stomach_tumor_T94

description: Affymetrix SNP6 - Stomach tumor tissue T94

source_name: Stomach tumor tissue T94


title: Stomach_tumor_T96

description: Affymetrix SNP6 - Stomach tumor tissue T96

source_name: Stomach tumor tissue T96


title: Stomach_tumor_T91

description: Affymetrix SNP6 - Stomach tumor tissue T91

source_name: Stomach tumor tissue T91


title: ADex #16

status: Public on Mar 08 2016

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: The labelled samples were hybridized to the Affymetrix Human Gene 2.1 ST Array for 16h at 45 C

scan_protocol: The arrays were scanned in an Affymetrix 3000 7G scanner

data_processing: Data were normalized using Robust Multichip Average (RMA) normalization in Expression Console, build 1.3.1.187 (Affymetrix). Please note, that this is a GENE level analysis.

source_name: Extrinsic AD lesional skin

label_protocol: WT_PLUS labeling kit (Affymetrix) according to the manufacturers´ instructions

extract_protocol: RNA was extracted with the mirVana kit (Life Technologies) following the manufacturer’s procedures.

treatment_protocol: Skin biopsies for RNA extraction were sampled in RNAlater and stored at -80°C. For purification, the biopsies were placed in Precellys tubes containing beads and lysis/binding buffer and homogenized using a Precellys.

value: Skin

tag: diagnosis

value: Extrinsic atopic dermatitis


title: kidney-high density-replicate1

description: Pool of 7 individual RNAs

source_name: kidney-high density-replicate1

value: mixed


title: CD56-ve cells subject 2

description: CD56-ve cells subject 2

source_name: Cultured cells

tag: cell type


title: spleen-moderate density-replicate1

description: Pool of 7 individual RNAs

source_name: spleen-moderate density-replicate1

value: spleen

tag: gender


title: kidney-low density-replicate1

description: Pool of 7 individual RNAs

source_name: kidney-low density-replicate1


title: liver-elevated density-replicate1

description: Pool of 7 individual RNAs

source_name: liver-elevated density-replicate1


title: spleen-elevated density-replicate1

description: Pool of 7 individual RNAs

source_name: spleen-elevated density-replicate1


title: kidney-moderate density-replicate2

description: Pool of 7 individual RNAs

source_name: kidney-moderate density-replicate2


title: liver-moderate density-replicate2

description: Pool of 7 individual RNAs

source_name: liver-moderate density-replicate2


title: liver-low density-replicate2

description: Pool of 7 individual RNAs

source_name: liver-low density-replicate2


title: kidney-elevated density-replicate1

description: Pool of 7 individual RNAs

source_name: kidney-elevated density-replicate1


title: spleen-elevated density-replicate2

description: Pool of 7 individual RNAs

source_name: spleen-elevated density-replicate2


title: Stomach_tumor_T87

description: Affymetrix SNP6 - Stomach tumor tissue T87

source_name: Stomach tumor tissue T87


title: liver-high density-replicate2

description: Pool of 7 individual RNAs

source_name: liver-high density-replicate2


title: liver-moderate density-replicate1

description: Pool of 7 individual RNAs

source_name: liver-moderate density-replicate1


title: spleen-moderate density-replicate2

description: Pool of 7 individual RNAs

source_name: spleen-moderate density-replicate2


title: Stomach_tumor_T85

description: Affymetrix SNP6 - Stomach tumor tissue T85

source_name: Stomach tumor tissue T85


title: Stomach_tumor_T83

description: Affymetrix SNP6 - Stomach tumor tissue T83

source_name: Stomach tumor tissue T83


title: Stomach_tumor_T86

description: Affymetrix SNP6 - Stomach tumor tissue T86

source_name: Stomach tumor tissue T86


title: liver-high density-replicate1

description: Pool of 7 individual RNAs

source_name: liver-high density-replicate1


title: Stomach_tumor_T84

description: Affymetrix SNP6 - Stomach tumor tissue T84

source_name: Stomach tumor tissue T84


title: Stomach_tumor_T81

description: Affymetrix SNP6 - Stomach tumor tissue T81

source_name: Stomach tumor tissue T81


title: Stomach_tumor_T80

description: Affymetrix SNP6 - Stomach tumor tissue T80

source_name: Stomach tumor tissue T80


title: Stomach_tumor_T584

description: Affymetrix SNP6 - Stomach tumor tissue T584

source_name: Stomach tumor tissue T584


title: Stomach_tumor_T586

description: Affymetrix SNP6 - Stomach tumor tissue T586

source_name: Stomach tumor tissue T586


title: Stomach_tumor_T58

description: Affymetrix SNP6 - Stomach tumor tissue T58

source_name: Stomach tumor tissue T58


title: Stomach_tumor_T561

description: Affymetrix SNP6 - Stomach tumor tissue T561

source_name: Stomach tumor tissue T561


title: Stomach_tumor_T566

description: Affymetrix SNP6 - Stomach tumor tissue T566

source_name: Stomach tumor tissue T566


title: Stomach_tumor_T571

description: Affymetrix SNP6 - Stomach tumor tissue T571

source_name: Stomach tumor tissue T571


title: Stomach_tumor_T595

description: Affymetrix SNP6 - Stomach tumor tissue T595

source_name: Stomach tumor tissue T595


title: Stomach_tumor_T592

description: Affymetrix SNP6 - Stomach tumor tissue T592

source_name: Stomach tumor tissue T592


title: Stomach_tumor_T78

description: Affymetrix SNP6 - Stomach tumor tissue T78

source_name: Stomach tumor tissue T78


title: Stomach_tumor_T588

description: Affymetrix SNP6 - Stomach tumor tissue T588

source_name: Stomach tumor tissue T588


title: Stomach_tumor_T589

description: Affymetrix SNP6 - Stomach tumor tissue T589

source_name: Stomach tumor tissue T589


title: Stomach_tumor_T77

description: Affymetrix SNP6 - Stomach tumor tissue T77

source_name: Stomach tumor tissue T77


title: Stomach_tumor_T596

description: Affymetrix SNP6 - Stomach tumor tissue T596

source_name: Stomach tumor tissue T596


title: Stomach_tumor_T75

description: Affymetrix SNP6 - Stomach tumor tissue T75

source_name: Stomach tumor tissue T75


title: Stomach_tumor_T559

description: Affymetrix SNP6 - Stomach tumor tissue T559

source_name: Stomach tumor tissue T559


title: Stomach_tumor_T560

description: Affymetrix SNP6 - Stomach tumor tissue T560

source_name: Stomach tumor tissue T560


title: Stomach_tumor_T557

description: Affymetrix SNP6 - Stomach tumor tissue T557

source_name: Stomach tumor tissue T557


title: Stomach_tumor_T68

description: Affymetrix SNP6 - Stomach tumor tissue T68

source_name: Stomach tumor tissue T68


title: Stomach_tumor_T601

description: Affymetrix SNP6 - Stomach tumor tissue T601

source_name: Stomach tumor tissue T601


title: Stomach_tumor_T603

description: Affymetrix SNP6 - Stomach tumor tissue T603

source_name: Stomach tumor tissue T603


title: Stomach_tumor_T554

description: Affymetrix SNP6 - Stomach tumor tissue T554

source_name: Stomach tumor tissue T554


title: Stomach_tumor_T556

description: Affymetrix SNP6 - Stomach tumor tissue T556

source_name: Stomach tumor tissue T556


title: Stomach_tumor_T553

description: Affymetrix SNP6 - Stomach tumor tissue T553

source_name: Stomach tumor tissue T553


title: Stomach_tumor_T550

description: Affymetrix SNP6 - Stomach tumor tissue T550

source_name: Stomach tumor tissue T550


title: Stomach_tumor_T552

description: Affymetrix SNP6 - Stomach tumor tissue T552

source_name: Stomach tumor tissue T552


title: Stomach_tumor_T551

description: Affymetrix SNP6 - Stomach tumor tissue T551

source_name: Stomach tumor tissue T551


title: Stomach_tumor_T547

description: Affymetrix SNP6 - Stomach tumor tissue T547

source_name: Stomach tumor tissue T547


title: Stomach_tumor_T544

description: Affymetrix SNP6 - Stomach tumor tissue T544

source_name: Stomach tumor tissue T544


title: Stomach_tumor_T542

description: Affymetrix SNP6 - Stomach tumor tissue T542

source_name: Stomach tumor tissue T542


title: Stomach_tumor_T53

description: Affymetrix SNP6 - Stomach tumor tissue T53

source_name: Stomach tumor tissue T53


title: Stomach_tumor_T534

description: Affymetrix SNP6 - Stomach tumor tissue T534

source_name: Stomach tumor tissue T534


title: Stomach_tumor_T524

description: Affymetrix SNP6 - Stomach tumor tissue T524

source_name: Stomach tumor tissue T524


title: Stomach_tumor_T522

description: Affymetrix SNP6 - Stomach tumor tissue T522

source_name: Stomach tumor tissue T522


title: Stomach_tumor_T52

description: Affymetrix SNP6 - Stomach tumor tissue T52

source_name: Stomach tumor tissue T52


title: Stomach_tumor_T525

description: Affymetrix SNP6 - Stomach tumor tissue T525

source_name: Stomach tumor tissue T525


title: Stomach_tumor_T540

description: Affymetrix SNP6 - Stomach tumor tissue T540

source_name: Stomach tumor tissue T540


title: Stomach_tumor_T532

description: Affymetrix SNP6 - Stomach tumor tissue T532

source_name: Stomach tumor tissue T532


title: Stomach_tumor_T528

description: Affymetrix SNP6 - Stomach tumor tissue T528

source_name: Stomach tumor tissue T528


title: Stomach_tumor_T54

description: Affymetrix SNP6 - Stomach tumor tissue T54

source_name: Stomach tumor tissue T54


title: Stomach_tumor_T523

description: Affymetrix SNP6 - Stomach tumor tissue T523

source_name: Stomach tumor tissue T523


title: Stomach_tumor_T538

description: Affymetrix SNP6 - Stomach tumor tissue T538

source_name: Stomach tumor tissue T538


title: Stomach_tumor_T533

description: Affymetrix SNP6 - Stomach tumor tissue T533

source_name: Stomach tumor tissue T533


title: Stomach_tumor_T520

description: Affymetrix SNP6 - Stomach tumor tissue T520

source_name: Stomach tumor tissue T520


title: Stomach_tumor_T529

description: Affymetrix SNP6 - Stomach tumor tissue T529

source_name: Stomach tumor tissue T529


title: Stomach_tumor_T518

description: Affymetrix SNP6 - Stomach tumor tissue T518

source_name: Stomach tumor tissue T518


title: Stomach_tumor_T519

description: Affymetrix SNP6 - Stomach tumor tissue T519

source_name: Stomach tumor tissue T519


title: Stomach_tumor_T517

description: Affymetrix SNP6 - Stomach tumor tissue T517

source_name: Stomach tumor tissue T517


title: Stomach_tumor_T510

description: Affymetrix SNP6 - Stomach tumor tissue T510

source_name: Stomach tumor tissue T510


title: Stomach_tumor_T516

description: Affymetrix SNP6 - Stomach tumor tissue T516

source_name: Stomach tumor tissue T516


title: Stomach_tumor_T51

description: Affymetrix SNP6 - Stomach tumor tissue T51

source_name: Stomach tumor tissue T51


title: Stomach_tumor_T505

description: Affymetrix SNP6 - Stomach tumor tissue T505

source_name: Stomach tumor tissue T505


title: Stomach_tumor_T503

description: Affymetrix SNP6 - Stomach tumor tissue T503

source_name: Stomach tumor tissue T503


title: Stomach_tumor_T541

description: Affymetrix SNP6 - Stomach tumor tissue T541

source_name: Stomach tumor tissue T541


title: Stomach_tumor_T499

description: Affymetrix SNP6 - Stomach tumor tissue T499

source_name: Stomach tumor tissue T499


title: Stomach_tumor_T501

description: Affymetrix SNP6 - Stomach tumor tissue T501

source_name: Stomach tumor tissue T501


title: Stomach_tumor_T50

description: Affymetrix SNP6 - Stomach tumor tissue T50

source_name: Stomach tumor tissue T50


title: Stomach_tumor_T492

description: Affymetrix SNP6 - Stomach tumor tissue T492

source_name: Stomach tumor tissue T492


title: Stomach_tumor_T489

description: Affymetrix SNP6 - Stomach tumor tissue T489

source_name: Stomach tumor tissue T489


title: Stomach_tumor_T493

description: Affymetrix SNP6 - Stomach tumor tissue T493

source_name: Stomach tumor tissue T493


title: Stomach_tumor_T486

description: Affymetrix SNP6 - Stomach tumor tissue T486

source_name: Stomach tumor tissue T486


title: Stomach_tumor_T482

description: Affymetrix SNP6 - Stomach tumor tissue T482

source_name: Stomach tumor tissue T482


title: Stomach_tumor_T488

description: Affymetrix SNP6 - Stomach tumor tissue T488

source_name: Stomach tumor tissue T488


title: Stomach_tumor_T483

description: Affymetrix SNP6 - Stomach tumor tissue T483

source_name: Stomach tumor tissue T483


title: Stomach_tumor_T485

description: Affymetrix SNP6 - Stomach tumor tissue T485

source_name: Stomach tumor tissue T485


title: Stomach_tumor_T514

description: Affymetrix SNP6 - Stomach tumor tissue T514

source_name: Stomach tumor tissue T514


title: Stomach_tumor_T480

description: Affymetrix SNP6 - Stomach tumor tissue T480

source_name: Stomach tumor tissue T480


title: Stomach_tumor_T502

description: Affymetrix SNP6 - Stomach tumor tissue T502

source_name: Stomach tumor tissue T502


title: Stomach_tumor_T469

description: Affymetrix SNP6 - Stomach tumor tissue T469

source_name: Stomach tumor tissue T469


title: Stomach_tumor_T473

description: Affymetrix SNP6 - Stomach tumor tissue T473

source_name: Stomach tumor tissue T473


title: Stomach_tumor_T475

description: Affymetrix SNP6 - Stomach tumor tissue T475

source_name: Stomach tumor tissue T475


title: Stomach_tumor_T462

description: Affymetrix SNP6 - Stomach tumor tissue T462

source_name: Stomach tumor tissue T462


title: Stomach_tumor_T476

description: Affymetrix SNP6 - Stomach tumor tissue T476

source_name: Stomach tumor tissue T476


title: Stomach_tumor_T470

description: Affymetrix SNP6 - Stomach tumor tissue T470

source_name: Stomach tumor tissue T470


title: Stomach_tumor_T47

description: Affymetrix SNP6 - Stomach tumor tissue T47

source_name: Stomach tumor tissue T47


title: Stomach_tumor_T465

description: Affymetrix SNP6 - Stomach tumor tissue T465

source_name: Stomach tumor tissue T465


title: Stomach_tumor_T460

description: Affymetrix SNP6 - Stomach tumor tissue T460

source_name: Stomach tumor tissue T460


title: Stomach_tumor_T46

description: Affymetrix SNP6 - Stomach tumor tissue T46

source_name: Stomach tumor tissue T46


title: Stomach_tumor_T459

description: Affymetrix SNP6 - Stomach tumor tissue T459

source_name: Stomach tumor tissue T459


title: Stomach_tumor_T456

description: Affymetrix SNP6 - Stomach tumor tissue T456

source_name: Stomach tumor tissue T456


title: Stomach_tumor_T477

description: Affymetrix SNP6 - Stomach tumor tissue T477

source_name: Stomach tumor tissue T477


title: Stomach_tumor_T471

description: Affymetrix SNP6 - Stomach tumor tissue T471

source_name: Stomach tumor tissue T471


title: Stomach_tumor_T457

description: Affymetrix SNP6 - Stomach tumor tissue T457

source_name: Stomach tumor tissue T457


title: Stomach_tumor_T448

description: Affymetrix SNP6 - Stomach tumor tissue T448

source_name: Stomach tumor tissue T448


title: Stomach_tumor_T423

description: Affymetrix SNP6 - Stomach tumor tissue T423

source_name: Stomach tumor tissue T423


title: Stomach_tumor_T452

description: Affymetrix SNP6 - Stomach tumor tissue T452

source_name: Stomach tumor tissue T452


title: Stomach_tumor_T447

description: Affymetrix SNP6 - Stomach tumor tissue T447

source_name: Stomach tumor tissue T447


title: Stomach_tumor_T450

description: Affymetrix SNP6 - Stomach tumor tissue T450

source_name: Stomach tumor tissue T450


title: Stomach_tumor_T422

description: Affymetrix SNP6 - Stomach tumor tissue T422

source_name: Stomach tumor tissue T422


title: Stomach_tumor_T455

description: Affymetrix SNP6 - Stomach tumor tissue T455

source_name: Stomach tumor tissue T455


title: Stomach_tumor_T428

description: Affymetrix SNP6 - Stomach tumor tissue T428

source_name: Stomach tumor tissue T428


title: Stomach_tumor_T421

description: Affymetrix SNP6 - Stomach tumor tissue T421

source_name: Stomach tumor tissue T421


title: Stomach_tumor_T424

description: Affymetrix SNP6 - Stomach tumor tissue T424

source_name: Stomach tumor tissue T424


title: Stomach_tumor_T451

description: Affymetrix SNP6 - Stomach tumor tissue T451

source_name: Stomach tumor tissue T451


title: Stomach_tumor_T44

description: Affymetrix SNP6 - Stomach tumor tissue T44

source_name: Stomach tumor tissue T44


title: Stomach_tumor_T446

description: Affymetrix SNP6 - Stomach tumor tissue T446

source_name: Stomach tumor tissue T446


title: Stomach_tumor_T432

description: Affymetrix SNP6 - Stomach tumor tissue T432

source_name: Stomach tumor tissue T432


title: Stomach_tumor_T443

description: Affymetrix SNP6 - Stomach tumor tissue T443

source_name: Stomach tumor tissue T443


title: Stomach_tumor_T433

description: Affymetrix SNP6 - Stomach tumor tissue T433

source_name: Stomach tumor tissue T433


title: Stomach_tumor_T440

description: Affymetrix SNP6 - Stomach tumor tissue T440

source_name: Stomach tumor tissue T440


title: Stomach_tumor_T442

description: Affymetrix SNP6 - Stomach tumor tissue T442

source_name: Stomach tumor tissue T442


title: Stomach_tumor_T42

description: Affymetrix SNP6 - Stomach tumor tissue T42

source_name: Stomach tumor tissue T42


title: Stomach_tumor_T441

description: Affymetrix SNP6 - Stomach tumor tissue T441

source_name: Stomach tumor tissue T441


title: Stomach_tumor_T444

description: Affymetrix SNP6 - Stomach tumor tissue T444

source_name: Stomach tumor tissue T444


title: Stomach_tumor_T445

description: Affymetrix SNP6 - Stomach tumor tissue T445

source_name: Stomach tumor tissue T445


title: Stomach_tumor_T430

description: Affymetrix SNP6 - Stomach tumor tissue T430

source_name: Stomach tumor tissue T430


title: Stomach_tumor_T419

description: Affymetrix SNP6 - Stomach tumor tissue T419

source_name: Stomach tumor tissue T419


title: Stomach_tumor_T416

description: Affymetrix SNP6 - Stomach tumor tissue T416

source_name: Stomach tumor tissue T416


title: Stomach_tumor_T426

description: Affymetrix SNP6 - Stomach tumor tissue T426

source_name: Stomach tumor tissue T426


title: Stomach_tumor_T437

description: Affymetrix SNP6 - Stomach tumor tissue T437

source_name: Stomach tumor tissue T437


title: Stomach_tumor_T420

description: Affymetrix SNP6 - Stomach tumor tissue T420

source_name: Stomach tumor tissue T420


title: Stomach_tumor_T415

description: Affymetrix SNP6 - Stomach tumor tissue T415

source_name: Stomach tumor tissue T415


title: Stomach_tumor_T413

description: Affymetrix SNP6 - Stomach tumor tissue T413

source_name: Stomach tumor tissue T413


title: Stomach_tumor_T405

description: Affymetrix SNP6 - Stomach tumor tissue T405

source_name: Stomach tumor tissue T405


title: Stomach_tumor_T412

description: Affymetrix SNP6 - Stomach tumor tissue T412

source_name: Stomach tumor tissue T412


title: Stomach_tumor_T407

description: Affymetrix SNP6 - Stomach tumor tissue T407

source_name: Stomach tumor tissue T407


title: Stomach_tumor_T41

description: Affymetrix SNP6 - Stomach tumor tissue T41

source_name: Stomach tumor tissue T41


title: Stomach_tumor_T395

description: Affymetrix SNP6 - Stomach tumor tissue T395

source_name: Stomach tumor tissue T395


title: Stomach_tumor_T39

description: Affymetrix SNP6 - Stomach tumor tissue T39

source_name: Stomach tumor tissue T39


title: Stomach_tumor_T399

description: Affymetrix SNP6 - Stomach tumor tissue T399

source_name: Stomach tumor tissue T399


title: Stomach_tumor_T396

description: Affymetrix SNP6 - Stomach tumor tissue T396

source_name: Stomach tumor tissue T396


title: Stomach_tumor_T397

description: Affymetrix SNP6 - Stomach tumor tissue T397

source_name: Stomach tumor tissue T397


title: Stomach_tumor_T402

description: Affymetrix SNP6 - Stomach tumor tissue T402

source_name: Stomach tumor tissue T402


title: Stomach_tumor_T372

description: Affymetrix SNP6 - Stomach tumor tissue T372

source_name: Stomach tumor tissue T372


title: Stomach_tumor_T361

description: Affymetrix SNP6 - Stomach tumor tissue T361

source_name: Stomach tumor tissue T361


title: Stomach_tumor_T355

description: Affymetrix SNP6 - Stomach tumor tissue T355

source_name: Stomach tumor tissue T355


title: Stomach_tumor_T340

description: Affymetrix SNP6 - Stomach tumor tissue T340

source_name: Stomach tumor tissue T340


title: Stomach_tumor_T346

description: Affymetrix SNP6 - Stomach tumor tissue T346

source_name: Stomach tumor tissue T346


title: Stomach_tumor_T375

description: Affymetrix SNP6 - Stomach tumor tissue T375

source_name: Stomach tumor tissue T375


title: Stomach_tumor_T377

description: Affymetrix SNP6 - Stomach tumor tissue T377

source_name: Stomach tumor tissue T377


title: Stomach_tumor_T34

description: Affymetrix SNP6 - Stomach tumor tissue T34

source_name: Stomach tumor tissue T34


title: Stomach_tumor_T341

description: Affymetrix SNP6 - Stomach tumor tissue T341

source_name: Stomach tumor tissue T341


title: Stomach_tumor_T343

description: Affymetrix SNP6 - Stomach tumor tissue T343

source_name: Stomach tumor tissue T343


title: Stomach_tumor_T338

description: Affymetrix SNP6 - Stomach tumor tissue T338

source_name: Stomach tumor tissue T338


title: Stomach_tumor_T339

description: Affymetrix SNP6 - Stomach tumor tissue T339

source_name: Stomach tumor tissue T339


title: Stomach_tumor_T385

description: Affymetrix SNP6 - Stomach tumor tissue T385

source_name: Stomach tumor tissue T385


title: Stomach_tumor_T394

description: Affymetrix SNP6 - Stomach tumor tissue T394

source_name: Stomach tumor tissue T394


title: Stomach_tumor_T337

description: Affymetrix SNP6 - Stomach tumor tissue T337

source_name: Stomach tumor tissue T337


title: Stomach_tumor_T336

description: Affymetrix SNP6 - Stomach tumor tissue T336

source_name: Stomach tumor tissue T336


title: Stomach_tumor_T363

description: Affymetrix SNP6 - Stomach tumor tissue T363

source_name: Stomach tumor tissue T363


title: Stomach_tumor_T35

description: Affymetrix SNP6 - Stomach tumor tissue T35

source_name: Stomach tumor tissue T35


title: Stomach_tumor_T388

description: Affymetrix SNP6 - Stomach tumor tissue T388

source_name: Stomach tumor tissue T388


title: Stomach_tumor_T332

description: Affymetrix SNP6 - Stomach tumor tissue T332

source_name: Stomach tumor tissue T332


title: Stomach_tumor_T331

description: Affymetrix SNP6 - Stomach tumor tissue T331

source_name: Stomach tumor tissue T331


title: Stomach_tumor_T33

description: Affymetrix SNP6 - Stomach tumor tissue T33

source_name: Stomach tumor tissue T33


title: Stomach_tumor_T330

description: Affymetrix SNP6 - Stomach tumor tissue T330

source_name: Stomach tumor tissue T330


title: Stomach_tumor_T328

description: Affymetrix SNP6 - Stomach tumor tissue T328

source_name: Stomach tumor tissue T328


title: Stomach_tumor_T326

description: Affymetrix SNP6 - Stomach tumor tissue T326

source_name: Stomach tumor tissue T326


title: Stomach_tumor_T325

description: Affymetrix SNP6 - Stomach tumor tissue T325

source_name: Stomach tumor tissue T325


title: Stomach_tumor_T323

description: Affymetrix SNP6 - Stomach tumor tissue T323

source_name: Stomach tumor tissue T323


title: Stomach_tumor_T327

description: Affymetrix SNP6 - Stomach tumor tissue T327

source_name: Stomach tumor tissue T327


title: Stomach_tumor_T324

description: Affymetrix SNP6 - Stomach tumor tissue T324

source_name: Stomach tumor tissue T324


title: Stomach_tumor_T319

description: Affymetrix SNP6 - Stomach tumor tissue T319

source_name: Stomach tumor tissue T319


title: Stomach_tumor_T288

description: Affymetrix SNP6 - Stomach tumor tissue T288

source_name: Stomach tumor tissue T288


title: Stomach_tumor_T287

description: Affymetrix SNP6 - Stomach tumor tissue T287

source_name: Stomach tumor tissue T287


title: Stomach_tumor_T31

description: Affymetrix SNP6 - Stomach tumor tissue T31

source_name: Stomach tumor tissue T31


title: Stomach_tumor_T301

description: Affymetrix SNP6 - Stomach tumor tissue T301

source_name: Stomach tumor tissue T301


title: Stomach_tumor_T318

description: Affymetrix SNP6 - Stomach tumor tissue T318

source_name: Stomach tumor tissue T318


title: Stomach_tumor_T269

description: Affymetrix SNP6 - Stomach tumor tissue T269

source_name: Stomach tumor tissue T269


title: Stomach_tumor_T275

description: Affymetrix SNP6 - Stomach tumor tissue T275

source_name: Stomach tumor tissue T275


title: Stomach_tumor_T321

description: Affymetrix SNP6 - Stomach tumor tissue T321

source_name: Stomach tumor tissue T321


title: Stomach_tumor_T27

description: Affymetrix SNP6 - Stomach tumor tissue T27

source_name: Stomach tumor tissue T27


title: Stomach_tumor_T282

description: Affymetrix SNP6 - Stomach tumor tissue T282

source_name: Stomach tumor tissue T282


title: Stomach_tumor_T256

description: Affymetrix SNP6 - Stomach tumor tissue T256

source_name: Stomach tumor tissue T256


title: Stomach_tumor_T263

description: Affymetrix SNP6 - Stomach tumor tissue T263

source_name: Stomach tumor tissue T263


title: Stomach_tumor_T268

description: Affymetrix SNP6 - Stomach tumor tissue T268

source_name: Stomach tumor tissue T268


title: Stomach_tumor_T82

description: Affymetrix SNP6 - Stomach tumor tissue T82

source_name: Stomach tumor tissue T82


title: Stomach_tumor_T255

description: Affymetrix SNP6 - Stomach tumor tissue T255

source_name: Stomach tumor tissue T255


title: Stomach_tumor_T253

description: Affymetrix SNP6 - Stomach tumor tissue T253

source_name: Stomach tumor tissue T253


title: Stomach_tumor_T333

description: Affymetrix SNP6 - Stomach tumor tissue T333

source_name: Stomach tumor tissue T333


title: Stomach_tumor_T244

description: Affymetrix SNP6 - Stomach tumor tissue T244

source_name: Stomach tumor tissue T244


title: Stomach_tumor_T246

description: Affymetrix SNP6 - Stomach tumor tissue T246

source_name: Stomach tumor tissue T246


title: Stomach_tumor_T241

description: Affymetrix SNP6 - Stomach tumor tissue T241

source_name: Stomach tumor tissue T241


title: Stomach_tumor_T240

description: Affymetrix SNP6 - Stomach tumor tissue T240

source_name: Stomach tumor tissue T240


title: Stomach_tumor_T299

description: Affymetrix SNP6 - Stomach tumor tissue T299

source_name: Stomach tumor tissue T299


title: Stomach_tumor_T24

description: Affymetrix SNP6 - Stomach tumor tissue T24

source_name: Stomach tumor tissue T24


title: Stomach_tumor_T238

description: Affymetrix SNP6 - Stomach tumor tissue T238

source_name: Stomach tumor tissue T238


title: Stomach_tumor_T236

description: Affymetrix SNP6 - Stomach tumor tissue T236

source_name: Stomach tumor tissue T236


title: Stomach_tumor_T235

description: Affymetrix SNP6 - Stomach tumor tissue T235

source_name: Stomach tumor tissue T235


title: Stomach_tumor_T227

description: Affymetrix SNP6 - Stomach tumor tissue T227

source_name: Stomach tumor tissue T227


title: Stomach_tumor_T226

description: Affymetrix SNP6 - Stomach tumor tissue T226

source_name: Stomach tumor tissue T226


title: Stomach_tumor_T237

description: Affymetrix SNP6 - Stomach tumor tissue T237

source_name: Stomach tumor tissue T237


title: Stomach_tumor_T225

description: Affymetrix SNP6 - Stomach tumor tissue T225

source_name: Stomach tumor tissue T225


title: Stomach_tumor_T206

description: Affymetrix SNP6 - Stomach tumor tissue T206

source_name: Stomach tumor tissue T206


title: Stomach_tumor_T204

description: Affymetrix SNP6 - Stomach tumor tissue T204

source_name: Stomach tumor tissue T204


title: Stomach_tumor_T205

description: Affymetrix SNP6 - Stomach tumor tissue T205

source_name: Stomach tumor tissue T205


title: Stomach_tumor_T213

description: Affymetrix SNP6 - Stomach tumor tissue T213

source_name: Stomach tumor tissue T213


title: Stomach_tumor_T209

description: Affymetrix SNP6 - Stomach tumor tissue T209

source_name: Stomach tumor tissue T209


title: Stomach_tumor_T201

description: Affymetrix SNP6 - Stomach tumor tissue T201

source_name: Stomach tumor tissue T201


title: Stomach_tumor_T202

description: Affymetrix SNP6 - Stomach tumor tissue T202

source_name: Stomach tumor tissue T202


title: Stomach_tumor_T207

description: Affymetrix SNP6 - Stomach tumor tissue T207

source_name: Stomach tumor tissue T207


title: Stomach_tumor_T192

description: Affymetrix SNP6 - Stomach tumor tissue T192

source_name: Stomach tumor tissue T192


title: Stomach_tumor_T197

description: Affymetrix SNP6 - Stomach tumor tissue T197

source_name: Stomach tumor tissue T197


title: Stomach_tumor_T193

description: Affymetrix SNP6 - Stomach tumor tissue T193

source_name: Stomach tumor tissue T193


title: Stomach_tumor_T187

description: Affymetrix SNP6 - Stomach tumor tissue T187

source_name: Stomach tumor tissue T187


title: Stomach_tumor_T190

description: Affymetrix SNP6 - Stomach tumor tissue T190

source_name: Stomach tumor tissue T190


title: Stomach_tumor_T186

description: Affymetrix SNP6 - Stomach tumor tissue T186

source_name: Stomach tumor tissue T186


title: Stomach_tumor_T188

description: Affymetrix SNP6 - Stomach tumor tissue T188

source_name: Stomach tumor tissue T188


title: Stomach_tumor_T228

description: Affymetrix SNP6 - Stomach tumor tissue T228

source_name: Stomach tumor tissue T228


title: Stomach_tumor_T189

description: Affymetrix SNP6 - Stomach tumor tissue T189

source_name: Stomach tumor tissue T189


title: Stomach_tumor_T182

description: Affymetrix SNP6 - Stomach tumor tissue T182

source_name: Stomach tumor tissue T182


title: Stomach_tumor_T177

description: Affymetrix SNP6 - Stomach tumor tissue T177

source_name: Stomach tumor tissue T177


title: Stomach_tumor_T185

description: Affymetrix SNP6 - Stomach tumor tissue T185

source_name: Stomach tumor tissue T185


title: Stomach_tumor_T212

description: Affymetrix SNP6 - Stomach tumor tissue T212

source_name: Stomach tumor tissue T212


title: Stomach_tumor_T180

description: Affymetrix SNP6 - Stomach tumor tissue T180

source_name: Stomach tumor tissue T180


title: Stomach_tumor_T173

description: Affymetrix SNP6 - Stomach tumor tissue T173

source_name: Stomach tumor tissue T173


title: Stomach_tumor_T175

description: Affymetrix SNP6 - Stomach tumor tissue T175

source_name: Stomach tumor tissue T175


title: Stomach_tumor_T172

description: Affymetrix SNP6 - Stomach tumor tissue T172

source_name: Stomach tumor tissue T172


title: Stomach_tumor_T168

description: Affymetrix SNP6 - Stomach tumor tissue T168

source_name: Stomach tumor tissue T168


title: Stomach_tumor_T169

description: Affymetrix SNP6 - Stomach tumor tissue T169

source_name: Stomach tumor tissue T169


title: Stomach_tumor_T171

description: Affymetrix SNP6 - Stomach tumor tissue T171

source_name: Stomach tumor tissue T171


title: Stomach_tumor_T165

description: Affymetrix SNP6 - Stomach tumor tissue T165

source_name: Stomach tumor tissue T165


title: Stomach_tumor_T164

description: Affymetrix SNP6 - Stomach tumor tissue T164

source_name: Stomach tumor tissue T164


title: Stomach_tumor_T155

description: Affymetrix SNP6 - Stomach tumor tissue T155

source_name: Stomach tumor tissue T155


title: Stomach_tumor_T160

description: Affymetrix SNP6 - Stomach tumor tissue T160

source_name: Stomach tumor tissue T160


title: Stomach_tumor_T157

description: Affymetrix SNP6 - Stomach tumor tissue T157

source_name: Stomach tumor tissue T157


title: Stomach_tumor_T16

description: Affymetrix SNP6 - Stomach tumor tissue T16

source_name: Stomach tumor tissue T16


title: Stomach_tumor_T154

description: Affymetrix SNP6 - Stomach tumor tissue T154

source_name: Stomach tumor tissue T154


title: Stomach_tumor_T152

description: Affymetrix SNP6 - Stomach tumor tissue T152

source_name: Stomach tumor tissue T152


title: Stomach_tumor_T150

description: Affymetrix SNP6 - Stomach tumor tissue T150

source_name: Stomach tumor tissue T150


title: Stomach_tumor_T148

description: Affymetrix SNP6 - Stomach tumor tissue T148

source_name: Stomach tumor tissue T148


title: Stomach_tumor_T146

description: Affymetrix SNP6 - Stomach tumor tissue T146

source_name: Stomach tumor tissue T146


title: Stomach_tumor_T143

description: Affymetrix SNP6 - Stomach tumor tissue T143

source_name: Stomach tumor tissue T143


title: Stomach_tumor_T142

description: Affymetrix SNP6 - Stomach tumor tissue T142

source_name: Stomach tumor tissue T142


title: Stomach_tumor_T141

description: Affymetrix SNP6 - Stomach tumor tissue T141

source_name: Stomach tumor tissue T141


title: Stomach_tumor_T138

description: Affymetrix SNP6 - Stomach tumor tissue T138

source_name: Stomach tumor tissue T138


title: Stomach_tumor_T140

description: Affymetrix SNP6 - Stomach tumor tissue T140

source_name: Stomach tumor tissue T140


title: Stomach_tumor_T139

description: Affymetrix SNP6 - Stomach tumor tissue T139

source_name: Stomach tumor tissue T139


title: Stomach_tumor_T144

description: Affymetrix SNP6 - Stomach tumor tissue T144

source_name: Stomach tumor tissue T144


title: Stomach_tumor_T137

description: Affymetrix SNP6 - Stomach tumor tissue T137

source_name: Stomach tumor tissue T137


title: Stomach_tumor_T136

description: Affymetrix SNP6 - Stomach tumor tissue T136

source_name: Stomach tumor tissue T136


title: Stomach_tumor_T135

description: Affymetrix SNP6 - Stomach tumor tissue T135

source_name: Stomach tumor tissue T135


title: Stomach_tumor_T132

description: Affymetrix SNP6 - Stomach tumor tissue T132

source_name: Stomach tumor tissue T132


title: Stomach_tumor_T133

description: Affymetrix SNP6 - Stomach tumor tissue T133

source_name: Stomach tumor tissue T133


title: Stomach_tumor_T134

description: Affymetrix SNP6 - Stomach tumor tissue T134

source_name: Stomach tumor tissue T134


title: Stomach_tumor_T129

description: Affymetrix SNP6 - Stomach tumor tissue T129

source_name: Stomach tumor tissue T129


title: Stomach_tumor_T121

description: Affymetrix SNP6 - Stomach tumor tissue T121

source_name: Stomach tumor tissue T121


title: Stomach_tumor_T118

description: Affymetrix SNP6 - Stomach tumor tissue T118

source_name: Stomach tumor tissue T118


title: Stomach_tumor_T124

description: Affymetrix SNP6 - Stomach tumor tissue T124

source_name: Stomach tumor tissue T124


title: Stomach_tumor_T116

description: Affymetrix SNP6 - Stomach tumor tissue T116

source_name: Stomach tumor tissue T116


title: Stomach_tumor_T128

description: Affymetrix SNP6 - Stomach tumor tissue T128

source_name: Stomach tumor tissue T128


title: Stomach_tumor_T115

description: Affymetrix SNP6 - Stomach tumor tissue T115

source_name: Stomach tumor tissue T115


title: Stomach_tumor_T114

description: Affymetrix SNP6 - Stomach tumor tissue T114

source_name: Stomach tumor tissue T114


title: Stomach_tumor_T117

description: Affymetrix SNP6 - Stomach tumor tissue T117

source_name: Stomach tumor tissue T117


title: Stomach_tumor_T145

description: Affymetrix SNP6 - Stomach tumor tissue T145

source_name: Stomach tumor tissue T145


title: Stomach_tumor_T112

description: Affymetrix SNP6 - Stomach tumor tissue T112

source_name: Stomach tumor tissue T112


title: Stomach_tumor_T107

description: Affymetrix SNP6 - Stomach tumor tissue T107

source_name: Stomach tumor tissue T107


title: Stomach_tumor_T113

description: Affymetrix SNP6 - Stomach tumor tissue T113

source_name: Stomach tumor tissue T113


title: Stomach_tumor_T109

description: Affymetrix SNP6 - Stomach tumor tissue T109

source_name: Stomach tumor tissue T109


title: Stomach_tumor_T108

description: Affymetrix SNP6 - Stomach tumor tissue T108

source_name: Stomach tumor tissue T108


title: Stomach_tumor_T11

description: Affymetrix SNP6 - Stomach tumor tissue T11

source_name: Stomach tumor tissue T11


title: Stomach_tumor_T106

description: Affymetrix SNP6 - Stomach tumor tissue T106

source_name: Stomach tumor tissue T106


title: Stomach_tumor_T105

description: Affymetrix SNP6 - Stomach tumor tissue T105

source_name: Stomach tumor tissue T105


title: Stomach_normal_N552

description: Affymetrix SNP6 - Stomach normal tissue N552

source_name: Stomach normal tissue N552

value: normal


title: Stomach_tumor_T1

description: Affymetrix SNP6 - Stomach tumor tissue T1

source_name: Stomach tumor tissue T1


title: Stomach_normal_N601

description: Affymetrix SNP6 - Stomach normal tissue N601

source_name: Stomach normal tissue N601


title: Stomach_normal_N499

description: Affymetrix SNP6 - Stomach normal tissue N499

source_name: Stomach normal tissue N499


title: Stomach_normal_N521

description: Affymetrix SNP6 - Stomach normal tissue N521

source_name: Stomach normal tissue N521


title: Stomach_tumor_T08

description: Affymetrix SNP6 - Stomach tumor tissue T08

source_name: Stomach tumor tissue T08


title: Stomach_tumor_T101

description: Affymetrix SNP6 - Stomach tumor tissue T101

source_name: Stomach tumor tissue T101


title: Stomach_normal_N462

description: Affymetrix SNP6 - Stomach normal tissue N462

source_name: Stomach normal tissue N462


title: Stomach_normal_N452

description: Affymetrix SNP6 - Stomach normal tissue N452

source_name: Stomach normal tissue N452


title: Stomach_normal_N412

description: Affymetrix SNP6 - Stomach normal tissue N412

source_name: Stomach normal tissue N412


title: Stomach_normal_N492

description: Affymetrix SNP6 - Stomach normal tissue N492

source_name: Stomach normal tissue N492


title: Stomach_normal_N473

description: Affymetrix SNP6 - Stomach normal tissue N473

source_name: Stomach normal tissue N473


title: Stomach_normal_N475

description: Affymetrix SNP6 - Stomach normal tissue N475

source_name: Stomach normal tissue N475


title: Stomach_normal_N486

description: Affymetrix SNP6 - Stomach normal tissue N486

source_name: Stomach normal tissue N486


title: Stomach_normal_N332

description: Affymetrix SNP6 - Stomach normal tissue N332

source_name: Stomach normal tissue N332


title: Stomach_normal_N407

description: Affymetrix SNP6 - Stomach normal tissue N407

source_name: Stomach normal tissue N407


title: Kidney_lupus NZB/W (late remission CTX+ CTLA4Ig + antiCD154) rep9

status: Public on Dec 31 2014

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description:
Sample name: Late9_V9LL_03
Kidney from lupus NZB/W mouse (late remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after late remission with triple therapy CTX+CTLA4Ig+anti-CD154

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

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

source_name: Kidney from NZB/W mouse under late remission (triple therapy)

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

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

tag: strain

value: NZB/W

tag: treatment

value: triple therapy CTX+CTLA4Ig+anti-CD154

value: late remission

value: Whole kidney


title: Kidney_lupus NZB/W (late remission CTX+ CTLA4Ig + antiCD154) rep6

description:
Sample name: Late6_V11LU_06
Kidney from lupus NZB/W mouse (late remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after late remission with triple therapy CTX+CTLA4Ig+anti-CD154

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


title: non-lesional_skin_control9

status: Public on Aug 26 2014

city: Kiel

first: Hansjoerg

last: Baurecht

address: Schittenhelmstr. 7

department: Department of Dermatology, Venereology and Allergology

institute: University Hospital Schleswig-Holstein, Campus Kiel

hyb_protocol: Standard Illumina hybridization protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: epidermal shave

label_protocol: In vitro transcription into cRNA and biotin-UTP labeling were performed using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Life Technologies, Carlsbad, CA)

extract_protocol: RNA was extracted with the PAXgene Tissue RNA Kit (Qiagen)

value: non-lesional skin

tag: phenotype

value: Control

value: m


title: non-lesional_skin_control10

value: f


title: non-lesional_skin_control11


title: non-lesional_skin_control8


title: non-lesional_skin_control14


title: non-lesional_skin_control12


title: Kidney_lupus NZB/W (late remission CTX+ CTLA4Ig + antiCD154) rep10

description:
Sample name: Late10_V11LL_05
Kidney from lupus NZB/W mouse (late remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after late remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: Kidney_lupus NZB/W (late remission CTX+ CTLA4Ig + antiCD154) rep11

description:
Sample name: Late11_V10_0_04
Kidney from lupus NZB/W mouse (late remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after late remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: Kidney_lupus NZB/W (late remission CTX+ CTLA4Ig + antiCD154) rep8

description:
Sample name: Late8_V90_02
Kidney from lupus NZB/W mouse (late remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after late remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: lesional_skin_case11

value: lesional skin

value: Atopic Dermatitis


title: Kidney_lupus NZB/W (late remission CTX+ CTLA4Ig + antiCD154) rep7

description:
Sample name: Late7_V7RU_01
Kidney from lupus NZB/W mouse (late remission after triple therapy CTX+CTLA4Ig+anti-CD154)
Gene expression data from NZB/W kidney after late remission with triple therapy CTX+CTLA4Ig+anti-CD154


title: non-lesional_skin_control13


title: non-lesional_skin_case12


title: non-lesional_skin_control5


title: non-lesional_skin_case11


title: non-lesional_skin_control7


title: non-lesional_skin_control2


title: non-lesional_skin_case8


title: non-lesional_skin_control4


title: non-lesional_skin_case9


title: lesional_skin_case13


title: lesional_skin_case12


title: lesional_skin_case10


title: non-lesional_skin_control6


title: non-lesional_skin_control1


title: lesional_skin_case9


title: non-lesional_skin_control3


title: lesional_skin_case5


title: lesional_skin_case4_(2 reps)

description: Sample_6, Sample_36


title: lesional_skin_case6


title: non-lesional_skin_case2


title: lesional_skin_case2


title: non-lesional_skin_case4


title: lesional_skin_case3_(3 reps)

description: Sample_5, Sample_34, Sample_35


title: lesional_skin_case1


title: non-lesional_skin_case1


title: Cerevisiae_cdc20_80min_rep2

status: Public on Jul 27 2014

city: Durham

first: Steven

last: Haase

state: NC

department: Biology

institute: Duke University

description: Cell cycle gene expression data from CDK on yeast synchronized by elutration

hyb_protocol: DNA microarray hybridization was performed according to standard Affymetrix protocols by the Duke Micorarray Core Facility.

scan_protocol: Array scanning was carried by the Duke Micorarray Core Facility using standard Affymetrix protocols.

data_processing: Data from all chips and data from Orlando et al 2008 was normalized together using the dChip implementation with default parameters from the affy package (1.32.1) within R/Bioconductor. S. pombe probes are removed before analysis.

source_name: Cerevisiae culture, cdc20, 80 min, rep2

label_protocol: Amplification and labeling using the GeneChip One-Cycle target Labeling (Affymetrix, Santa Clara, CA).

growth_protocol: YEPDextrose/1M sorbitol at 30c

extract_protocol: RNA was extracted using standard yeast methods.

treatment_protocol: synchronous G1 populations collected by elutration.


title: Cerevisiae_cdc20_360min_rep2

source_name: Cerevisiae culture, cdc20, 360 min, rep2


title: Cerevisiae_cdc20_260min_rep2

source_name: Cerevisiae culture, cdc20, 260 min, rep2


title: Cerevisiae_cdc20_140min_rep2

source_name: Cerevisiae culture, cdc20, 140 min, rep2


title: Cerevisiae_cdc20_300min_rep1

source_name: Cerevisiae culture, cdc20, 300 min, rep1


title: Cerevisiae_cdc20_160min_rep2

source_name: Cerevisiae culture, cdc20, 160 min, rep2


title: Cerevisiae_cdc20_280min_rep2

source_name: Cerevisiae culture, cdc20, 280 min, rep2


title: Cerevisiae_cdc20_300min_rep2

source_name: Cerevisiae culture, cdc20, 300 min, rep2


title: Cerevisiae_cdc20_20min_rep2

source_name: Cerevisiae culture, cdc20, 20 min, rep2


title: Cerevisiae_cdc20_180min_rep2

source_name: Cerevisiae culture, cdc20, 180 min, rep2


title: Cerevisiae_cdc20_120min_rep2

source_name: Cerevisiae culture, cdc20, 120 min, rep2


title: Cerevisiae_cdc20_200min_rep2

source_name: Cerevisiae culture, cdc20, 200 min, rep2


title: Cerevisiae_cdc20_40min_rep2

source_name: Cerevisiae culture, cdc20, 40 min, rep2


title: Cerevisiae_cdc20_320min_rep2

source_name: Cerevisiae culture, cdc20, 320 min, rep2


title: Cerevisiae_cdc20_280min_rep1

source_name: Cerevisiae culture, cdc20, 280 min, rep1


title: Cerevisiae_cdc20_240min_rep2

source_name: Cerevisiae culture, cdc20, 240 min, rep2


title: Cerevisiae_cdc20_100min_rep2

source_name: Cerevisiae culture, cdc20, 100 min, rep2


title: Cerevisiae_cdc20_220min_rep2

source_name: Cerevisiae culture, cdc20, 220 min, rep2


title: Cerevisiae_cdc20_340min_rep2

source_name: Cerevisiae culture, cdc20, 340 min, rep2


title: lesional_skin_case7

source_name: epidermal shave


title: Cerevisiae_cdc20_240min_rep1

source_name: Cerevisiae culture, cdc20, 240 min, rep1


title: Cerevisiae_cdc20_260min_rep1

source_name: Cerevisiae culture, cdc20, 260 min, rep1


title: Cerevisiae_cdc20_220min_rep1

source_name: Cerevisiae culture, cdc20, 220 min, rep1


title: Cerevisiae_cdc20_60min_rep2

source_name: Cerevisiae culture, cdc20, 60 min, rep2


title: Cerevisiae_cdc20_200min_rep1

source_name: Cerevisiae culture, cdc20, 200 min, rep1


title: Cerevisiae_cdc20_160min_rep1

source_name: Cerevisiae culture, cdc20, 160 min, rep1


title: Cerevisiae_cdc20_120min_rep1

source_name: Cerevisiae culture, cdc20, 120 min, rep1


title: Cerevisiae_cdc20_60min_rep1

source_name: Cerevisiae culture, cdc20, 60 min, rep1


title: Cerevisiae_cdc20_100min_rep1

source_name: Cerevisiae culture, cdc20, 100 min, rep1


title: Cerevisiae_cdc20_80min_rep1

source_name: Cerevisiae culture, cdc20, 80 min, rep1


title: Cerevisiae_cdc20_40min_rep1

source_name: Cerevisiae culture, cdc20, 40 min, rep1


title: Cerevisiae_cdc20_180min_rep1

source_name: Cerevisiae culture, cdc20, 180 min, rep1


title: Cerevisiae_cdc20_140min_rep1

source_name: Cerevisiae culture, cdc20, 140 min, rep1


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 36

status: Public on Jul 08 2014

city: London

first: Jocelyn

last: Charlton

address: 30 Guilford Street

department: Institute of Child Health

institute: University College London

description: SAMPLE 94

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 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: Cy5 and Cy3

source_name: Wilms tumour 36

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from formalin fixed paraffin embedded tissue using the Dneasy kit (QIAGEN)

value: Wilms tumour

tag: matched trios

value: matched trio 19

tag: matched pairs

value: matched pair 21

tag: Sex

tag: laterality

value: bilateral

tag: overall tumour histology

value: regressive

value: cancer

tag: age (months)


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 33

description: SAMPLE 91

source_name: Wilms tumour 33

tag: tissue

value: matched trio 17

value: matched pair 19

value: F

value: stromal


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 34

description: SAMPLE 92

source_name: Wilms tumour 34

value: blastemal

tag: disease state


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 23

description: SAMPLE 81

source_name: Wilms tumour 23

value: matched trio 11

value: matched pair 12

value: epithelial


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 29

description: SAMPLE 87

source_name: Wilms tumour 29

value: matched trio 14

value: matched pair 15

value: M

value: unilateral


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 9

description: SAMPLE 67

source_name: Wilms tumour 9

value: Wilms tumour


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 22

description: SAMPLE 80

source_name: Wilms tumour 22

value: diffuse anaplasia


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 31

description: SAMPLE 89

source_name: Wilms tumour 31

value: matched trio 15

value: matched pair 17

value: bilateral


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 21

description: SAMPLE 79

source_name: Wilms tumour 21

value: regressive

value: cancer


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 25

description: SAMPLE 83

source_name: Wilms tumour 25

value: matched trio 13

value: matched pair 14


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 20

description: SAMPLE 78

source_name: Wilms tumour 20

value: matched trio 10

value: matched pair 11

value: F

value: mixed


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 35

description: SAMPLE 93

source_name: Wilms tumour 35

value: matched trio 18

value: matched pair 20


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 16

description: SAMPLE 74

source_name: Wilms tumour 16

value: matched trio 7

value: matched pair 8


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 17

description: SAMPLE 75

source_name: Wilms tumour 17

value: Wilms tumour

value: matched trio 8

value: matched pair 9

value: M


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 15

description: SAMPLE 73

source_name: Wilms tumour 15

value: unilateral


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 27

description: SAMPLE 85

source_name: Wilms tumour 27


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 28

description: SAMPLE 86

source_name: Wilms tumour 28

value: bilateral

value: stromal


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 26

description: SAMPLE 84

source_name: Wilms tumour 26

value: cancer


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 37

description: SAMPLE 95

source_name: Wilms tumour 37

value: matched trio 20

value: matched pair 22

value: blastemal


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 32

description: SAMPLE 90

source_name: Wilms tumour 32

value: matched trio 16

value: matched pair 18

value: F

value: regressive


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 24

description: SAMPLE 82

source_name: Wilms tumour 24

value: matched trio 12

value: matched pair 13

value: mixed


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 13

description: SAMPLE 71

source_name: Wilms tumour 13

value: Wilms tumour

value: matched trio 6

value: matched pair 7

value: epithelial


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 14

description: SAMPLE 72

source_name: Wilms tumour 14

value: unilateral


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 8

description: SAMPLE 66

source_name: Wilms tumour 8

value: M


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 12

description: SAMPLE 70

source_name: Wilms tumour 12

value: matched trio 5

value: matched pair 6

value: cancer


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 18

description: SAMPLE 76

source_name: Wilms tumour 18

value: matched trio 9

value: matched pair 10

value: bilateral

value: anaplastic


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 30

description: SAMPLE 88

source_name: Wilms tumour 30

value: matched pair 16

value: necrotic


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 11

description: SAMPLE 69

source_name: Wilms tumour 11

value: matched trio 4

value: matched pair 5

value: blastemal


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 19

description: SAMPLE 77

source_name: Wilms tumour 19

value: Wilms tumour

value: F

value: regressive


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 10

description: SAMPLE 68

source_name: Wilms tumour 10

value: mixed


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 13

description: SAMPLE 49

source_name: nephrogenic rest 13

value: nephrogenic rest

value: matched trio 12

value: M

value: precursor


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 7

description: SAMPLE 65

source_name: Wilms tumour 7

value: unilateral

value: cancer


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 6

description: SAMPLE 64

source_name: Wilms tumour 6


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 15

description: SAMPLE 51

source_name: nephrogenic rest 15


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 9

description: SAMPLE 45

source_name: nephrogenic rest 9

value: matched trio 9


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 7

description: SAMPLE 43

source_name: nephrogenic rest 7

value: matched trio 7


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 5

description: SAMPLE 63

source_name: Wilms tumour 5

value: matched trio 3

value: matched pair 4


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 12

description: SAMPLE 48

source_name: nephrogenic rest 12

value: matched trio 11


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 18

description: SAMPLE 54

source_name: nephrogenic rest 18

value: matched trio 16


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 4

description: SAMPLE 40

source_name: nephrogenic rest 4

value: matched trio 4


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 3

description: SAMPLE 61

source_name: Wilms tumour 3

value: Wilms tumour

value: matched trio 2

value: matched pair 3

value: bilateral


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 19

description: SAMPLE 55

source_name: nephrogenic rest 19

value: nephrogenic rest

value: matched trio 17

value: F


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 2

description: SAMPLE 38

source_name: nephrogenic rest 2

value: precursor


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 1

description: SAMPLE 59

source_name: Wilms tumour 1

value: matched trio 1

value: matched pair 1

value: M

value: mixed

value: unknown


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 20

description: SAMPLE 56

source_name: nephrogenic rest 20

value: matched trio 18


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 6

description: SAMPLE 42

source_name: nephrogenic rest 6

value: matched trio 6


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 21

description: SAMPLE 57

source_name: nephrogenic rest 21

value: matched trio 19


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 22

description: SAMPLE 58

source_name: nephrogenic rest 22

value: matched trio 20


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 1

description: SAMPLE 37

source_name: nephrogenic rest 1


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 2

description: SAMPLE 60

source_name: Wilms tumour 2

value: Wilms tumour

value: matched pair 2

value: stromal

value: cancer


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 10

description: SAMPLE 46

source_name: nephrogenic rest 10

value: nephrogenic rest

value: matched trio 10


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 11

description: SAMPLE 47

source_name: nephrogenic rest 11

value: F


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 16

description: SAMPLE 52

source_name: nephrogenic rest 16

value: matched trio 14

value: precursor


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 8

description: SAMPLE 44

source_name: nephrogenic rest 8

value: matched trio 8


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 14

description: SAMPLE 50

source_name: nephrogenic rest 14

value: matched trio 13

value: M


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 3

description: SAMPLE 39

source_name: nephrogenic rest 3

value: matched trio 3


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 5

description: SAMPLE 41

source_name: nephrogenic rest 5

value: matched trio 5


title: genomic DNA from formalin fixed paraffin embedded nephrogenic rest 17

description: SAMPLE 53

source_name: nephrogenic rest 17

value: matched trio 15


title: genomic DNA from formalin fixed paraffin embedded Wilms tumour 4

description: SAMPLE 62

source_name: Wilms tumour 4

value: unilateral

value: mixed


title: genomic DNA from formalin fixed paraffin embedded normal kidney 32

description: SAMPLE 32

source_name: normal kidney 32

value: normal kidney

value: matched trio 17

value: matched pair 19

value: normal


title: genomic DNA from formalin fixed paraffin embedded normal kidney 36

description: SAMPLE 36

source_name: normal kidney 36

value: matched trio 20

value: matched pair 22


title: genomic DNA from formalin fixed paraffin embedded normal kidney 35

description: SAMPLE 35

source_name: normal kidney 35

value: matched trio 19

value: matched pair 21

value: F


title: genomic DNA from formalin fixed paraffin embedded normal kidney 28

description: SAMPLE 28

source_name: normal kidney 28

value: matched trio 14

value: matched pair 15


title: genomic DNA from formalin fixed paraffin embedded normal kidney 29

description: SAMPLE 29

source_name: normal kidney 29

value: matched pair 16

value: M


title: genomic DNA from formalin fixed paraffin embedded normal kidney 27

description: SAMPLE 27

source_name: normal kidney 27


title: genomic DNA from formalin fixed paraffin embedded normal kidney 20

description: SAMPLE 20

source_name: normal kidney 20


title: genomic DNA from formalin fixed paraffin embedded normal kidney 26

description: SAMPLE 26

source_name: normal kidney 26

value: matched trio 13

value: matched pair 14


title: genomic DNA from formalin fixed paraffin embedded normal kidney 19

description: SAMPLE 19

source_name: normal kidney 19

value: matched trio 9

value: matched pair 10


title: genomic DNA from formalin fixed paraffin embedded normal kidney 16

description: SAMPLE 16

source_name: normal kidney 16

value: normal kidney

value: matched trio 7

value: matched pair 8


title: genomic DNA from formalin fixed paraffin embedded normal kidney 30

description: SAMPLE 30

source_name: normal kidney 30

value: matched trio 15

value: matched pair 17

value: normal


title: genomic DNA from formalin fixed paraffin embedded normal kidney 23

description: SAMPLE 23

source_name: normal kidney 23


title: genomic DNA from formalin fixed paraffin embedded normal kidney 13

description: SAMPLE 13

source_name: normal kidney 13

value: matched trio 6

value: matched pair 7


title: genomic DNA from formalin fixed paraffin embedded normal kidney 8

description: SAMPLE 8

source_name: normal kidney 8


title: genomic DNA from formalin fixed paraffin embedded normal kidney 31

description: SAMPLE 31

source_name: normal kidney 31

value: matched trio 16

value: matched pair 18

value: F


title: genomic DNA from formalin fixed paraffin embedded normal kidney 17

description: SAMPLE 17

source_name: normal kidney 17


title: genomic DNA from formalin fixed paraffin embedded normal kidney 25

description: SAMPLE 25

source_name: normal kidney 25

value: matched trio 12

value: matched pair 13


title: genomic DNA from formalin fixed paraffin embedded normal kidney 33

description: SAMPLE 33

source_name: normal kidney 33


title: genomic DNA from formalin fixed paraffin embedded normal kidney 21

description: SAMPLE 21

source_name: normal kidney 21

value: matched trio 10

value: matched pair 11


title: genomic DNA from formalin fixed paraffin embedded normal kidney 22

description: SAMPLE 22

source_name: normal kidney 22


title: genomic DNA from formalin fixed paraffin embedded normal kidney 18

description: SAMPLE 18

source_name: normal kidney 18

value: matched trio 8

value: matched pair 9

value: M


title: genomic DNA from formalin fixed paraffin embedded normal kidney 12

description: SAMPLE 12

source_name: normal kidney 12

value: normal kidney

value: matched trio 5

value: matched pair 6


title: genomic DNA from formalin fixed paraffin embedded normal kidney 11

description: SAMPLE 11

source_name: normal kidney 11

value: matched trio 4

value: matched pair 5


title: genomic DNA from formalin fixed paraffin embedded normal kidney 14

description: SAMPLE 14

source_name: normal kidney 14

value: normal


title: genomic DNA from formalin fixed paraffin embedded normal kidney 9

description: SAMPLE 9

source_name: normal kidney 9


title: genomic DNA from formalin fixed paraffin embedded normal kidney 10

description: SAMPLE 10

source_name: normal kidney 10


title: genomic DNA from formalin fixed paraffin embedded normal kidney 15

description: SAMPLE 15

source_name: normal kidney 15


title: genomic DNA from formalin fixed paraffin embedded normal kidney 34

description: SAMPLE 34

source_name: normal kidney 34

value: matched trio 18

value: matched pair 20


title: genomic DNA from formalin fixed paraffin embedded normal kidney 24

description: SAMPLE 24

source_name: normal kidney 24

value: matched trio 11

value: matched pair 12


title: FLIGHT TAGES 2B plate4 ROOTS Rep2

status: Public on Apr 10 2014

hyb_protocol: Amplified and labeled cDNA (5 µg/sample) was fragmented and hybridized with rotation onto Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays for 16h at 45°C. Arrays were washed on a Fluidics Station 450 (Affymetrix) with the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004.

data_processing: The MAS5 data was generated by using the Affymetrix Expression Console software using default analysis settings and global scaling as normalization method.

source_name: solid 0.5x MS media plates; Advanced Biological Research System (ABRS); The EXPRESS Rack

label_protocol: cDNA was synthesized using Ovation Pico WTA System (NuGEN Technologies Inc.) and cDNA was labeled using Encore Biotin Module (NuGEN Technologies Inc.)

growth_protocol: Plant Lines and Seed Dormancy: Arabidopsis thaliana (Arabidopsis) plants were grown in a vertical configuration on the surface of 10 cm2 solid media plates.  Three GFP (Green fluorescent Protein reporter gene lines were used:  Adh::GFP (alcohol dehydrogenase promoter), DR5::GFP (synthetic auxin response element) and UB::GFP (35sCaMV constitutive promoter). Seeds, and the seeded plates, were prepared in such a way as to maintain dormancy until the initiation of the experiment on orbit. Seeds were surface sterilized with 75% ethanol for 10 minutes, dried on sterile filter paper and stored at 4°C until use. Immediately before planting onto media plates, a small amount of seed was suspended in sterile water and the seeds were dispersed individually to the surface of the plate.  The plate was then immediately wrapped in light-tight black cloth (Duvatyne) and stored at room temperature until launch. After launch (Shuttle launch STS-131, Orbiter Discovery, April, 2010) and transition to the International Space Station (ISS), the wrapped plates were stowed at ambient temperature for 12 days until the initiation of the experiment on orbit.  The dry-sterilized seeds remained dormant until activated by exposure to light.

treatment_protocol: Experiment Unique Equipment and Environmental Conditions:Both the flight and ground control components of the experiment were grown in specialized growth chamber units developed by Kennedy Space Center referred to as ABRS (Advanced Biological Research System) growth chamber.  Seeded plates were unwrapped from their light-tight coverings and installed in a specialized GFP imaging system (GIS) designed to hold six plates – one in the direct line of fluorescent excitation LEDs and the imaging camera, plus five additional plates. GFP expression data were collected on orbit form the imaging plate, and after 12 days of growth, all plates were harvested on orbit to RNAlater-filled KSC Fixation Tubes (KFTs) and then stowed below -40°C on station.  The Ground Control was housed in the Orbital Environmental Simulator (OES) chamber in the Spaceflight Life Sciences Laboratory at Kennedy Space Center. The Ground Control was initiated with a precise 48 hour delay to enable the OES environment to be programed with those environmental conditions that can be replicated on the ground, such as cabin temperature and CO2 levels, taken from ISS telemetry. Sample Preparation: Plants harvested to RNAlater-filled KFTs were returned from ISS stowage with Orbiter Atlantis for the return flight of STS-132 and transferred to the PIs. Total RNA was isolated form sets of intact 12 day old seedlings, and from seedlings separated into three tissue types: leaves (cut from the plant at base of each petiole), hypocotyls (the region between the root/shoot junction and the start of the leaf rosette) and roots.

tag: cultivar

tag: material type

value: plant tissue

tag: organism part

value: roots

tag: age

value: seeds germinated with light stimulus 12 days into the flight

tag: biosource type

value: in-flight fixed sample


title: GROUND CONTROL TAGES 2B plate4 ROOTS Rep2

source_name: solid 0.5x MS media plates; Advanced solid media plates; Advanced Biological Research System (ABRS); GC Unit, OES chamber at KSC

value: fixed sample


title: FLIGHT TAGES 2B plate4 ROOTS Rep1


title: FLIGHT TAGES 2B plate6 ROOTS Rep1


title: GROUND CONTROL TAGES 2B plate4 HYPOCOTYLS Rep1

value: hypocotyls


title: FLIGHT TAGES 2B plate6 HYPOCOTYLS Rep2


title: genomic DNA from formalin fixed paraffin embedded normal kidney 6

description: SAMPLE 6

source_name: normal kidney 6

value: M


title: GROUND CONTROL TAGES 2B plate6 HYPOCOTYLS Rep1


title: genomic DNA from formalin fixed paraffin embedded normal kidney 7

description: SAMPLE 7

source_name: normal kidney 7

value: normal kidney


title: GROUND CONTROL TAGES 2B plate2 ROOTS Rep1


title: FLIGHT TAGES 2B plate4 HYPOCOTYLS Rep1


title: FLIGHT TAGES 2B plate2 HYPOCOTYLS Rep1


title: GROUND CONTROL TAGES 2B plate2 HYPOCOTYLS Rep1


title: GROUND CONTROL TAGES 2B plate6 SHOOTS Rep2

value: shoots


title: GROUND CONTROL TAGES 2B plate6 HYPOCOTYLS Rep2


title: GROUND CONTROL TAGES 2B plate6 SHOOTS Rep1


title: FLIGHT TAGES 2B plate6 HYPOCOTYLS Rep1


title: FLIGHT TAGES 2B plate2 ROOTS Rep1


title: GROUND CONTROL TAGES 2B plate4 ROOTS Rep1


title: GROUND CONTROL TAGES 2B plate4 SHOOTS Rep2


title: FLIGHT TAGES 2B plate6 SHOOTS Rep1


title: FLIGHT TAGES 2B plate6 SHOOTS Rep2


title: GROUND CONTROL TAGES 2B plate4 SHOOTS Rep1


title: FLIGHT TAGES 2B plate4 SHOOTS Rep2


title: FLIGHT TAGES 2B plate2 SHOOTS Rep1


title: GROUND CONTROL TAGES 2B plate2 SHOOTS Rep1


title: FLIGHT TAGES 2B plate4 SHOOTS Rep1


title: genomic DNA from formalin fixed paraffin embedded normal kidney 5

description: SAMPLE 5

source_name: normal kidney 5

value: matched trio 3

value: matched pair 4

value: F


title: GROUND CONTROL TAGES 2B plate6 ROOTS Rep2


title: GROUND CONTROL TAGES 2B plate6

value: WS

value: whole plant


title: FLIGHT TAGES 2B plate4


title: FLIGHT TAGES 2B plate6


title: FLIGHT TAGES 2B plate4 HYPOCOTYLS Rep2


title: GROUND CONTROL TAGES 2B plate2


title: genomic DNA from formalin fixed paraffin embedded normal kidney 3

description: SAMPLE 3

source_name: normal kidney 3

value: matched trio 2

value: matched pair 3

value: normal


title: GROUND CONTROL TAGES 2B plate6 ROOTS Rep1

value: plant tissue


title: FLIGHT TAGES 2B plate2


title: genomic DNA from formalin fixed paraffin embedded normal kidney 2

description: SAMPLE 2

source_name: normal kidney 2

value: matched pair 2


title: GROUND CONTROL BRIC A PDFU-4 314 seedlings

source_name: solid media plates; BRIC-16; OES chamber: BRIC-A PDFU-4

growth_protocol: General biology operations   Wild-type (non-transgenic) Arabidopsis plants and Arabidopsis tissue culture cells were planted on 60mm round, nutrient agar Petri plates cultured in a horizontal position until turnover and installation into the BRIC hardware.  All of the sub-culturing on the plates was conducted in the laboratory of the PIs and the University of Florida.  Some planting of the seeded plates was conducted at KSC. Plates were planted in a laminar flow hood and stored in sterile Biotransfer Boxes (BT). Plates with both seeds and cells were kept in the dark, and the seeds vernalized at 4 deg C.  Preparation of specialized plates and biology  Petri plates.   Because of their configuration within the BRIC flight hardware, sterility was maintained on all surfaces (interior and exterior) of the Petri plates. The media in the plates for BRIC had to be 5mm deep or less to accommodate the biology and the PDFU cover hardware. For a 60mm dish, this calculates out to 6.7 mLs. After pouring, the plates are allowed to solidify, and then transferred to a sterile Biotransporter (to maintain sterility of external surface) until planting.  Preparation of seeded plates. Arabidopsis seed was surface sterilized working in a laminar flow hood. Seeds were planted on the surface of the Petri plates at a density of about 75 seeds per plate.  The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at 4 deg C until Turn Over.  Preparation of cell culture plates.  The liquid media from a sterile cell suspension was decanted, and the cells were washed once with fresh liquid media, and then decanted again. A sterile scoop was used to place about 1 gram of cells in the surface on the plate and disperse evenly across the surface. The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at room temperature until Turn Over.  BRIC Spaceflight Hardware  The hardware for this experiment was the NASA BRIC-LED (Biological Research In a Canister – Light Emitting Diode). The LED component of the hardware was disabled and all biology was held in the dark for the duration of the experiment. The BRIC-LED canisters hold six 60 mm diameter Petri plates in small sub-compartments called PDFUs (Petri Dish Fixation Units). The PDFUs allow an externally activated fixation step without manipulating the samples. We were allocated 13 PDFUs: 5 in BRIC A, 5 in BRIC B and 3 in BRIC G. The six replicate plates of seedlings and six replicate plates cultured cells (12 plates total) were distributed among three BRIC canisters. We were allocated 13 PDFUs: 5 in BRIC A, 5 in BRIC B and 3 in BRIC G. One of the PDFU slots in each BRIC was used to hold a HOBO™ data logger to record temperature. The HOBO temperature data collection begins immediately after the biology is sealed in the BRICs, 24 hours before launch. The BRICs were contained within a foam-lined tray for launch and stowage in a Shuttle Middeck Locker for the flight.   An additional set of Petri plates within BRIC hardware, identical to that launched for Spaceflight, was prepared for the Ground Control. The Ground Control was housed in the OES (Orbital Environmental Simulator) chamber in the Spaceflight Life Sciences Laboratory (SLSL) at Kennedy Space Center (KSC). The Ground Control was initiated with a precise 24 hour delay to enable the OES environment to be programmed with the environmental profile taken from telemetry of the Space Shuttle. Nominally, the Ground Control BRIC hardware and samples experienced the same external environment profile as the hardware and samples on the Space Shuttle. Environmental parameters that are controlled on the OES and made identical to flight are cabin temperature, humidity and CO2 concentration.

treatment_protocol: The BRIC-16 experiment was turned over to payload engineers in the SLSL at KSC 24 hours before the scheduled launch time. The payload launched on STS-131 on April 5th, 2010, at 06:25, and achieved orbit approximately eight minutes later. The biology was in orbit 12 days and 21 hours (04/05/10 06:25:28 to 04/18/10 03:37:28) before being fixed on orbit with RNAlater. The orbiter landed on April 20th (04/20/10 07:37:28) and the biology was returned to the PIs at SLSL approximately 7 hours later.

value: Etiolated seedlings

value: germinated seeds

value: 7 days old


title: GROUND CONTROL BRIC A PDFU-5 319 seedlings

source_name: solid media plates; BRIC-16; OES chamber: BRIC-A PDFU-5

value: fixed sample


title: genomic DNA from formalin fixed paraffin embedded normal kidney 1

description: SAMPLE 1

source_name: normal kidney 1

value: matched trio 1

value: matched pair 1

value: M

value: unknown


title: FLIGHT  BRIC A PDFU-5 099 seedlings

source_name: solid media plates; BRIC-16; middeck : BRIC-A PDFU-5

value: in-flight fixed sample


title: GROUND BRIC G PDFU-3 334 tissue

source_name: solid media plates; BRIC-16; OES chamber: BRIC-G PDFU-3

value: Tissue culture cells

value: derived from hypocotyls


title: FLIGHT TAGES 2B plate6 ROOTS Rep2

value: roots

value: seeds germinated with light stimulus 12 days into the flight


title: GROUND BRIC B PDFU-5 318 tissue

source_name: solid media plates; BRIC-16; OES chamber: BRIC-B PDFU-5


title: FLIGHT  BRIC A PDFU-4 135 seedlings

source_name: solid media plates; BRIC-16; middeck : BRIC-A PDFU-4