title: ND 06229 Cm

status: Public on Feb 04 2010

city: Syracuse

first: Frank

middle: A

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: One of 16 samples in series

hyb_protocol: Standard GeneChip Expression Analysis Technical Manual 701021 rev 5

source_name: Lymphoblasts

label_protocol: Standard One-Cycle cRNA IVT method (Affymetrix Expression Analysis Technical Manual 701021 rev 5)

growth_protocol: RPMI 1640

extract_protocol: RNeasy (QIagen)

tag: coriell catalog id

tag: disease state

value: control

tag: sample type

value: B lymphocytes from peripheral blood were transformed with EBV


title: ND 02852 Pm

type: RNA

state: NY

country: USA

description: One of 16 samples in series

scan_protocol: Standard GeneChip Expression Analysis Technical Manual 701021 rev 5

label: biotin

molecule: total RNA

organism: Homo sapiens

value: Parkinson's disease

tag: gender

value: male


title: ND 04158 Pf

description: One of 16 samples in series

value: female


title: ND 00397 Cf

description: One of 16 samples in series


title: ND 03432 Pf

description: One of 16 samples in series


title: ND 00051 Cf

description: One of 16 samples in series


title: ND 03367 Cm

description: One of 16 samples in series


title: ND 06449 Pm

description: One of 16 samples in series


title: ND 00268 Cm

description: One of 16 samples in series


title: ND 00259 Cf

description: One of 16 samples in series


title: ND 01173 Pf

description: One of 16 samples in series


title: ND 01737 Pf

description: One of 16 samples in series


title: ND 04424 Pm

description: One of 16 samples in series


title: ND 00151 Cf

description: One of 16 samples in series


title: ND 02579 Pm

description: One of 16 samples in series


title: 3805 GPi Cm

description: One of 20 samples in series

source_name: Globus pallidus interna

label_protocol: WT-Ovation (Nugen)

extract_protocol: RNeasy Mini (Qiagen)

tag: tissue

value: Globus pallidus interna


title: 3780 GPi Pf

description: One of 20 samples in series


title: ND 00022 Cm

description: One of 16 samples in series


title: 3790 GPi Pf

description: One of 20 samples in series


title: 3746 GPi Pf

description: One of 20 samples in series


title: 3880 GPi Pm

description: One of 20 samples in series


title: 3885 GPi Pm

description: One of 20 samples in series


title: 3750 GPi Cm

description: One of 20 samples in series


title: 3643 GPi Pm

description: One of 20 samples in series


title: 3795 GPi Cf

description: One of 20 samples in series


title: 3740 GPi Cf

description: One of 20 samples in series


title: 3641 GPi Cm

description: One of 20 samples in series


title: 3733 GPi Cf

description: One of 20 samples in series


title: 3698 GPi Cf

description: One of 20 samples in series


title: 3769 GPi Pm

description: One of 20 samples in series


title: 3083 GPi Pm

description: One of 20 samples in series


title: 3856 GPi Pm

description: One of 20 samples in series


title: 3642 GPi Pf

description: One of 20 samples in series


title: PD-5138-SNc

description: One of 18 samples in series

data_processing: MAS 5

source_name: Substantia Nigra pars compacta

label_protocol: WT Ovation (Nugen)

value: Substantia Nigra pars compacta


title: Peripheral T-Cell lymphoma, unspecified 30

status: Public on Feb 08 2010

city: omaha

first: Javeed

last: Iqbal

state: NE

address: 40th street

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description:
Gene expression data from PTCL pre-treated biopsy.
CLN-122

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Scanning Protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Further analysis (e.g., clustering, classification) was carried using BRB-ArrayTools version (3.7.0).

source_name: Pre-treated fresh frozen biopsy, PTCL

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All the tissues used in the study were fresh frozen and stored below -70 degree C.

extract_protocol: Total RNA was extracted with Trizol and further purified with RNeasy Mini Columns (Qiagen, Valencia, CA) before aliquots were run in agarose gel electrophoresis and measured by spectrophotometer at 260 and 280 nm to assess the quality of the RNA.

treatment_protocol: The cryopreserved tissues from pre-treated biopsies obtained at the time of diagnosis had been stored in liquid nitrogen or -80 degree C before total RNA extraction.

tag: cell type

value: PTCL

tag: age


title: PD-2515p-SNc

description: One of 18 samples in series


title: PD-3769p-SNc

description: One of 18 samples in series


title: PD-5476-SNc

description: One of 18 samples in series


title: PD-3790p-SNc

description: One of 18 samples in series


title: PD-3803p-SNc

description: One of 18 samples in series


title: PD-2525-SNc

description: One of 18 samples in series


title: C-5220-SNc

description: One of 18 samples in series


title: 3777 GPi Cm

description: One of 20 samples in series


title: PD-1401-SNc

description: One of 18 samples in series


title: C-2829-SNc

description: One of 18 samples in series


title: C-1074p-SNc

description: One of 18 samples in series


title: C-3132p-SNc

description: One of 18 samples in series


title: C-1271p-SNc

description: One of 18 samples in series


title: PD-1647-SNc

description: One of 18 samples in series


title: C-3603-SNc

description: One of 18 samples in series


title: C-3543-SNc

description: One of 18 samples in series


title: C-3397-SNc

description: One of 18 samples in series


title: 3632 GPi Cm

description: One of 20 samples in series


title: PD-1364-SNc

description: One of 18 samples in series


title: patient 042, cancer, homogenized

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description: Gene expression profile of surgically resected material

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.

source_name: surgically resected material

label_protocol: cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.

tag: metastasis

value: cancer, homogenized


title: patient 032, cancer, homogenized


title: patient 044, cancer, homogenized


title: patient 033, cancer, homogenized


title: patient 047, cancer, homogenized


title: patient 047, normal, homogenized

value: normal, homogenized


title: patient 035, cancer, homogenized

value: metastasis


title: patient 031, cancer, homogenized


title: patient 041, cancer, homogenized

value: metastatic recurrence


title: patient 038, cancer, homogenized


title: patient 006, cancer, homogenized


title: patient 030, cancer, homogenized


title: patient 011, cancer, homogenized


title: patient 024, cancer, homogenized


title: patient 027, cancer, homogenized


title: patient 036, cancer, homogenized


title: patient 045, cancer, homogenized


title: patient 028, cancer, homogenized


title: patient 044, normal, homogenized


title: patient 035, normal, homogenized


title: patient 042, normal, homogenized


title: patient 041, normal, homogenized


title: patient 038, normal, homogenized


title: patient 045, normal, homogenized


title: patient 036, normal, homogenized


title: patient 033, normal, homogenized


title: 3637 GPi Cm

description: One of 20 samples in series


title: patient 032, normal, homogenized


title: patient 031, normal, homogenized


title: patient 030, normal, homogenized


title: patient 011, normal, homogenized


title: patient 006, normal, homogenized


title: patient 090, cancer, LCM

value: cancer, LCM


title: patient 024, normal, homogenized


title: patient 059, cancer, LCM


title: patient 086, cancer, LCM


title: patient 084, cancer, LCM


title: patient 027, normal, homogenized


title: patient 028, normal, homogenized


title: patient 064, cancer, LCM


title: patient 096, cancer, LCM


title: patient 035, cancer, LCM


title: patient 042, cancer, LCM


title: patient 027, cancer, LCM


title: patient 149, cancer, LCM


title: patient 019, cancer, LCM


title: patient 079, cancer, LCM


title: patient 045, cancer, LCM


title: patient 141, cancer, LCM


title: patient 140, cancer, LCM


title: patient 133, cancer, LCM


title: patient 146, cancer, LCM


title: patient 129, cancer, LCM


title: patient 032, cancer, LCM


title: patient 106, cancer, LCM


title: patient 121, cancer, LCM


title: patient 130, cancer, LCM


title: patient 131, cancer, LCM


title: patient 083, cancer, LCM


title: patient 081, cancer, LCM


title: patient 078, cancer, LCM


title: patient 077, cancer, LCM


title: patient 034, cancer, LCM


title: patient 053, cancer, LCM


title: patient 057, cancer, LCM


title: patient 046, cancer, LCM


title: patient 038, cancer, LCM


title: patient 033, cancer, LCM


title: patient 037, cancer, LCM


title: patient 025, cancer, LCM


title: patient 024, cancer, LCM


title: patient 048, cancer, LCM


title: patient 036, cancer, LCM


title: patient 015, cancer, LCM


title: patient 156, cancer, LCM


title: patient 073, cancer, LCM


title: patient 155, cancer, LCM


title: patient 022, cancer, LCM


title: patient 154, cancer, LCM


title: patient 152, cancer, LCM


title: patient 148, cancer, LCM


title: patient 150, cancer, LCM


title: patient 153, cancer, LCM


title: patient 145, cancer, LCM


title: patient 143, cancer, LCM


title: patient 142, cancer, LCM


title: patient 139, cancer, LCM


title: patient 144, cancer, LCM


title: patient 138, cancer, LCM


title: patient 128, cancer, LCM


title: patient 134, cancer, LCM


title: patient 147, cancer, LCM


title: patient 123, cancer, LCM


title: patient 118, cancer, LCM


title: patient 127, cancer, LCM


title: patient 135, cancer, LCM


title: patient 011, cancer, LCM


title: patient 125, cancer, LCM


title: patient 136, cancer, LCM


title: patient 124, cancer, LCM


title: patient 119, cancer, LCM


title: patient 117, cancer, LCM


title: patient 116, cancer, LCM


title: patient 104, cancer, LCM


title: patient 111, cancer, LCM


title: patient 107, cancer, LCM


title: patient 101, cancer, LCM


title: patient 115, cancer, LCM


title: TSC 4

status: Public on Feb 02 2010

city: Amsterdam

first: Floyd

last: Wittink

address: Kruislaan 318

department: MAD

country: Netherlands

institute: Universiteit van Amsterdam

description: Gene expression data from cortical tuber of TSC-diagnosed patients.

hyb_protocol: Following fragmentation, 10 ug cRNA were hybridized for 16 hours at 45C on GeneChip Human Genome U133 Plus 2.0 Array. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 G7 scanner.

data_processing: The data were analyzed with MicroArray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Robust Multi-Array Average (RMA) analysis as normalization method. The trimmed mean target intensity of each array was set arbitrarily to 100.

source_name: cortical tuber, TSC

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical manual, 2005  Affymetrix).

growth_protocol: Cortical tuber specimens were obtained during epilepsy surgery from 4 patients diagnosed for TSC with perituberal tissue as surgical control samples.

extract_protocol: Trizol LS extraction was perfomed according to manufacturer's instructions.

treatment_protocol: Fixed in liquid nitrogen.

value: surgical

tag: disease

value: tuberous sclerosis complex

value: brain

tag: sub-brain

value: cortical tuber


title: patient 102, cancer, LCM


title: patient 113, cancer, LCM


title: patient 103, cancer, LCM


title: patient 100, cancer, LCM


title: TSC 3


title: surgical 2

description: Gene expression data from perituberal tissue of affected patients.

source_name: perituberal tissue, TSC

value: perituberal tissue

tag: patient

value: TSC 2


title: TSC 1

value: TSC 1


title: control 5

description: Gene expression data from cortex of unaffected patients.

source_name: cortex, unaffected

value: autopsy

value: unaffected

value: cortex


title: control 2


title: surgical 1


title: control 4


title: control 3


title: Swiss22_Non-adipogenic_rep2

status: Public on Feb 01 2010

city: Boston

first: Rana

middle: K

last: Gupta

state: MA

address: 44 Binney Street CLSB 11119

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: clonal cell line derived from parental Swiss 3T3 fibroblasts

hyb_protocol: The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45°C.  The chip was then transferred to a fluidics instrument for washes to remove unbound cRNA. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were added using biotinylated anti-streptavidin antibody and SAPE.

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

data_processing: Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values

organism: Mus musculus

source_name: proliferating Swiss 22 fibroblasts

label_protocol: cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).

growth_protocol: All cells were propagated in DMEM containing 10% bovine serum

extract_protocol: Trizol (Invitrogen) extraction, followed by purification using Qiagen RNeasy column

treatment_protocol: Cells used in experiment were grown in DMEM containing 10% bovine serum (non-differentiating conditions) and harvested prior to growth arrest

tag: cell line

tag: stage

value: immortalized embryonic fibroblast


title: Swiss3_Non-adipogenic_rep3

source_name: proliferating Swiss 3 fibroblasts


title: Swiss5_Non-adipogenic_rep3

source_name: proliferating Swiss 5 fibroblasts


title: Swiss19_Preadipocyte_rep1

source_name: proliferating Swiss 19 fibroblasts


title: minicircle-derived iPSC subclone 1

city: Stanford

first: Kitchener

middle: D.

last: Wilson

state: CA

address: S140 Grant Bldg

institute: Stanford University

hyb_protocol: Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.

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

data_processing:
The data were analyzed with AGCC (Affymetrix Genechip Command Console).
Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.

source_name: iPSC derived from hASC using minicircle reprogramming vector

label_protocol: Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.

growth_protocol: Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes  with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen)

tag: developmental stage

value: undifferentiated


title: Swiss22_Non-adipogenic_rep3


title: Swiss22_Non-adipogenic_rep1


title: Swiss9_Preadipocyte_rep2

source_name: proliferating Swiss 9 fibroblasts


title: Swiss19_Preadipocyte_rep2


title: Swiss5_Non-adipogenic_rep1


title: minicircle-derived iPSC subclone 2

value: iPSC derived from hASC using minicircle reprogramming vector


title: Swiss8_Preadipocyte_rep3

source_name: proliferating Swiss 8 fibroblasts


title: FrontalC_HIV_3

city: La Jolla

first: Erick

middle: T

last: Tatro

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California San Diego

description: Gene expression data from frontal cortex of patient CC147

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction per manufacturer's protocols.

value: Brain, frontal cortex

tag: latest mdd visit

value: NO

tag: hiv status

value: HIV+

value: Male

tag: pmi


title: Swiss5_Non-adipogenic_rep2


title: Swiss9_Preadipocyte_rep1


title: Swiss9_Preadipocyte_rep3


title: FrontalC_HIVMDD_3

description: Gene expression data from frontal cortex of patient CC207


title: Swiss3_Non-adipogenic_rep1


title: Swiss8_Preadipocyte_rep2


title: Swiss3_Non-adipogenic_rep2


title: FrontalC_HIV_1

description: Gene expression data from frontal cortex of patient CC103


title: FrontalC_HIV_2

description: Gene expression data from frontal cortex of patient CC141


title: Swiss2_Preadipocyte_rep3

source_name: proliferating Swiss 2 fibroblasts


title: Swiss8_Preadipocyte_rep1


title: FrontalC_HIVMDD_2

description: Gene expression data from frontal cortex of patient CA143

value: 12 mo


title: FrontalC_HIVMDD_1

description: Gene expression data from frontal cortex of patient CA110

value: 6 mo


title: FrontalC_HIV_4

description: Gene expression data from frontal cortex of patient CA146


title: Swiss2_Preadipocyte_rep2


title: FrontalC_HIVMDD_4

description: Gene expression data from frontal cortex of patient CA236


title: Swiss2_Preadipocyte_rep1


title: minicircle-derived iPSC subclone 3


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 48 hours post infection #1

city: Galveston

first: Tomoki

last: Yoshikawa

state: TX

address: 301 University BLVD

institute: University of Texas Medical Branch

hyb_protocol: According to standard Affymetrix protocol.

data_processing:
For comparison across different arrays, the data for each array were normalized by Robust Multi-chip Average (RMA) using Spotfire DecisionSite (Spotfire, Inc., Somerville, MA) and GeneSifter (VizX Labs, Seattle, WA), and probe sets with expression values below the level of background noise (as determined by detection p value) were disregarded in further analyses. Results of these analyses indicated that the RNA samples used and the data generated after the normalization were of sufficiently high quality for subsequent analyses (data not shown).
For statistical purposes, all 27 arrays were analyzed as nine separate groups (mock-, SARS-CoV-, and DHOV-infected cells at 12-, 24-, and 48-hrs). The GeneSifter-based normalization was followed by pairwise comparisons of average group values and Student's t test with Benjamini and Hochberg correction. Criteria for selection of genes were as follows: All pairwise comparisons for one group versus another (e.g., mock-versus SARS-CoV-versus DHOV-infected cells at 12 hr) were expected to be at least 1.5-fold and at least 50% greater than the fold-change observed between any two controls (e.g., mock-infected replicate 1 versus mock-infected replicate 2 at 12 hr). Exceptions were made for those probe sets that were significantly altered (fold change ≥ 1.5, p value < 0.05) at an earlier or later time point, with a magnitude that exceeded the observed fold-change between replicate controls by at least 50%. This allowed for more accurate identification of those genes that increased or decreased in expression levels over time but that fell below the stringent statistical criteria at the lower transcriptional levels. In order to ensure that results obtained from comparison of SARS-CoV- and DHOV-infected cells were specific to infection, any probe set determined to be significantly different in hybridization signal based on the above criteria was further expected to have been detected as altered (fold-change ≥ 1.5 and at least 50% greater in magnitude than any change observed between control samples, p value ≤ 0.05) between mock-infected and SARS- or DHOV-infected cells. In other words, any gene with an expression level that differed between cells infected with the two different viruses was considered as irrelevant if not altered by either virus, as determined by comparison to mock-infected control cells at that same time point.

label: Biotin

extract_protocol: total RNA extraction by using an RNAqueous-4PCR kit and following the protocol recommended by the manufacturer (Ambion, Austin, TX)

value: Bronchial  epithelial cell line 2B4

tag: infection

value: SARS-CoV-infected (MOI=0.1)

tag: time

value: 48 hours post infection


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 48 hours post infection #２

scan_protocol: According to standard Affymetrix protocol.

value: DOHV-infected (MOI=0.1)


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 48 hours post infection #1

label_protocol: According to standard Affymetrix protocol.


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 48 hours post infection #3


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 24 hours post infection #3

value: 24 hours post infection


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 24 hours post infection #2


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #1

value: 12 hours post infection


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 24 hours post infection #2


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 24 hours post infection #1


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 24 hours post infection #3


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 48 hours post infection #3


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #3


title: DOHV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #2


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #3


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #1


title: Mock-infected Calu-3 subclone 2B4 at 48 hours post infection #1

value: Mock-infected


title: Mock-infected Calu-3 subclone 2B4 at 24 hours post infection #3


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 24 hours post infection #1


title: Mock-infected Calu-3 subclone 2B4 at 48 hours post infection #2


title: Mock-infected Calu-3 subclone 2B4 at 48 hours post infection #3


title: Mock-infected Calu-3 subclone 2B4 at 24 hours post infection #1


title: Mock-infected Calu-3 subclone 2B4 at 12 hours post infection #3


title: Mock-infected Calu-3 subclone 2B4 at 24 hours post infection #2


title: Mock-infected Calu-3 subclone 2B4 at 12 hours post infection #2


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 12 hours post infection #2


title: WT mouse, 24 months of age (rlcstriat1)

status: Public on Jan 31 2010

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

hyb_protocol: According to the manufacturer's instructions.

data_processing: All CEL files in the series were processed using RMA in R using justRMA with default parameters.

label_protocol: RNA was prepared according to the manufacturer.s two-cycle target labeling procedure (Affymetrix Inc.) with a starting amount 25 ng total RNA per sample.

extract_protocol: Striatal tissue was collected from 12 and 24 month old YAC128 mice and wildtype littermates. Animals were anaesthetized using Avertine and tissue was collected in RNAlater (Ambion) and stored at -80 prior to RNA isolation. Homogenization of tissue was performed using a Fastprep Homogenizer (ThermoScientific). Total RNA from mouse striatum was extracted using the Qiagen RNeasy mini kit and eluted in 30 microliters RNase free water according to manufacturer's instructions. Total RNA was quantified using the Nanodrop spectrophotometer (ThermoScientific) and the integrity of the total RNA was determined electrophoretically on the RNA Nano Assay Chip run on the Bioanalyzer 2100 (Agilent Tech).

value: 24 months

value: whole striatum

tag: genotype

value: WT


title: YAC128 mouse, 24 months of age (rlcstriat4)

scan_protocol: According to the manufacturer's instructions.


title: Mock-infected Calu-3 subclone 2B4 at 12 hours post infection #1


title: YAC128 mouse, 24 months of age (rlcstriat2)


title: YAC128 mouse, 24 months of age (rlcstriat3)


title: WT mouse, 24 months of age (rlcstriat5)


title: WT mouse, 12 months of age (S8)

value: 12 months


title: YAC128 mouse, 24 months of age (rlcstriat7)


title: WT mouse, 24 months of age (rlcstriat8)


title: WT mouse, 12 months of age (S7)


title: YAC128 mouse, 24 months of age (rlcstriat6)


title: WT mouse, 24 months of age (rlcstriat10)


title: YAC128 mouse, 12 months of age (S3bis)


title: WT mouse, 12 months of age (S5)


title: WT mouse, 12 months of age (S6)


title: YAC128 mouse, 12 months of age (S4)


title: YAC128 mouse, 12 months of age (S1bis)


title: YAC128 mouse, 12 months of age (S2)


title: YAC128 mouse, 24 months of age (rlcstriat9)


title: Saline, D2 biological rep 2

city: blacksburg

first: Saroj

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

description: Gene expression data from saline-pretreated mouse liver 48 hours after infection

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Staining with R-phycoerythrin-streptavidin (Molecular Probes) was followed by antibody amplification with a biotinylated streptavidin antibody (Vector Laboratories).

scan_protocol: Scanning was carried out by using the 7G scanner (Hewlett-Packard).

data_processing: All analysis was done in R statistical environment (version 2.8.1). Data were read with bioconductor package affy (version 1.20.2) and normalized by gcRMA method with package gcrma (version 2.14.1). The probe sets were further selected in an unbiased manner by removing those associated with a very low degree of variability (inter-quartile range less than 0.5) across all the samples. This reduced the number of probe sets from 45101 to 19535. Statistical analysis was performed using the package limma (version 2.16.4) by applying a linear model to the expression measurement (log intensities) for each gene. For each comparison of interest, the genes were assigned p-values after controlling for false discovery rate. For assessment of differential expression, empirical Bayes method was applied. A cutoff of p<0.05 and >2-fold change was used as the criterion for whether or not a gene was significantly modulated by treatment.

source_name: Saline pretreatment on day -2; Ft LVS inoculation on day 0; sacrificed on day 2

label_protocol: Standard Affy metrix labelling

growth_protocol: Francisella tularensis LVS was streaked onto plates consisting of Mueller Hinton Broth  (Becton Dickinson Microbiology Systems, Sparks, MD) supplemented with IsoVitaleX  (Becton Dickinson, Cockeysville, MD), 0.1% glucose and 0.025% Ferric PPi (Sigma 10% defibrinated sheep blood.  These plates were incubated overnight.  The next day, 5 ml of liquid Mueller Hinton Broth supplemented with IsoVitaleX, 0.1% glucose and 0.025% Ferric PPi s inoculated with fresh bacteria.  The inoculated medium was incubated overnight with shaking.  The following day 2 ml of this overnight culture was transferred to 30 ml of fresh medium and this culture was incubated with shaking until it reached 0.4-0.8 OD600 nm.  This culture is used to prepare frozen Francisella tularensis stocks.  Frozen stocks are stored in aliquots at –70C.  Thawed bacteria are quantified by plating serial dilutions.  Frozen stocks are used a single time.  Mice were injected with Francisella tularensis LVS taken from a frozen stock that was diluted in sterile saline.

extract_protocol: Liver tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA).  After homogenization, total RNA was extracted and purified using the RNAesy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.

treatment_protocol: Female 8 week old  C57BL/6J (Jackson Labs, Bar Harbor, ME) were i.p. injected with either 100 ng of Ft LVS LPS or an equivalent volume of saline 48 hours prior to Ft LVS challenge.  On the day of challenge, 3 saline- and 3 Ft LVS LPS-pretreated animals were sacrificed (uninfected controls), while all remaining mice were challenged i.p. with ~4-5  105 Ft LVS.  Ft LVS-challenged mice were sacrificed (in groups of 3) at 24 and 48 hours post-infection.  This entire experiment was performed 3 times.  Within each individual experiment, equal amounts of extracted RNA from biological replicate samples were pooled.  RNA from separate experiments was never combined.

value: Liver

tag: strain

value: 8 weeks


title: Saline, D0 biological rep 2

description: Gene expression data from saline-pretreated uninfected mouse liver

source_name: Saline pretreatment on day -2; sacrificed on day 0

tag: tissue


title: LPS, D0 biological rep 3

description: Gene expression data from  LPS-pretreated uninfected mouse liver

source_name: 100 ng Ft LVS LPS pretreatment on day -2; sacrificed on day 0


title: Saline, D0 biological rep 3


title: LPS, D1 biological rep 3

description: Gene expression data from  LPS-pretreated mouse liver 24 hours after infection

source_name: 100 ng Ft LVS LPS pretreatment on day -2; Ft LVS inoculation on day 0; sacrificed on day 1


title: LPS, D1 biological rep 2


title: LPS, D1 biological rep 1

description: Gene expression data from LPS-pretreated mouse liver  24 hours after infection


title: LPS, D0 biological rep 2


title: LPS, D2 biological rep 2

description: Gene expression data from  LPS-pretreated mouse liver 48 hours after infection

source_name: 100 ng Ft LVS LPS pretreatment on day -2; Ft LVS inoculation on day 0; sacrificed on day 2


title: Saline, D2 biological rep 3


title: LPS, D2 biological rep 3


title: Saline, D1 biological rep 2

description: Gene expression data from saline-pretreated mouse liver 24 hours after infection

source_name: Saline pretreatment on day -2; Ft LVS inoculation on day 0; sacrificed on day 1


title: LPS, D0 biological rep 1

description: Gene expression data from LPS-pretreated uninfected mouse liver


title: Saline, D2 biological rep 1


title: LPS, D2 biological rep 1


title: Saline, D0 biological rep 1


title: Saline, D1 biological rep 3


title: Relative gene expression value from wildtype 3 retinas at birth

status: Public on Jan 29 2010

first: Frederic

middle: Emile

last: Bienvenu

address: 1 Jimmy Fund Way

description:
The dataset was analyzed for statistically significant differential expression using the online NIA Array Analysis Tool REF (http://lgsun.grc.nia.nih.gov/ANOVA/).
Probesets were tested for differential expression using the following settings:
Threshold z-value to remove outliers: 10000
Error Model: Max(Average, Bayesian)
Error variance averaging window: 200
Proportion of highest error variances to be removed: 0.01
Bayesian degrees of freedom: 5
FDR threshold: 0.10
Probesets that did not map to genes for which we had cyclin D1 binding data and probesets that mapped to multiple genes were excluded.  In the cases where multiple probesets map to one gene, the probeset with the largest differential expression was retained.

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix GeneChip Mouse Expression Set 430 2.0 arrays at the Microarray Core Facility (Dana-Farber Cancer Institute).

scan_protocol: Arrays were stained, scanned, and quantified according to standard Affymetrix protocols. Data were annotated according the NetAffx database (http://www.affymetrix.com/analysis/index.affx) as of March, 2006.

data_processing: Quantile normalization was performed, and expression data were ranked within each sample. Within each sample, each probeset was given a signal value of the average signal of the probesets of that rank, across the dataset.

source_name: Pool of Wildtype 3 neonates retinas

label_protocol: Biotinylated antisense cRNA probes were prepared according to the Affymetrix standard labeling protocol (one amplification round).

growth_protocol: Normal mouse breeding in state-of-the-art mouse facility.

extract_protocol: Qiagen RNeasy mini extraction kit

treatment_protocol: Retina extraction in 1x PBS under binoccular

tag: Relative gene expression value from wildtype retinas at birth


title: Relative gene expression value from Cyclin D1 -/- 2 retinas at birth

source_name: Pool of Cyclin D1 -/- 2 neonates retinas

tag: C57BL/6 129SV Mixed genetic background


title: E161K heart, technical replicate B Mas5

status: Public on Jan 30 2010

city: Chicago

first: Stephanie

last: Mewborn

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: University of Chicago

description: Gene expression data from left ventricle of human heart with E161K LMNA mutation

hyb_protocol: cDNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array.  Microarrays were washed, stained, and scanned according to standard procedures.

scan_protocol: Standard Affymetrix protocols were used.

data_processing: Robust Microarray Analysis (RMA) and Affymetrix Microarray Suite 5.0 (Mas5) background correction and normalization were applied independently to the raw data sets using the Bioconductor open source software.  RankProducts (RP) was used to rank the probesets by fold change.

source_name: left ventricle patient with E161K LMNA mutation

label_protocol: cDNA was synthesized from 10 µg of total RNA using the Superscript Choice System (Invitrogen) and labeled using the BioArray High Yield RNA Transcript Labeling kit (Enzo Diagnostics).

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

tag: gender

value: male

value: adult

tag: organ

value: heart

value: left ventricle

value: LMNA E161K

tag: data analysis algorithm


title: Relative gene expression value from wildtype 1 retinas at birth

source_name: Pool of Wildtype 1 neonates retinas


title: ISC Control heart, technical replicate B Mas5

description: Gene expression data from left ventricle of human heart with no LMNA mutation

source_name: left ventricle patient with ischemic cardiomyopathy

value: LMNA wt


title: Arabidopsis bWS-2

status: Public on Jan 27 2010

city: Davis

first: John

middle: J

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

description:
Laser capture microdissected (LCM) whole seeds at the bending cotyledon stage, biological replicate 2
Serial sections of whole seeds collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

hyb_protocol: Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.

organism: Arabidopsis thaliana

source_name: Arabidopsis bending cotyledon whole seeds captured by LCM

label_protocol: 5 to 6 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50%-70% relative humidity.

extract_protocol: Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.

treatment_protocol: Siliques containing bending cotyledon stage seeds were collected from 38-46 day old plants. Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin. Microdissection of compartments was carried out on sections using a Leica LMD6000 system.

tag: genome/variation

tag: cell type

value: whole seeds

value: bending cotyledon stage


title: Relative gene expression value from Cyclin D1 -/- 1 retinas at birth

source_name: Pool of Cyclin D1 -/- 1 neonates retinas


title: E161K heart, technical replicate A Mas5


title: Saline, D1 biological rep 1

tag: age


title: SARS-CoV-infected (MOI=0.1) Calu-3 subclone 2B4 at 48 hours post infection #2

tag: cell line

value: Bronchial  epithelial cell line 2B4

value: SARS-CoV-infected (MOI=0.1)

value: 48 hours post infection


title: ISC Control heart, technical replicate A Mas5

tag: developmental stage


title: Relative gene expression value from Cyclin D1 -/- 3 retinas at birth

source_name: Pool of Cyclin D1 -/- 3 neonates retinas


title: Relative gene expression value from wildtype 2 retinas at birth

source_name: Pool of Wildtype 2 neonates retinas


title: Arabidopsis bPEN1

description:
Laser capture microdissected (LCM) peripherial endosperm at the bending cotyledon stage, biological replicate 1
Peripherial endosperm collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis bending cotyledon stage peripherial endosperm captured by LCM

value: peripherial endosperm


title: Arabidopsis bWS-1

description:
Laser capture microdissected (LCM) whole seeds at the bending cotyledon stage, biological replicate 1
Serial sections of whole seeds collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.


title: Arabidopsis bCZSC1

description:
Laser capture microdissected (LCM) chalazal seed coat at the bending cotyledon stage, biological replicate 1
Chalazal seed coat collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis bending cotyledon stage chalazal seed coat captured by LCM

value: chalazal seed coat


title: Arabidopsis bPEN2

description:
Laser capture microdissected (LCM) peripherial endosperm at the bending cotyledon stage, biological replicate 2
Peripherial endosperm collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.


title: Arabidopsis bEP2

description:
Laser capture microdissected (LCM) embryo proper at the bending cotyledon stage, biological replicate 2
Embryo proper collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis bending cotyledon stage embryo proper captured by LCM

value: embryo proper


title: Arabidopsis bEP1

description:
Laser capture microdissected (LCM) embryo proper at the bending cotyledon stage, biological replicate 1
Embryo proper collected from seeds containing embryo proper with both 100 -140 um long cotyledons bent at an angle relative to the embryo axis and pockets of cellularized endosperm between the cotyledons and chalazal endosperm when examined using the LEICA LMD6000 system for microdissection.


title: Laser capture microdissected (LCM) micropylar endosperm at the linear-cotyledon stage, biological replicate 1

status: Public on Jan 22 2010

description:
Arabidopsis lcMCE1
Whole seeds collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis linear-cotyledon stage micropylar endosperm captured by LCM

label_protocol: 2 to 5 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

treatment_protocol: Siliques between 1.6 and 1.9 cm  long containing linear-cotyledon stage seeds were collected from 38-46 day old plants.  Siliques were sub-divided and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin.  Microdissection of compartments was carried out on sections using a Leica LMD6000 system.


title: poxn homozygous mutant proboscis_rep1

city: Berkeley

first: Peter

last: Cameron

address: GL71 Koshland, UC-Berkeley

institute: UC-Berkeley

hyb_protocol: cRNA was hybridized for 16h at 45oC to Drosophila 2.0 arrays. Affymetrix fluidics station 450 was used for washing and staining.

scan_protocol: Affymetrix scanner 3000 was used to read arrays.

data_processing: data was processed and normalized using GC-RMA

organism: Drosophila melanogaster

source_name: proboscis RNA

label_protocol: Twice amplified biotinylated cRNA was prepared from about 50ng total RNA.

growth_protocol: male flies were reared for 8-18 days post eclosure at room temperature.

treatment_protocol: Proboscises were dissected and homogenized in Trizol in several batches for each biological replicate.

value: homozygous


title: poxn homozygous mutant proboscis_rep3


title: poxn heterozygous mutant proboscis_rep1

value: heterozygous


title: poxn heterozygous mutant proboscis_rep3


title: Laser capture microdissected (LCM) micropylar endosperm at the linear-cotyledon stage, biological replicate 2

description:
Arabidopsis lcMCE2
Whole seeds collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.


title: Arabidopsis gWS1

description:
Laser capture microdissected (LCM) whole seeds at the globular stage, biological replicate 1
Whole seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage whole seeds captured by LCM

label_protocol: 2 to 4 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

treatment_protocol: Siliques with length between 1.1 and 1.4 cm containing globular stage seeds were collected from 38-46 day old plants. Seeds were either dissected out of siliques or left in sub-divided siliques and fixed in 3:1 (v/v) ethanol:acetic acid and embedded in paraffin.  Microdissection of compartments was carried out on 5 or 7 um sections using a Leica LMD6000 system. Compartments were only captured from seeds with globular embryos 24-32 um in diameter, as determined by a medial section through the embryo proper.


title: poxn homozygous mutant proboscis_rep2


title: Arabidopsis gWS2

description:
Laser capture microdissected (LCM) whole seeds at the globular stage, biological replicate 2
Whole seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Laser capture microdissected (LCM) whole seeds at the linear-cotyledon stage, biological replicate 1

description:
Arabidopsis lcWS4
Whole seeds collected from seeds containing linear-cotyledon embryos 175 (+/- 11) microns in length  as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis linear-cotyledon stage whole seeds captured by LCM


title: poxn heterozygous mutant proboscis_rep2


title: dsT3

status: Public on Jan 19 2010

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Gene expression data from early embryonic SL2 cells treated with dTip60-RNAi for 5 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome_2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned in a GeneChip Scanner 3000 with G7 update.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: SL2 cells, treated with dsRNA against Tip60, position 190-807

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual v2, 2004, Affymetrix).

growth_protocol: Cells were cultured at 26°C in InsectExpress Sf9-S2 Medium (PAA). Unless noted otherwise, the medium was supplemented with 10% fetal calf serum (FCS, from PAA).

extract_protocol: Cells were harvested after 5 days and RNA was extracted using the NucleoSpin RNA II kit (Macherey –Nagel)

treatment_protocol: 10^6 SL2 cells were incubated with 10 µg dsRNA in 1 ml serum-free medium with Pen/Strep (50 U/ ml) with agitation at room temperature for 10 min and for 50 min at 26°C without agitation. 2 ml medium with Pen/Strep and FCS to a final concentration of 10% were added.


title: eGFP2.2

description: Gene expression data from early embryonic SL2 cells mock-treated with eGFP-RNAi for 5 days

source_name: SL2 cells, mock-treated with dsRNA against GFP


title: dsT1


title: eGFP3.1


title: Laer, treat with paclobutrazol (PAC), Biological Rep 2

status: Public on Jan 15 2010

city: Norwich

first: Daniel

last: MacLean

address: Colney Lane

department: Bioinformatics

country: United Kingdom

institute: The Sainsbury Laboratory

description: Gene expression data from Arabidopsis leaves treated with paclobutrazol

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis Genome ATH1 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: background corrected using RMA, quantile normalized, values summarised by median-polish

source_name: leaf discs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in SANYO cabinets under short day conditions (8h light, 16h dark), 120μE light intensity.

extract_protocol: RNA was extracted using Qiagen Rneasy plant mini kit according to the manufacturer's instructions.

treatment_protocol: Five weeks old short day grown Arabidopsis leaf discs were used to treat with 100nM flg22 and samples were collected after 1 hour and 2 hour time points. For Alternaria brassicicola, five weeks old plants were drop inoculated with 4x 5µl droplets of Alternaria brassicicola spores (5x105 spores/ml) and samples were collected 3 days post inoculation. Five weeks old plants were infiltrated with Pst DC3000 (2x105cfu/ml) bacteria and samples were collected after 12 hours post infiltration. For methyl jasmonate treatments, five weeks old plants were sprayed with 10µM Methyl Jasmonate solution, covered with plastic bags and samples were collected after one hour.

value: leaf discs


title: Laer, pretreat with GA+JA, Flg22, 2h, Biological Rep 3

description: Gene expression data from Arabidopsis leaves pre-treated with GA+JA and induced with flg22


title: eRNAi1

source_name: SL2 cells, treated with dsRNA against Tip60, position 1321-1618


title: HFA3

source_name: SL2 cells, treated with dsRNA against Tip60, position 603-1116


title: eRNAi2


title: HFA1


title: eGFP2.1


title: Laer, pretreat with GA+JA, Flg22, 0h, Biological Rep 2


title: Laer, pretreat with GA+JA, Flg22, 1h, Biological Rep 1


title: eGFP3.2


title: Laer, pretreat with GA+JA, Flg22, 1h, Biological Rep 3


title: Laer, treat with paclobutrazol (PAC), Biological Rep 3


title: Laer, pretreat with GA+JA, Flg22, 1h, Biological Rep 2


title: Laer, pretreat with GA+JA, Flg22, 0h, Biological Rep 3


title: Laer, pretreat with GA+JA, Flg22, 0h, Biological Rep 1


title: Laer, pretreat with GA, Flg22, 1h, Biological Rep 1

description: Gene expression data from Arabidopsis leaves pre-treated with GA and induced with flg22


title: Laer, pretreat with GA, Flg22, 0h, Biological Rep 1


title: Laer, pretreat with JA, Flg22, 2h, Biological Rep 3

description: Gene expression data from Arabidopsis leaves pre-treated with JA and induced with flg22


title: Laer, pretreat with GA, Flg22, 0h, Biological Rep 2


title: Laer, pretreat with JA, Flg22, 1h, Biological Rep 3


title: Laer, pretreat with JA, Flg22, 2h, Biological Rep 2


title: Laer, pretreat with JA, Flg22, 1h, Biological Rep 1


title: Laer, pretreat with JA, Flg22, 2h, Biological Rep 1


title: Laer, pretreat with JA, Flg22, 1h, Biological Rep 2


title: Laer, pretreat with JA, Flg22, 0h, Biological Rep 1


title: Laer, pretreat with JA, Flg22, 0h, Biological Rep 3


title: penta, Pst DC3000, 12hpi, Biological Rep 2

description: Gene expression data from Arabidopsis leaves infiltrated with Pseudomonas syringae pv tomato DC3000


title: penta, Pst DC3000, 12hpi, Biological Rep 3


title: Laer, Pst DC3000, 12hpi, Biological Rep 3


title: penta, MeJA, 1h, Biological Rep 1

description: Gene expression data from Arabidopsis leaves treated with Methyl Jasmonate


title: gai, MeJA, 1h, Biological Rep 1


title: Laer, Pst DC3000, 12hpi, Biological Rep 2


title: Laer, Pst DC3000, 12hpi, Biological Rep 1


title: penta, MeJA, 1h, Biological Rep 3


title: gai, MeJA, 1h, Biological Rep 2


title: penta, MeJA, 1h, Biological Rep 2


title: Laer, pretreat with water, control, Biological Rep 2

description: Gene expression data from Arabidopsis leaves pre-treated with water


title: penta, Alternaria, 3dpi, Biological Rep 1

description: Gene expression data from Arabidopsis leaves infected with Alternaria brassicicola


title: Laer, MeJA, 1h, Biological Rep 3


title: Laer, MeJA, 1h, Biological Rep 2


title: Laer, MeJA, 1h, Biological Rep 1


title: gai, MeJA, 1h, Biological Rep 3


title: Laer, pretreat with water, control, Biological Rep 3


title: penta, Pst DC3000, 12hpi, Biological Rep 1


title: Laer, Alternaria, 3dpi, Biological Rep 3


title: Laer, Alternaria, 3dpi, Biological Rep 2


title: penta, Alternaria, 3dpi, Biological Rep 2


title: gai, Flg22, 2h, Biological Rep 3

description: Gene expression data from Arabidopsis leaves treated with flg22


title: gai, Flg22, 1h, Biological Rep 2


title: gai, Flg22, 2h, Biological Rep 2


title: gai, Flg22, 1h, Biological Rep 1


title: gai, Control, Biological Rep 2


title: gai, Flg22, 1h, Biological Rep 3


title: gai, Control, Biological Rep 3


title: Laer, Alternaria, 3dpi, Biological Rep 1


title: penta, Flg22, 2h, Biological Rep 1


title: penta, Flg22, 1h, Biological Rep 2


title: penta, Flg22, 1h, Biological Rep 3


title: penta, Flg22, 2h, Biological Rep 3


title: penta, Alternaria, 3dpi, Biological Rep 3


title: penta, Control, Biological Rep 3


title: gai, Flg22, 2h, Biological Rep 1


title: penta, Flg22, 1h, Biological Rep 1


title: penta, Control, Biological Rep 2


title: penta, Control, Biological Rep 1


title: Laer, Flg22+GA, 2h, Biological Rep 2


title: penta, Flg22, 2h, Biological Rep 2


title: Laer, Flg22+GA, 2h, Biological Rep 1


title: Laer, Flg22+GA, 2h, Biological Rep 3


title: gai, Control, Biological Rep 1


title: Laer, Flg22+GA, 1h, Biological Rep 3


title: Laer, Flg22+GA, 1h, Biological Rep 2


title: shRB-B (Senescent)  E2

city: Cold Spring Harbor

first: Agustin

last: Chicas

address: One Bungtown Road

institute: Memorial Sloan Kettering

description: Senescent cells expressing shRNA targeting RB replicate 2, experiment 2

hyb_protocol: Hybridization was as described in Expression Analysis Technical Manual Affymetrix P/N 702232 Rev 2, (16 hours, 45 degress at 60 rpm), the Wash and Stain Protocol was as described in FS450_0004 using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Scanning was performed using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with the gc-RMA (Robust Multi-Array Averaging with GC content correction) method of BioConductor R package to subtract background normalize intensities and summarize gene expression level.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: IMR90 cells were grown in 10% FBS DMEM media unless otherwise stated

extract_protocol: RNA was extracted using the RNAeasy Mini Kit from Quiegen accordingtheto the manufacturer's instructions.

tag: growth state

value: ras-induced senescence


title: shp107-B (Senescent)

description: Senescent cells expressing shRNA targeting p107 replicate 2


title: Growing A E2

description: Growing cells expressing a vector control replicate 1, experiment 2

value: Growing


title: shRB-A (senescent) E2

description: Senescent cells expressing shRNA targeting RB  replicate 1, experiment 2


title: shp130-B (Senescent)

description: Senescent cells expressing shRNA targeting p130 replicate 2


title: shp130-A (Senescent)

description: Senescent cells expressing shRNA targeting p130 replicate 1


title: Senescent B  E2

description: Senescent cells expressing a vector control replicate 2, experiment 2


title: shp107-A (Senescent)

description: Senescent cells expressing shRNA targeting p107 replicate 1


title: shRB-B (Senescent)

description: Senescent cells expressing shRNA targeting RB replicate 2


title: Growing B E2

description: Growing cells expressing a vector control replicate 2, experiment 2


title: Senescent A  E2

description: Senescent cells expressing a vector control replicate 1, experiment 2


title: Laer, GA, 2h, Biological Rep 1


title: Laer, GA, 2h, Biological Rep 3


title: Laer, Flg22+GA, 1h, Biological Rep 1


title: Laer, GA, 1h, Biological Rep 3


title: Laer, GA, 2h, Biological Rep 2


title: shRB-A (Senescent)

description: Senescent cells expressing shRNA targeting RB replicate 1


title: MLP-B (Senescent)

description: Senescent cells expressing a vector control replicate 2


title: shp130-B (Confluent)

description: Quiescent cells expressing shRNA targeting p130 replicate 2

value: Confluent quiescent


title: shp107-B (Confluent)

description: Quiescent cells expressing shRNA targeting p107 replicate 2


title: Laer, Flg22(Agrobacterium), 2h, Biological Rep 2


title: Laer, GA, 1h, Biological Rep 2


title: MLP-A (Senescent)

description: Senescent cells expressing a vector control replicate 1


title: Laer, GA, 1h, Biological Rep 1

description: Gene expression data from Arabidopsis leaves treated with flg22


title: Laer, Flg22, 2h, Biological Rep 2


title: Laer, Flg22, 2h, Biological Rep 3


title: shRB-A (Confluent)

description: Quiescent cells expressing shRNA targeting RB replicate 1


title: Laer, Flg22(Agrobacterium), 1h, Biological Rep 2


title: shRB-B (Confluent)

description: Quiescent cells expressing shRNA targeting RB replicate 2


title: shp130-A (Confluent)

description: Quiescent cells expressing shRNA targeting p130 replicate 1


title: Laer, Flg22(Agrobacterium), 2h, Biological Rep 1


title: shp130-B  (0.1% FBS)

source_name: Quiescent cells expressing shRNA targeting p130

value: Low serum quiescence


title: shp107-A   (0.1% FBS)

description: Quiescent cells expressing shRNA targeting p107 replicate 1


title: Laer, Flg22, 2h, Biological Rep 1


title: Laer, Flg22(Agrobacterium), 1h, Biological Rep 1


title: Laer, Flg22(Agrobacterium), 1h, Biological Rep 3


title: shp107-A (Confluent)

source_name: Quiescent cells expressing shRNA targeting p107


title: MLP-B  (Confluent)

description: Quiescent cells expressing a vector control replicate 2


title: shp130-A   (0.1% FBS)


title: Laer, Flg22, 1h, Biological Rep 3


title: MLP-A (Confluent)

description: Quiescent cells expressing a vector control replicate 1


title: shp107-B  (0.1% FBS)


title: shRB-B  (0.1% FBS)

source_name: Quiescent cells expressing shRNA targeting RB


title: Laer, Flg22, 1h, Biological Rep 2


title: shRB-A  (0.1% FBS)


title: Laer, Control, Biological Rep 3


title: Laer, Control, Biological Rep 1


title: Laer, Flg22, 1h, Biological Rep 1


title: MLP-A (0.1% FBS)

source_name: Quiescent cells expressing a vector control


title: shp130-A  (Growing)

description: Growing cells expressing shRNA targeting p130 replicate 1


title: shp130-B   (Growing)

description: Growing cells expressing shRNA targeting p130 replicate 2


title: shp107-A  (Growing)

description: Growing cells expressing shRNA targeting p107 replicate 1


title: MLP-B  (0.1% FBS)


title: shp107-B  (Growing)

description: Growing cells expressing shRNA targeting p107 replicate 2


title: shRB-B  (Growing)

description: Growing cells expressing shRNA targeting RB replicate 2


title: shRB-A  (Growing)

description: Growing cells expressing shRNA targeting RB replicate 1


title: High Hyperdiploid-ALL, ICH data set (SI-HD-31)

status: Public on Jan 13 2010

city: Rehovot

first: Libi

last: Hertzberg

address: Herzel 145

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: Affymetrix Expression Console (EC) software Version 1.1 was used to median-normalize the data and then apply RMA.

source_name: White blood human cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: No growth protocol used

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation

tag: condition

value: High Hyperdiploid with acute lymphoblastic leukemia

tag: genetic aberration

value: High Hyperdiploid

value: white blood cells


title: MLP-A (Growing)

description: Growing cells expressing a vector control replicate 1


title: TEL-AML1-ALL, ICH data set (SI-TEL-33)


title: PTL ECs

status: Public on Jan 14 2010

city: wuhan

first: ding

last: ma

address: jiefang avenue 1095#

country: China

institute: cancer biology research center, tongji hospital, tongji medical college, huazhong university of science and technology

description: Gene expression data from PTL endothelium cells

hyb_protocol: Following fragmentation, 20ug of cRNA were hybridized for 16 hr at 45C on HG-U133Plus2.0 gene chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000.

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

source_name: endothelium cells from peripheral T cell lymphoma

label_protocol: Biotinylated  cRNA were prepared according to the single round amplification protocol (Affymetrix) from 10ug RNA

extract_protocol: The total RNA was extracted using the RNAqueous micro kit and the purified RNA was linearly amplified in-vitro.

treatment_protocol: The pure lymphoma and reactive lymph node-derived Ecs were isolated by LCM after immunohistochemical staining of CD34.


title: TEL-AML1-ALL, ICH data set (SI-TEL-30)


title: DS-ALL, ICH data set (SI-DS-ALL-49)

value: Down's syndrome with acute lymphoblastic leukemia

tag: snp dataset

tag: gene expression dataset

value: ICH

tag: jak2 r683 mutation

tag: crlf2 mutation

value: normal, wild type

tag: crlf2 fish

tag: crlf2 expression levels (gene expression arrays - log2)

tag: crlf2 expression levels (qrt-pcr - relative to si-ds-all-12)

tag: crlf2 expression levels stratification

value: High/medium


title: High Hyperdiploid-ALL, ICH data set (SI-HD-28)


title: reactive lymph node-derived ECs, case2

description: Gene expression data from reactive lymph node-derived endothelium cells of case 2

source_name: endothelium cells from reactive lymph nodes, case 2


title: High Hyperdiploid-ALL, ICH data set (SI-HD-29)


title: reactive lymph node-derived ECs, case1

description: Gene expression data from reactive lymph node-derived endothelium cells of case 1

source_name: endothelium cells from reactive lymph nodes, case1


title: TEL-AML1-ALL, ICH data set (SI-TEL-31)


title: DLBCL ECs, case 1

description: Gene expression data from DLBCL endothelium cells of case 1

source_name: endothelium cells from diffuse large B-cell lymphoma, case 1


title: TEL-AML1-ALL, ICH data set (SI-TEL-32)


title: High Hyperdiploid-ALL, ICH data set (SI-HD-30)


title: High Hyperdiploid-ALL, ICH data set (SI-HD-27)


title: DS-ALL, ICH data set (SI-DS-ALL-45)

value: Deletion


title: DS-ALL, ICH data set (SI-DS-ALL-31)


title: MLL-ALL, AIEOP data set (SI-MLL-6)

value: MLL-ALL

value: MLL


title: MLP-B  (Growing)

description: Growing cells expressing a vector control replicate 2


title: MLL-ALL, AIEOP data set (SI-MLL-1)


title: MLL-ALL, AIEOP data set (SI-MLL-5)


title: MLL-ALL, AIEOP data set (SI-MLL-4)


title: MLL-ALL, AIEOP data set (SI-MLL-2)


title: DS-ALL, ICH data set (SI-DS-ALL-32)

value: Normal


title: MLL-ALL, AIEOP data set (SI-MLL-3)


title: DS-ALL, ICH data set (SI-DS-ALL-30)


title: E2A-PBX1-ALL, AIEOP data set (SI-E2A-4)


title: Laer, Control, Biological Rep 2

description: Gene expression data from Arabidopsis leaves treated with flg22

tag: tissue


title: DS-ALL, ICH data set (SI-DS-ALL-38)


title: DLBCL ECs, case 2

description: Gene expression data from DLBCL endothelium cells of case 2

source_name: endothelium cells from diffuse large B-cell lymphoma, case 2


title: BCR-ABL-ALL, AIEOP data set (SI-BCR-5)

value: BCR-ABL-ALL

value: BCR-ABL


title: BCR-ABL-ALL, AIEOP data set (SI-BCR-1)


title: BCR-ABL-ALL, AIEOP data set (SI-BCR-4)


title: E2A-PBX1-ALL, AIEOP data set (SI-E2A-1)


title: BCR-ABL-ALL, AIEOP data set (SI-BCR-6)


title: E2A-PBX1-ALL, AIEOP data set (SI-E2A-2)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-23)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-22)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-27)


title: E2A-PBX1-ALL, AIEOP data set (SI-E2A-3)


title: BCR-ABL-ALL, AIEOP data set (SI-BCR-2)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-26)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-20)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-25)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-29)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-16)


title: BCR-ABL-ALL, AIEOP data set (SI-BCR-7)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-17)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-28)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-15)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-13)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-12)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-18)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-19)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-21)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-14)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-11)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-8)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-9)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-7)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-10)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-6)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-22)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-4)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-25)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-2)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-24)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-5)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-1)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-21)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-20)


title: TEL-AML1-ALL, AIEOP data set (SI-TEL-3)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-26)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-19)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-16)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-18)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-15)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-14)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-13)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-8)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-12)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-9)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-24)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-6)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-11)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-10)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-5)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-17)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-4)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-7)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-3)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-2)


title: DS-ALL, AIEOP data set (SI-DS-ALL-90)

value: AIEOP

value: No/low


title: DS-ALL, AIEOP data set (SI-DS-ALL-82)


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-1)


title: DS-ALL, AIEOP data set (SI-DS-ALL-11)

value: IL

value: IL, AIEOP


title: DS-ALL, AIEOP data set (SI-DS-ALL-14)


title: BCR-ABL-ALL, AIEOP data set (SI-BCR-3)


title: DS-ALL, AIEOP data set (SI-DS-ALL-86)


title: DS-ALL, AIEOP data set (SI-DS-ALL-15)


title: DS-ALL, AIEOP data set (SI-DS-ALL-85)


title: DS-ALL, AIEOP data set (SI-DS-ALL-81)


title: DS-ALL, AIEOP data set (SI-DS-ALL-18)


title: DS-ALL, AIEOP data set (SI-DS-ALL-77)


title: DS-ALL, AIEOP data set (SI-DS-ALL-80)


title: DS-ALL, AIEOP data set (SI-DS-ALL-73)


title: DS-ALL, AIEOP data set (SI-DS-ALL-92)


title: DS-ALL, AIEOP data set (SI-DS-ALL-74)


title: DS-ALL, AIEOP data set (SI-DS-ALL-95)


title: DS-ALL, AIEOP data set (SI-DS-ALL-93)


title: DS-ALL, AIEOP data set (SI-DS-ALL-84)


title: DS-ALL, AIEOP data set (SI-DS-ALL-17)


title: DS-ALL, AIEOP data set (SI-DS-ALL-10)


title: DS-ALL, AIEOP data set (SI-DS-ALL-83)


title: DS-ALL, AIEOP data set (SI-DS-ALL-76)


title: DS-ALL, AIEOP data set (SI-DS-ALL-87)


title: DS-ALL, AIEOP data set (SI-DS-ALL-91)


title: DS-ALL, AIEOP data set (SI-DS-ALL-96)


title: DS-ALL, AIEOP data set (SI-DS-ALL-69)


title: CB2008210-7T

status: Public on Jan 12 2010

city: Shanghai

first: zhihai

last: peng

state: Shanghai

address: 85 Wujin Road

department: Department of General Surgery

institute: Shanghai Jiao Tong University Affiliated First People's Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed with GCOS1.4, using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: gastric cancer tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

treatment_protocol: Selected tissue were taken out from nitrogen, cut into small pieces and placed on ice in the Trizol solution (invitrogen).

tag: tissue type

value: gastric cancer tissue

tag: stage

value: IV


title: CB2008210-13N

source_name: noncancer tissue

value: noncancer tissue


title: CB2008210-15T

value: I


title: CB2008210-12N


title: CB2008210-9N


title: CB2008210-7N


title: CB2008210-12T

value: II


title: CB2008210-14N


title: CB2008210-14T

value: III


title: CB2008210-9C

source_name: normal gastric tissue

value: normal gastric tissue


title: CB2008210-15N


title: CB2008210-5C


title: CB2008210-9T


title: CB2008210-13T


title: CB2008210-3C


title: CB2008210-6N


title: CB2008210-6T


title: CB2008210-5N


title: CB2008210-1N


title: CB2008210-4N


title: CB2008210-2N


title: CB2008210-5T


title: CB2008210-3N


title: CB2008210-4T


title: CB2008210-3T


title: CB2008210-1T


title: High Hyperdiploid-ALL, AIEOP data set (SI-HD-23)

value: High Hyperdiploid with acute lymphoblastic leukemia

value: High Hyperdiploid

tag: cell type

value: white blood cells


title: CB2008210-2T


title: male wild type, biological rep3

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

country: Spain

institute: Universidad Pablo de Olavide

description: male wild type, biological rep3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45ºC on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 High-Resolution.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: 1 day old wilf type male

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA using kits provied by Quiagen

growth_protocol: Stocks were maintained in standard oatmeal and molasses medium containing 1.5% (w/v) sucrose (Merck), 3% glucose (Sigma), 3.5% Instant Dry Baker’s Yeast (European), 1.5% Maize flour (Oriola), 1% Wheat germ (Oriola), 1% Soya flour (Oriola), 1% agar (Oriola) and 3% Lyle’s black treacle (Tate & Lyle, UK), to which was added 0.1% Nipagin M (Sigma) and 0.5% (v/v) propionic acid (JT Baker).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Afterwars, RNA was cleaned using the RNeasy® MinElute™ Cleanup kit (Qiagen). RNA concentration and purity were checked spectrophotometrically and RNA quality was verified electrophoretically. RNA was stored at –20 ºC in RNase-free water.

treatment_protocol: Adult flies were collected and aged to 1 day old in vials containing 4 ml food

tag: Gender

value: male

tag: Genotype

value: F1 generation, by crossing virgin Canton S wild type females with Oregon R wild type males

tag: Age

value: 1 day old


title: male tko25t mutant, biological rep3

description: male tko25t mutant, biological rep3

source_name: 1 day old tko25t mutant male

value: F1 generation, by crossing virgin Canton S tko25t homozygous mutant females with Oregon R tko25t males


title: male wild type, biological rep2

description: male wild type, biological rep2


title: female wild type, biological rep2

description: female wild type, biological rep2

source_name: 1 day old wilf type female

value: female


title: female tko25t mutant, biological rep2

description: female tko25t mutant, biological rep2

source_name: 1 day old tko25t mutant female


title: female tko25t mutant, biological rep3

description: female tko25t mutant, biological rep3


title: male tko25t mutant, biological rep2

description: male tko25t mutant, biological rep2


title: female wild type, biological rep1

description: female wild type, biological rep1


title: female wild type, biological rep3

description: female wild type, biological rep3


title: female tko25t mutant, biological rep1

description: female tko25t mutant, biological rep1


title: male wild type, biological rep1

description: male wild type, biological rep1


title: male tko25t mutant, biological rep1

description: male tko25t mutant, biological rep1


title: pil5, dark, biological rep3

city: Daejeon

first: Giltsu

last: Choi

address: 335 Gwahangno

department: Biological Sciences

country: South Korea

institute: KAIST

description: Gene expression data from pil5 imbibied seeds incubated in the dark for 12 hours after far-red light irradiation

hyb_protocol: Following fragmentation, the labeled cRNA were hybridized to GeneChip microarray (ATH1 GenomeArray; Affymetrix, Santa Clara CA) for 16 hr at 42C.

scan_protocol: CeneChips were scanned using a confocal microscope scanner (Gene Array Scanner; Hewlett-Packard, Palo Alto, CA) at 570 nm

data_processing: The data were analyzed with Microarray Suite software (version 5.0, Affymetrix) and signal intensities were normalized using robust multiple-array average (RMA) method

source_name: pil5 imbibed seeds incubated in the dark for 12 hours after far-red light irradiation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds were incubated for 12 hours dark either after far-red light or far-red/red light irradiation on aqueous medium.

extract_protocol: Total RNA was extracted using the Spectrum plant total RNA kit (Sigma, St. Louis, MO, USA) according to the manufacturer’s protocol.

treatment_protocol: Far-red light treatment (3.2 μmol m-2 s-1, 5 mins), Red light treatment (13 μmol m-2 s-1, 5mins)


title: Col-0, red light, biological rep3

description: Gene expression data from Col-0 imbibied seeds incubated in the dark for 12 hours after far-red/red light irradiation

source_name: Col-0 imbibed seeds incubated in the dark for 12 hours after far-red/red light irradiation

value: Col-0 wild type


title: pil5, red light, biological rep2

description: Gene expression data from pil5 imbibied seeds incubated in the dark for 12 hours after far-red/red light irradiation

source_name: pil5 imbibed seeds incubated in the dark for 12 hours after far-red/red light irradiation


title: pil5, dark, biological rep2


title: Col-0, dark, biological rep3

description: Gene expression data from Col-0 imbibied seeds incubated in the dark for 12 hours after far-red light irradiation

source_name: Col-0 imbibed seeds incubated in the dark for 12 hours after far-red light irradiation


title: pil5, red light, biological rep3


title: Col-0, dark, biological rep2


title: pil5, dark, biological rep1


title: pil5, red light, biological rep1


title: Col-0, red light, biological rep2


title: Col-0, red light, biological rep1


title: Col-0, dark, biological rep1


title: PaTu8988s replicate 2

status: Public on Jan 10 2010

city: London

first: yaohe

last: Wang

address: Charterhouse Square

institute: Institute of Cancer

description: gene expression data from pancreatic cancer cell line PaTu8988s

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: RMA robust multi-array analysis using R

source_name: pancreatic cancer cell line PaTu8988s

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

growth_protocol: Cell lines were maintained in DMEM with 10% FBS

extract_protocol: extraction of total RNA was performed using TRIzol solution(Gibco BRL) according to the manufacturer's instructions

treatment_protocol: cells were grown to 70-80% confluence before RNA extraction.

tag: pancreatic cancer cell line PaTu8988s


title: T5573A1

status: Public on Jan 08 2010

city: Parkville

first: Oliver

last: Sieber

state: Victoria

address: 6th floor, Centre for Medical Research,  Royal Melbourne Hospital,  Royal Parade

department: Melbourne Tumour Biology Branch

country: Australia

institute: Ludwig Institute for Cancer Research

description: Location: Left; DukesStage: D; Age_Diag: 68; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Use the simpleaffy package in R/Bioconductor to calculate MAS5.0 calls. These values were subsequently normalized using quantile normalization.

source_name: primary colorectal adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

tag: Location

value: Left; DukesStage:D; Age_Diag:68; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: PaTu8988t replicate 2

description: gene expression data from pancreatic cancer cell line PaTu8988t

source_name: pancreatic cancer cell line PaTu8988t

tag: pancreatic cancer cell line PaTu8988t


title: PaTu8988s replicate 3


title: PaTu8988s replicate 1


title: T6190A1

description: Location: Left; DukesStage: D; Age_Diag: 47; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:47; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T5536C4

description: Location: Right; DukesStage: D; Age_Diag: 66; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:66; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T694C

description: Location: Left; DukesStage: D; Age_Diag: 46; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:46; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: 03-TB-002-1B

description: Location: Right; DukesStage: D; Age_Diag: 65; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: ; AdjCTX:

value: Right; DukesStage:D; Age_Diag:65; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:; AdjCTX:


title: T4750A1

description: Location: Left; DukesStage: D; Age_Diag: 51; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:51; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T4354H

description: Location: Right; DukesStage: D; Age_Diag: 42; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:42; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T377A

description: Location: Right; DukesStage: D; Age_Diag: 59; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:59; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T4975A1

description: Location: Right; DukesStage: D; Age_Diag: 73; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:73; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T5513A1.1

description: Location: Right; DukesStage: D; Age_Diag: 78; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:78; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: PaTu8988t replicate 1


title: PaTu8988t replicate 3


title: T3779A

description: Location: Right; DukesStage: D; Age_Diag: 58; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:58; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: 02-567-P1453

description: Location: Right; DukesStage: D; Age_Diag: 76; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:76; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T5063A

description: Location: Left; DukesStage: D; Age_Diag: 82; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:82; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 03-1514-P3083

description: Location: Rectum; DukesStage: D; Age_Diag: 67; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:D; Age_Diag:67; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 04-TB-017-1A

description: Location: Left; DukesStage: D; Age_Diag: 79; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:79; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T4449E1

description: Location: Rectum; DukesStage: D; Age_Diag: 78; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Rectum; DukesStage:D; Age_Diag:78; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T4926A1

description: Location: Right; DukesStage: D; Age_Diag: 63; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:63; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: 02-156-P1182

description: Location: Colon; DukesStage: D; Age_Diag: 59; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Colon; DukesStage:D; Age_Diag:59; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T4148A2.2

description: Location: Right; DukesStage: D; Age_Diag: 69; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:69; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T4956A1

description: Location: Left; DukesStage: D; Age_Diag: 66; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:66; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T4984A1

description: Location: Right; DukesStage: D; Age_Diag: 62; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:62; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T3734A1

description: Location: Right; DukesStage: D; Age_Diag: 76; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:76; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T5102A1

description: Location: Left; DukesStage: D; Age_Diag: 76; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:76; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T3289A

description: Location: ; DukesStage: D; Age_Diag: 56; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: Y; AdjCTX: Y

value: ; DukesStage:D; Age_Diag:56; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:Y; AdjCTX:Y


title: T3025B1

description: Location: Right; DukesStage: D; Age_Diag: 82; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:82; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T3437A

description: Location: Right; DukesStage: D; Age_Diag: 65; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:65; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T2528C

description: Location: Rectum; DukesStage: D; Age_Diag: 52; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: Y; AdjCTX: Y

value: Rectum; DukesStage:D; Age_Diag:52; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:Y; AdjCTX:Y


title: T3426B1

description: Location: Left; DukesStage: D; Age_Diag: 63; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:63; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T3072A1

description: Location: Left; DukesStage: D; Age_Diag: 60; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:60; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T2404A1

description: Location: Right; DukesStage: D; Age_Diag: 69; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:69; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T2057A

description: Location: Left; DukesStage: D; Age_Diag: 82; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:82; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T2419A1

description: Location: Left; DukesStage: D; Age_Diag: 51; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:51; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T2369A

description: Location: Left; DukesStage: D; Age_Diag: 58; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:58; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T288C

description: Location: Right; DukesStage: D; Age_Diag: 72; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:72; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T220A

description: Location: Left; DukesStage: D; Age_Diag: 64; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:64; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T3087B

description: Location: Rectum; DukesStage: D; Age_Diag: 57; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: Y; AdjCTX: Y

value: Rectum; DukesStage:D; Age_Diag:57; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:Y; AdjCTX:Y


title: T1889A1

description: Location: Left; DukesStage: D; Age_Diag: 58; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:58; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T1311B

description: Location: Left; DukesStage: D; Age_Diag: 73; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:73; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:Y; AdjCTX:Y


title: T1535A

description: Location: Left; DukesStage: D; Age_Diag: 63; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:D; Age_Diag:63; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T3159B

description: Location: Right; DukesStage: D; Age_Diag: 52; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:52; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T3277B

description: Location: Right; DukesStage: D; Age_Diag: 59; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:59; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T1700A

description: Location: Left; DukesStage: D; Age_Diag: 54; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:54; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: T3650A

description: Location: Right; DukesStage: D; Age_Diag: 54; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:54; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: 2000-287

description: Location: Right; DukesStage: C; Age_Diag: 51; Gender: M; DFS_Time: 40; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:51; Gender:M; DFS_Time:40; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T1356B

description: Location: Left; DukesStage: D; Age_Diag: 66; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:D; Age_Diag:66; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: 99-62-P51

description: Location: Right; DukesStage: C; Age_Diag: 81; Gender: M; DFS_Time: 18; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:81; Gender:M; DFS_Time:18; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T2759A

description: Location: Right; DukesStage: D; Age_Diag: 70; Gender: F; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:D; Age_Diag:70; Gender:F; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:Y


title: 99-52-P49

description: Location: Left; DukesStage: C; Age_Diag: 53; Gender: F; DFS_Time: 72.9; DFS_Cens: 0; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:53; Gender:F; DFS_Time:72.9; DFS_Cens:0; AdjXRT:N; AdjCTX:Y


title: T1094A1

description: Location: Rectum; DukesStage: D; Age_Diag: 69; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Rectum; DukesStage:D; Age_Diag:69; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: T1792A1

description: Location: Right; DukesStage: D; Age_Diag: 88; Gender: M; DFS_Time: NA; DFS_Cens: NA; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:D; Age_Diag:88; Gender:M; DFS_Time:NA; DFS_Cens:NA; AdjXRT:N; AdjCTX:N


title: 02-863-P1654

description: Location: Right; DukesStage: C; Age_Diag: 82; Gender: F; DFS_Time: 4.44; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:82; Gender:F; DFS_Time:4.44; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: 003-230-P541

description: Location: Left; DukesStage: C; Age_Diag: 43; Gender: M; DFS_Time: 70.8; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:43; Gender:M; DFS_Time:70.8; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T573A

description: Location: Right; DukesStage: C; Age_Diag: 64; Gender: F; DFS_Time: 112.33; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Right; DukesStage:C; Age_Diag:64; Gender:F; DFS_Time:112.33; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T451A

description: Location: Right; DukesStage: C; Age_Diag: 71; Gender: F; DFS_Time: 95.07; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:71; Gender:F; DFS_Time:95.07; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T5133A

description: Location: Right; DukesStage: C; Age_Diag: 74; Gender: M; DFS_Time: 85.84; DFS_Cens: 0; AdjXRT: Y; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:74; Gender:M; DFS_Time:85.84; DFS_Cens:0; AdjXRT:Y; AdjCTX:Y


title: T251A

description: Location: Left; DukesStage: C; Age_Diag: 39; Gender: M; DFS_Time: 105.17; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:39; Gender:M; DFS_Time:105.17; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T252A

description: Location: Left; DukesStage: C; Age_Diag: 60; Gender: M; DFS_Time: 79.46; DFS_Cens: 0; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:60; Gender:M; DFS_Time:79.46; DFS_Cens:0; AdjXRT:N; AdjCTX:N


title: T3351B

description: Location: Left; DukesStage: C; Age_Diag: 65; Gender: F; DFS_Time: 65.55; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:65; Gender:F; DFS_Time:65.55; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T3040A

description: Location: Left; DukesStage: C; Age_Diag: 62; Gender: M; DFS_Time: 64.93; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:62; Gender:M; DFS_Time:64.93; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T1204A

description: Location: Right; DukesStage: C; Age_Diag: 48; Gender: F; DFS_Time: 99.51; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:48; Gender:F; DFS_Time:99.51; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T3701A1

description: Location: Right; DukesStage: C; Age_Diag: 69; Gender: M; DFS_Time: 59.34; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:69; Gender:M; DFS_Time:59.34; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T2549C

description: Location: Left; DukesStage: C; Age_Diag: 30; Gender: M; DFS_Time: 47.8; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:30; Gender:M; DFS_Time:47.8; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T1612C

description: Location: Left; DukesStage: C; Age_Diag: 46; Gender: M; DFS_Time: 89.62; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:46; Gender:M; DFS_Time:89.62; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T2651C

description: Location: Rectum; DukesStage: C; Age_Diag: 50; Gender: F; DFS_Time: 74.36; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Rectum; DukesStage:C; Age_Diag:50; Gender:F; DFS_Time:74.36; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T4088A

description: Location: Left; DukesStage: C; Age_Diag: 72; Gender: M; DFS_Time: 52.86; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:72; Gender:M; DFS_Time:52.86; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T1954A

description: Location: Rectum; DukesStage: C; Age_Diag: 71; Gender: F; DFS_Time: 85.61; DFS_Cens: 1; AdjXRT: Y; AdjCTX: Y

value: Rectum; DukesStage:C; Age_Diag:71; Gender:F; DFS_Time:85.61; DFS_Cens:1; AdjXRT:Y; AdjCTX:Y


title: T2130A

description: Location: Left; DukesStage: C; Age_Diag: 63; Gender: M; DFS_Time: 64.33; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:63; Gender:M; DFS_Time:64.33; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4475A1

description: Location: Right; DukesStage: C; Age_Diag: 60; Gender: F; DFS_Time: 38.07; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:60; Gender:F; DFS_Time:38.07; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4452A2

description: Location: Right; DukesStage: C; Age_Diag: 71; Gender: F; DFS_Time: 49.11; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:71; Gender:F; DFS_Time:49.11; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T2465G

description: Location: Right; DukesStage: C; Age_Diag: 87; Gender: M; DFS_Time: 59.07; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:87; Gender:M; DFS_Time:59.07; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T3085B

description: Location: Right; DukesStage: C; Age_Diag: 67; Gender: F; DFS_Time: 50.59; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:67; Gender:F; DFS_Time:50.59; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4489A1

description: Location: Left; DukesStage: C; Age_Diag: 46; Gender: M; DFS_Time: 44.74; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Left; DukesStage:C; Age_Diag:46; Gender:M; DFS_Time:44.74; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T2421A

description: Location: Left; DukesStage: C; Age_Diag: 63; Gender: M; DFS_Time: 74.53; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:63; Gender:M; DFS_Time:74.53; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T2660A

description: Location: Right; DukesStage: C; Age_Diag: 55; Gender: M; DFS_Time: 72.09; DFS_Cens: 1; AdjXRT: N; AdjCTX: Y

value: Right; DukesStage:C; Age_Diag:55; Gender:M; DFS_Time:72.09; DFS_Cens:1; AdjXRT:N; AdjCTX:Y


title: T4111A

description: Location: Left; DukesStage: C; Age_Diag: 67; Gender: M; DFS_Time: 44.67; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:67; Gender:M; DFS_Time:44.67; DFS_Cens:1; AdjXRT:N; AdjCTX:N


title: T3552B

description: Location: Left; DukesStage: C; Age_Diag: 63; Gender: F; DFS_Time: 58.45; DFS_Cens: 1; AdjXRT: N; AdjCTX: N

value: Left; DukesStage:C; Age_Diag:63; Gender:F; DFS_Time:58.45; DFS_Cens:1; AdjXRT:N; AdjCTX:N