title: Spleen_PBS_24HPI_fish4

status: Public on Nov 05 2010

city: St. John's

first: Marije

last: Booman

state: NL

address: 1 Marine Lab Road

institute: Memorial University of Newfoundland

hyb_protocol: Arrays were prehybridized at 42°C in Nexterion Oligo Prehyb Buffer (Schott Nexterion cat. nr 1116889) for at least 2 hours. Arrays were washed at room temperature for with 0.1% SDS for 5 minutes, followed by 3 5-minute washes with water. Slides were dried by spinning them for 5 minutes at 200x g and kept at 42°C. LifterSlips were prepared by washing them sequentially with water, water, 70% ethanol and 100% ethanol and drying them using compressed air. For each array two labeled cDNAs were combined (one sample, one reference) and 2 μl of LNA blocker (Genisphere) and 40 μl of prewarmed 2x formamide-based hybridization buffer (Genisphere) was added. These samples were incubated at 80°C for 10 minutes and then kept at 42°C. Pre-warmed arrays were put in Corning hybridization chambers, LifterSlips were applied and the samples were loaded under the LifterSlips. Hybridizations were performed overnight for ~16 hours in a water bath at 42°C. After hybridization, arrays were washed at room temperature for 15 minutes with 2xSSC/0.2% SDS which was pre-warmed at 42°C. Next slides were washed  at room temperature for 15 minutes with 2xSSC, followed by 2 15-minute washes with 0.2xSSC. Slides were dried by spinning them for 5 minutes at 200x g.

scan_protocol: Arrays were scanned at a resolution of 5 μm using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer).

data_processing: Signal intensity data was extracted from tiff images using Imagene v7.5. In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot  was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 2* SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene. Logratios of duplicate spots were averaged.

label: AlexaFluor 647

organism: Gadus morhua

source_name: Spleen tissue, PBS group, 24 hours post-injection

label_protocol: 5 μg of DNAse-treated column-purified total RNA was labeled using Invitrogen SuperScript Direct cDNA Labeling kit according to the manufacturer's protocol. Test samples were always labeled with AlexaFluor 647, the common reference was always labeled with AlexaFluor 555.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) following manufacturer's instructions. Total RNA was treated with DNAse I and column-purified using the RNeasy Mi-Elute Cleanup kit (Qiagen) following manufacturer's instructions.

treatment_protocol: At sampling time fish were euthanized by a lethal dose (0.4 g/l) of tricaine methanesulphonate and spleens were collected in RNAse-free 1.5 ml tubes, flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: Spleen

tag: life stage

value: Juvenile

tag: agent

value: PBS

label: AlexaFluor 555

source_name: Pooled total RNA from spleen tissue, undisturbed control group

tag: sample type


title: Spleen_PBS_24HPI_fish7

type: RNA

department: Ocean Sciences

country: Canada

molecule: total RNA

tag: tissue

value: Pooled total RNA from spleen tissue, undisturbed control group


title: Spleen_PBS_24HPI_fish6


title: Spleen_PBS_PreInjection_fish8

source_name: Spleen tissue, PBS group, pre-injection


title: Spleen_PBS_PreInjection_fish2


title: Spleen_PBS_PreInjection_fish4


title: Spleen_PBS_24HPI_fish8


title: Spleen_PBS_PreInjection_fish3


title: Spleen_PBS_PreInjection_fish5


title: Spleen_PBS_24HPI_fish5


title: Spleen_Asal_24HPI_fish5

source_name: Spleen tissue, Asal group, 24 hours post-injection

value: Asal


title: Spleen_PBS_24HPI_fish3


title: Spleen_Asal_24HPI_fish3


title: Spleen_Asal_24HPI_fish6


title: Spleen_Asal_PreInjection_fish8

source_name: Spleen tissue, Asal group, pre-injection


title: Spleen_Asal_PreInjection_fish6


title: Spleen_Asal_24HPI_fish7


title: Spleen_Asal_PreInjection_fish7


title: Spleen_Asal_PreInjection_fish4


title: Spleen_Asal_24HPI_fish8


title: Spleen_Asal_PreInjection_fish2


title: breast tumor part_IDC_rep1 5389

status: Public on Nov 04 2010

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

country: Taiwan

institute: National Taiwan University

description: breast tumor part_IDC_rep1

scan_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0 with Agilent scanner and Feature Extraction 6.0.

data_processing: Agilent Two-Color Microarray-Based Gene Expression Analysis, version 4.0. The log2 ratio for each gene was centered by subtracting the median across all samples to discriminate the subclass of the dataset.

organism: Homo sapiens

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(+), PR(+).

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0

growth_protocol: The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit

treatment_protocol: The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately before RNA extraction.

tag: status

tag: gender

value: female

value: primary tumor

source_name: Commercially available.

value: Stratagene's human common reference RNA


title: Spleen_Asal_24HPI_fish4


title: breast tumor part_IDC_rep1 5383

description: breast tumor part_IDC_rep1

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0


title: breast tumor part_IDC_rep1 5397

description: breast tumor part_IDC_rep1

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(-), PR(+).

tag: er/pr/her status


title: breast tumor part_IDC_rep1 5381

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5379

description: breast tumor part_IDC_rep1


title: Spleen_Asal_PreInjection_fish3


title: breast tumor part_IDC_rep1 5377

description: breast tumor part_IDC_rep1

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(+), PR(-).


title: breast tumor part_IDC_rep1 5365

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5391

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5369

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5349

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5353

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5361

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5351

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5355

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5315

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5309

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5331

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5311

description: breast tumor part_IDC_rep1


title: HBEC38-KT

status: Public on Jun 18 2012

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

country: USA

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

label: biotin

source_name: Immortalized human bronchial epithelial cells

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: K-SFM (Keratinocyte Serum-Free Media, Gibco)

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

tag: cell type

tag: cell line

tag: atcc alias

tag: histology

tag: age

tag: race

value: F


title: breast tumor part_IDC_rep1 5299

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5303

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5367

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4439

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5313

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4441

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4443

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5297

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4435

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4433

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4437

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4427

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4431

description: breast tumor part_IDC_rep1

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(-), PR(-).


title: breast tumor part_IDC_rep1 4429

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5295

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 2401

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 2399

description: breast tumor part_IDC_rep1


title: Patient 18, before month24 IFN-beta injection_chipB

status: Public on Sep 29 2010

city: Rostock

first: Robert

last: Goertsches

address: Gehlsheimer Strasse 20

department: Neurology

country: Germany

institute: University

description: Gene expression data from a multiple sclerosis patient treated with IFN-beta

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133A and B arrays, respectively. Microarrays 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 raw probe-level signals were converted to expression values using the MAS5.0 algorithm. Accordingly, probeset specific detection calls (Absent/Present) and changes with respect to baseline (Increase/Decrease/NoChange) were ascertained.

label: Biotin

source_name: Peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 µg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Patient blood samples were drawn immediately before first IFN-beta injection as well as two days, one, twelve and twenty-four months post therapy initiation.

extract_protocol: Blood was separated using isopycnic centrifugation (Ficoll), and peripheral blood mononuclear cells were lysed using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocol.

treatment_protocol: Patients were treated with subcutaneous IFN-beta-1b (Betaferon, Bayer Healthcare) at standard dose (250 µg every other day).

tag: age at ifn-beta therapy onset (baseline blood sampling)

tag: duration from ms diagnosis to therapy initiation (in months)

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 5 years

tag: number of relapses during the year prior to treatment

tag: number of relapses during 1-year follow-up

tag: number of relapses during 2-year follow-up

tag: number of relapses during 5-year follow-up

tag: time from start of therapy to the first relapse (in months)

tag: completed years of ifn-beta therapy


title: Patient 18, before first IFN-beta injection_chipB

tag: gender


title: Patient 18, before month1 IFN-beta injection_chipA


title: Patient 10, before month12 IFN-beta injection_chipB

value: male


title: Patient 10, before month1 IFN-beta injection_chipB


title: Patient 18, before month12 IFN-beta injection_chipA


title: Patient 18, before month24 IFN-beta injection_chipA


title: Patient 18, before month1 IFN-beta injection_chipB


title: Patient 18, before second IFN-beta injection_chipB


title: Patient 18, before second IFN-beta injection_chipA


title: Patient 10, before month24 IFN-beta injection_chipB


title: Patient 10, before second IFN-beta injection_chipB


title: Patient 18, before first IFN-beta injection_chipA


title: Patient 10, before first IFN-beta injection_chipA


title: Patient 10, before month12 IFN-beta injection_chipA


title: Patient 10, before month1 IFN-beta injection_chipA


title: Patient 18, before month12 IFN-beta injection_chipB


title: Patient 10, before first IFN-beta injection_chipB


title: Patient 10, before month24 IFN-beta injection_chipA


title: Patient 10, before second IFN-beta injection_chipA


title: Patient 16, before second IFN-beta injection U133B

status: Public on Dec 03 2009

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133B arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 1.5.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each B-chip yielded mRNA abundances of 6,771 human genes.

growth_protocol: Patient blood samples were taken immediately before first IFN-beta injection as well as one and four weeks post therapy initiation.

extract_protocol: Blood was separated using isopycnic centrifugation (Ficoll), and peripheral blood mononuclear cells were lysated using chaotropic buffer and cleaned by RNeasy (Qiagen) according to the manufacturers' protocol.

treatment_protocol: Patients were treated with intramuscular IFN-beta-1a (Avonex, Biogen Idec) at standard dose.


title: Patient 16, before fifth IFN-beta injection U133B


title: Patient 15, before first IFN-beta injection U133A

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 h at 45°C on Affymetrix HG-U133A arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The raw probe-level signals were converted to expression values using the MAS5.0 algorithm and custom GeneAnnot-based chip definition files (version 1.5.0, available at http://www.xlab.unimo.it/GA_CDF). Data normalization was performed by a loess fit to the data with span=0.05 (using R package affy). Each A-chip yielded mRNA abundances of 11,220 human genes.


title: Patient 16, before first IFN-beta injection U133B


title: Patient 16, before first IFN-beta injection U133A


title: Patient 15, before fifth IFN-beta injection U133A


title: Patient 15, before first IFN-beta injection U133B


title: Patient 15, before fifth IFN-beta injection U133B


title: Patient 15, before second IFN-beta injection U133B


title: Patient 16, before fifth IFN-beta injection U133A


title: Patient 16, before second IFN-beta injection U133A


title: Patient 15, before second IFN-beta injection U133A


title: S791N [gene level]

status: Public on Sep 24 2009

city: shanghai

first: Zhang

last: Qinghua

address: 151# libing road

country: China

institute: Shanghai shbiochip co

description: Gene expression and alternative splicing between cancer and normal mucosa.

hyb_protocol: 5 ug of cDNA were hybridized for 17 hr at 45C and 60 rpm on GeneChip Human Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using the Genechip scanner 3000.

data_processing:
The Expression Console software version 1.0 integrated RMA algorithm was selected to derive the signal intensities for both gene-level and probeset (exon level), and “Detection Above Background” (DABG) p-value for each probeset from the .CEL files of the 25 sample pairs. Core exons and transcripts were selected in later analysis.
HuEx-1_0-st-v2.annot.hg18.csv core.

source_name: S791N,surgically resected from patient of gastric cancer

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA(GENECHIP WHOLE TRANSCRIPT (WT) SENSE TARGET LABELING ASSAY MANUAL,Affymetrix).

extract_protocol: Total RNA were isolated by RNAqueous-Micro kit (Ambion) according to the manufacturer’s instructions.

treatment_protocol: Sample was frozen in liquid nitrogen after surgically resected. 8 um cryostat sections was made and pathologically re-inspected by another pathologist with H&E staining. Pure normal gastric mucosa cells were obtained by LCM before RNA extraction.

tag: Lymph Nodes:NA


title: S791T [gene level]

source_name: S791T,surgically resected from patient of gastric cancer

treatment_protocol: Sample was frozen in liquid nitrogen after surgically resected. 8 um cryostat sections was made and pathologically re-inspected by another pathologist with H&E staining. Pure tumor cells were obtained by LCM before RNA extraction.

tag: Histopathology:Adenocarcinoma,partial signet-ring cell carcinoma

tag: Lymph Nodes:N3

tag: Differentiation:Poor differentiation


title: S800N [gene level]

source_name: S800N,surgically resected from patient of gastric cancer


title: S800T [gene level]

source_name: S800T,surgically resected from patient of gastric cancer

tag: Lymph Nodes:N0


title: S787N [gene level]

source_name: S787N,surgically resected from patient of gastric cancer


title: S766N [gene level]

source_name: S766N,surgically resected from patient of gastric cancer


title: S740T [gene level]

source_name: S740T,surgically resected from patient of gastric cancer

tag: Lymph Nodes:N2


title: S737N [gene level]

source_name: S737N,surgically resected from patient of gastric cancer


title: S740N [gene level]

source_name: S740N,surgically resected from patient of gastric cancer


title: S726N [gene level]

source_name: S726N,surgically resected from patient of gastric cancer


title: S736T [gene level]

source_name: S736T,surgically resected from patient of gastric cancer


title: S736N [gene level]

source_name: S736N,surgically resected from patient of gastric cancer


title: S766T [gene level]

source_name: S766T,surgically resected from patient of gastric cancer


title: S787T [gene level]

source_name: S787T,surgically resected from patient of gastric cancer


title: S729T [gene level]

source_name: S729T,surgically resected from patient of gastric cancer


title: S729N [gene level]

source_name: S729N,surgically resected from patient of gastric cancer


title: S723N [gene level]

source_name: S723N,surgically resected from patient of gastric cancer


title: S737T [gene level]

source_name: S737T,surgically resected from patient of gastric cancer


title: S723T [gene level]

source_name: S723T,surgically resected from patient of gastric cancer


title: S575T [gene level]

source_name: S575T,surgically resected from patient of gastric cancer


title: S574N [gene level]

source_name: S574N,surgically resected from patient of gastric cancer


title: S575N [gene level]

source_name: S575N,surgically resected from patient of gastric cancer


title: S726T [gene level]

source_name: S726T,surgically resected from patient of gastric cancer


title: S574T [gene level]

source_name: S574T,surgically resected from patient of gastric cancer


title: S554N [gene level]

source_name: S554N,surgically resected from patient of gastric cancer


title: S553T [gene level]

source_name: S553T,surgically resected from patient of gastric cancer


title: S554T [gene level]

source_name: S554T,surgically resected from patient of gastric cancer


title: S442T [gene level]

source_name: S442T,surgically resected from patient of gastric cancer


title: S543T [gene level]

source_name: S543T,surgically resected from patient of gastric cancer


title: S439N [gene level]

source_name: S439N,surgically resected from patient of gastric cancer


title: S553N [gene level]

source_name: S553N,surgically resected from patient of gastric cancer


title: S439T [gene level]

source_name: S439T,surgically resected from patient of gastric cancer


title: S442N [gene level]

source_name: S442N,surgically resected from patient of gastric cancer


title: S543N [gene level]

source_name: S543N,surgically resected from patient of gastric cancer


title: S414T [gene level]

source_name: S414T,surgically resected from patient of gastric cancer

tag: Histopathology:Tubular adenocarcinoma


title: S800T [exon level]

data_processing: The Expression Console software version 1.0 integrated RMA algorithm was selected to derive the signal intensities for both gene-level and probeset (exon level), and “Detection Above Background” (DABG) p-value for each probeset from the .CEL files of the 25 sample pairs. Core exons and transcripts were selected in later analysis.

source_name: S800T,surgically resected from patient of gastric cancer


title: S791T [exon level]

source_name: S791T,surgically resected from patient of gastric cancer


title: S800N [exon level]

source_name: S800N,surgically resected from patient of gastric cancer


title: S791N [exon level]

source_name: S791N,surgically resected from patient of gastric cancer


title: S414N [gene level]

source_name: S414N,surgically resected from patient of gastric cancer


title: S737T [exon level]

source_name: S737T,surgically resected from patient of gastric cancer


title: S740N [exon level]

source_name: S740N,surgically resected from patient of gastric cancer


title: S395T [gene level]

source_name: S395T,surgically resected from patient of gastric cancer


title: S395N [gene level]

source_name: S395N,surgically resected from patient of gastric cancer


title: S384N [gene level]

source_name: S384N,surgically resected from patient of gastric cancer


title: S177T [gene level]

source_name: S177T,surgically resected from patient of gastric cancer


title: S766N [exon level]

source_name: S766N,surgically resected from patient of gastric cancer


title: S177N [gene level]

source_name: S177N,surgically resected from patient of gastric cancer


title: S384T [gene level]

source_name: S384T,surgically resected from patient of gastric cancer


title: S175N [gene level]

source_name: S175N,surgically resected from patient of gastric cancer


title: S787T [exon level]

source_name: S787T,surgically resected from patient of gastric cancer


title: S766T [exon level]

source_name: S766T,surgically resected from patient of gastric cancer


title: S736N [exon level]

source_name: S736N,surgically resected from patient of gastric cancer


title: S787N [exon level]

source_name: S787N,surgically resected from patient of gastric cancer


title: S729T [exon level]

source_name: S729T,surgically resected from patient of gastric cancer


title: S736T [exon level]

source_name: S736T,surgically resected from patient of gastric cancer


title: S175T [gene level]

source_name: S175T,surgically resected from patient of gastric cancer


title: S740T [exon level]

source_name: S740T,surgically resected from patient of gastric cancer


title: S737N [exon level]

source_name: S737N,surgically resected from patient of gastric cancer


title: S168N [gene level]

source_name: S168N,surgically resected from patient of gastric cancer


title: S168T [gene level]

source_name: S168T,surgically resected from patient of gastric cancer


title: S729N [exon level]

source_name: S729N,surgically resected from patient of gastric cancer


title: S726N [exon level]

source_name: S726N,surgically resected from patient of gastric cancer


title: S723T [exon level]

source_name: S723T,surgically resected from patient of gastric cancer


title: S723N [exon level]

source_name: S723N,surgically resected from patient of gastric cancer


title: S134N [gene level]

source_name: S134N,surgically resected from patient of gastric cancer


title: S134T [gene level]

source_name: S134T,surgically resected from patient of gastric cancer


title: S159N [gene level]

source_name: S159N,surgically resected from patient of gastric cancer


title: S726T [exon level]

source_name: S726T,surgically resected from patient of gastric cancer


title: S575T [exon level]

source_name: S575T,surgically resected from patient of gastric cancer


title: S574N [exon level]

source_name: S574N,surgically resected from patient of gastric cancer


title: S574T [exon level]

source_name: S574T,surgically resected from patient of gastric cancer


title: S554N [exon level]

source_name: S554N,surgically resected from patient of gastric cancer


title: S159T [gene level]

source_name: S159T,surgically resected from patient of gastric cancer


title: S554T [exon level]

source_name: S554T,surgically resected from patient of gastric cancer


title: S543N [exon level]

source_name: S543N,surgically resected from patient of gastric cancer


title: S553T [exon level]

source_name: S553T,surgically resected from patient of gastric cancer


title: S442T [exon level]

source_name: S442T,surgically resected from patient of gastric cancer


title: S395T [exon level]

source_name: S395T,surgically resected from patient of gastric cancer


title: S414N [exon level]

source_name: S414N,surgically resected from patient of gastric cancer


title: S159N [exon level]


title: S442N [exon level]

source_name: S442N,surgically resected from patient of gastric cancer


title: S159T [exon level]


title: S177T [exon level]

source_name: S177T,surgically resected from patient of gastric cancer


title: breast tumor part_IDC_rep1_4423

status: Public on Jul 24 2009

description: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(+), PR(-).

data_processing: Agilent Two-Color Microarray-Based Gene Expression Analysis, version 4.0

source_name: Infiltrating Ductal Carcinoma (IDC)

extract_protocol: Trizol reagent combined with Rneasy mini kit

tag: tissue

tag: estrogen receptor status

tag: progesterone receptor status

source_name: Stratagene's human common reference RNA

tag: reference


title: S553N [exon level]

source_name: S553N,surgically resected from patient of gastric cancer


title: S439T [exon level]

source_name: S439T,surgically resected from patient of gastric cancer


title: S175N [exon level]

source_name: S175N,surgically resected from patient of gastric cancer


title: S168T [exon level]

source_name: S168T,surgically resected from patient of gastric cancer


title: S439N [exon level]

source_name: S439N,surgically resected from patient of gastric cancer


title: S575N [exon level]

source_name: S575N,surgically resected from patient of gastric cancer


title: S543T [exon level]

source_name: S543T,surgically resected from patient of gastric cancer


title: S175T [exon level]

source_name: S175T,surgically resected from patient of gastric cancer


title: S168N [exon level]

source_name: S168N,surgically resected from patient of gastric cancer


title: MN, biological rep 3

status: Public on Mar 31 2008

city: stockholm

first: Jesper

last: Ryge

address: retziusvag 8

department: neuroscience

country: Sweden

institute: karolinska institutet

description: Gene expression data of fluorescently labelled neurons laser microdissected from 10 micro meter thick cryo-sections.

hyb_protocol: Following fragmentation, 5 ug of aRNA were hybridized for 16 hr at 45 °C on GeneChip Rat Neurobiology U34. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression values were calculated using R and Bioconductor using the affy package.  Li-wong expression summaries were calculated based on PM intensity values that were normalised (linear quantile plus quantile projection) and background subtracted (global minimization) (Ryge et al, 2007).  The genes were filtered prior to analysis such that only probe sets annotated in the Ensembl database was included (using biomaRt bioconductor package), so the probe set was reduced from 1322 to 1050.

organism: Rattus norvegicus

source_name: Ca. 70 MNs from neonatal spinal cord

label_protocol: Biotin labelled aRNA was generated from cDNA of the two-round amplification procedure using the GeneChip® Expression 3´-Amplification Reagents (Affymetrix).

extract_protocol: Spinal cords were snap frozen using CO2, cryosectioned into 10 micro meter slices, which were mounted onto POL-membrane metal frame slides (Leica) and fluorescently identied neurons were laser microdissected into a collector tube. Total RNA was extrated using the Picopure RNA isolation kit (Arcturus), which were then subject to a two round amplification using the RiboAmp HS RNA amplification kit (Arcturus) according to manufactors instructions.  A DNAse treatment was included in the isolation protocol.

treatment_protocol: The spinal cords were disected out from neonatal animals, the tracer applied to cut axons to retrogradely label neurons through a ca. 3 hour incubation time in oxygenated normal calcium ringer at room temperature.

tag: Wistar rats, age P0-P2


title: MN, biological rep 4

source_name: Ca. 115 MNs from neonatal spinal cord


title: MN, biological rep 7

source_name: Ca. 55 MNs from neonatal spinal cord


title: S384N [exon level]

source_name: S384N,surgically resected from patient of gastric cancer


title: S384T [exon level]

source_name: S384T,surgically resected from patient of gastric cancer


title: MN, biological rep 5

source_name: Ca. 100 MNs from neonatal spinal cord


title: MN, biological rep 2

source_name: Ca. 230 MNs from neonatal spinal cord


title: MN, biological rep 1

source_name: Ca. 250 MNs from neonatal spinal cord


title: MIX, biological rep 4

source_name: Ca. 125 MIX from neonatal spinal cord


title: MIX, biological rep 3

source_name: Ca. 100 MIX from neonatal spinal cord


title: MIX, biological rep 6


title: MIX, biological rep 5

source_name: Ca. 95 MIX from neonatal spinal cord


title: MIX, biological rep 7


title: CIN, biological rep 7

source_name: Ca. 50 CINs from neonatal spinal cord


title: MIX, biological rep 1

source_name: Ca. 187 MIX from neonatal spinal cord


title: MIX, biological rep 2


title: S134N [exon level]

source_name: S134N,surgically resected from patient of gastric cancer


title: CIN, biological rep 4

source_name: Ca. 80 CINs from neonatal spinal cord


title: CIN, biological rep 5


title: CIN, biological rep 3


title: CIN, biological rep 2

source_name: Ca. 75 CINs from neonatal spinal cord


title: CIN, biological rep 1

source_name: Ca. 60 CINs from neonatal spinal cord


title: breast tumor part_IDC_rep1_4425

source_name: Infiltrating Ductal Carcinoma (IDC)

source_name: Stratagene's human common reference RNA


title: CIN, biological rep 6

source_name: Ca. 100 CINs from neonatal spinal cord


title: S395N [exon level]

source_name: S395N,surgically resected from patient of gastric cancer


title: S134T [exon level]

source_name: S134T,surgically resected from patient of gastric cancer


title: S177N [exon level]

source_name: S177N,surgically resected from patient of gastric cancer


title: MIX, biological rep 8

source_name: Ca. 145 MIX from neonatal spinal cord


title: breast tumor part_IDC_rep1_2467

status: Public on Oct 20 2007

first: Hsin-Chieh

last: Yao

address: 1,  Rd. Roosevelt,  Sec. 4

department: CHE

description: Same tissue as sample 2079 but hybridized with Buffer1

treatment_protocol: The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately  before RNA extraction.


title: breast tumor part_IDC_rep1_2453

description: Same tissue as sample 2065 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2457

description: Same tissue as sample 2069 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2451

description: Same tissue as sample 2063 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2465

description: Same tissue as sample 2077 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2431

description: Same tissue as sample 2043 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2445

description: Same tissue as sample 2057 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2471

description: Same tissue as sample 2083 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2437

description: Same tissue as sample 2049 but hybridized with Buffer1

value: recurrent tumor


title: S414T [exon level]

source_name: S414T,surgically resected from patient of gastric cancer


title: breast tumor part_IDC_rep1_2427

description: Same tissue as sample 2039 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2449

description: Same tissue as sample 2061 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2423

description: Same tissue as sample 2035 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2429

description: Same tissue as sample 2041 but hybridized with Buffer1

tag: er/pr/her status


title: breast tumor part_IDC_rep1_2443

description: Same tissue as sample 2055 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2421

description: Same tissue as sample 2033 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2419

description: Same tissue as sample 2031 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2415

description: Same tissue as sample 2027 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2473

description: Same tissue as sample 2085 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2417

description: Same tissue as sample 2029 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2409

description: Same tissue as sample 2021 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2435

description: Same tissue as sample 2047 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2407

description: Same tissue as sample 2019 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_1703

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1707

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1705

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1711

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1653

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1687

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1713

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1701

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1649

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1655

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1643

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1617

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1645

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1619

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1623

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1667

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1651

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1597

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1581

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1685

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1647

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1599

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1583

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1587

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1579

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1577

description: Hybridized with Buffer1


title: MN, biological rep 6

description: Gene expression data of fluorescently labelled neurons laser microdissected from 10 micro meter thick cryo-sections.

source_name: Ca. 80 MNs from neonatal spinal cord


title: breast tumor part_IDC_rep1_1509

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1507

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_2439

description: Same tissue as sample 2051 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_1453

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1531

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1511

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1451

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1533

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1513

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1449

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1431

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1329

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1257

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1353

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1261

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1433

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_1331

description: Hybridized with Buffer1


title: breast tumor part_IDC_rep1_2459

description: Same tissue as sample 2071 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2405

description: Same tissue as sample 2017 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2425

description: Same tissue as sample 2037 but hybridized with Buffer1


title: breast tumor part_IDC_rep1_2413

description: Same tissue as sample 2025 but hybridized with Buffer1