title: iPSC cultured with feeder free condition rep3

city: Suehiro-cho, Tsurumi-ku

first: Yuki

last: Hasegawa

state: Yokohama-city

department: OSC

institute: RIKEN

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization of Illumina data and B-statistic calculations were carried out using the lumi and limma packages of Bioconductor in the R statistical language.

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

growth_protocol: Cells in the feeder condition were cultured on mitomycin C -treated SNL76/7 cells . miPS cells under feeder-free condition were cultured without feeder cells after adding 1000 units/ml of LIF  into the media containing 15% FBS, 0.1mM NEAA, 0.1mM 2-Mercaptoethanol in DMEM (high glucose without sodium pyruvate)

extract_protocol: RNA was purified for expression analysis by RNeasy mini kit (Qiagen, Washington DC, MA, http://www.qiagen.com/) after DNaseI treatment.

treatment_protocol: Cells were dissociating with 0.25% trypsin and lysised in Trizol solution.

tag: culture condition

tag: strain

value: induced-pluripotent stem cells


title: Pca_WCIPC-000032

status: Public on Jun 01 2011

type: RNA

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

country: USA

institute: Emory University

description: Prostate Cancer

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: SAMs were scanned using Illumina BeadArray Scanner

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.1

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

extract_protocol: Ambion Recoverall on MagMax Express 96 as described in Abramovitz et al, Biotechniques, 44(3): 417-23.

tag: disease state

value: Prostate Cancer

tag: tissue

value: Prostate cancer tumor

tag: group

tag: biochemical recurrence

value: Recurrence

tag: time f/u

tag: time no bcr

tag: time bcr

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa

tag: gleason score

tag: tumor stage

tag: patient number


title: 92% of iPSC cultured with feeder free condition signal mixed with 8% of MSTO signal in silico rep2

country: Japan

organism: Mus musculus

tag: cell type


title: Pca_WCIPC-000033

description: Prostate Cancer


title: 92% of iPSC cultured with feeder free condition signal mixed with 8% of MSTO signal in silico rep3


title: iPSC cultured on feeder cells rep3

source_name: iPSC cultured on feeder cells rep3

value: iPSC cultured on feeder cells


title: RR5b

description: RefRNA

source_name: Commercial

value: RefRNA


title: iPSC cultured with feeder free condition rep1


title: iPSC cultured on feeder cells rep2

source_name: iPSC cultured on feeder cells rep2


title: RR5a

description: RefRNA


title: RDb

description: RefDNA

value: RefDNA


title: RDa

description: RefDNA


title: Pca_PCS-000478_2

description: Prostate Cancer

value: Unknown


title: RR5c

description: RefRNA


title: iPSC cultured on feeder cells rep1

source_name: iPSC cultured on feeder cells rep1


title: N_PCS-000478_1

description: Normal

value: Normal

value: normal prostate


title: control vs MEHP 10uM biol rep 3, tech rep

city: Dunee

first: simon

middle: matthew

last: plummer

state: Angus

address: 2 James Lindsay Place

department: CXR

country: United Kingdom

institute: CXR Biosciences ltd

hyb_protocol: Agilent 2 colour hyb protocol

scan_protocol: Agilent FE 8.5.1.1 software, GE2 scan protocol, Agilent G2565B scanner

data_processing: The normalisation method was Agilent Feature Extraction 9.1 - Lowess. Rosetta resolver processing to generate signture lists of significantly altered genes (p<0.01)

organism: Rattus norvegicus

source_name: rat fetal testes explants

label_protocol: Agilent low input labelling kit 2 colour

growth_protocol: 0.5 ml of medium M199 (Invitrogen, Gibco), supplemented with gentamycin (50µg/ml; Life technologies, Cergy-Pontoise France) and fungizone (2.5 µg/ml;

extract_protocol: Qiagen Rneasy mini

treatment_protocol: Explanted testis was cultured either with medium containing vehicle,  1uM or 10uM  MEHP for 72 hrs

tag: agent

value: 10uM MEHP

treatment_protocol: Explanted testis was cultured with medium containing vehicle for 72 hrs

value: vehicle


title: control vs MEHP 10uM biol rep 2, tech rep


title: N_PCS-000473_1

description: Normal


title: Pca_PCS-000472_2

description: Prostate Cancer


title: Feeder cells (MSTO)  rep2

source_name: Feeder cells(MSTO)  rep2

value: Embryonic fibroblast expressing LIF


title: control vs MEHP 1uM, tech rep

value: 1uM MEHP


title: N_PCS-000472_1

description: Normal


title: 92% of iPSC cultured with feeder free condition signal mixed with 8% of MSTO signal in silico rep1

tag: culture condition


title: control vs MEHP 10uM biol rep 2


title: Feeder cells (MSTO)  rep1

source_name: Feeder cells(MSTO)  rep1

tag: strain


title: control vs MEHP 10uM biol rep 1


title: control vs MEHP 10uM biol rep 3


title: Pca_PCS-000293

description: Prostate Cancer

tag: disease state


title: iPSC cultured with feeder free condition rep2


title: Pca_PCS-000291

description: Prostate Cancer

tag: tissue


title: control vs MEHP 10uM biol rep 1, tech rep


title: Pca_PCS-000290

description: Prostate Cancer

tag: group


title: Pca_PCS-000473_2

description: Prostate Cancer

tag: biochemical recurrence


title: Pca_PCS-000289

description: Prostate Cancer

tag: time f/u


title: Pca_PCS-000287

description: Prostate Cancer

tag: time no bcr


title: A151 (TTAGGG) ODN + CpG ODN 3hr - repeat 3 - mAdbID:94933

city: Frederick

first: Dennis

middle: M

last: Klinman

state: MD

department: CIP

institute: NCI Frederick

description: mAdb experiment ID: 94933

hyb_protocol: Sample Hybridization Protocol Other: Murine oligonucleotide microarrays were produced by the NCI microarray facility (Gaithersburg, MD). Cy3 labeled reference and Cy5 labeled sample cDNAs (10 ìl each) were combined, denaturated by heating for 2 min at 98 oC and mixed with 36 ìl of hybridization solution at 42 oC (Ambion). Microarrays were overlaid with this solution and hybridized for 18 h at 42 oC using an actively mixing MAUI hybridization system (BioMicro Systems). Post hybridization, the arrays were washed in 1X SSC/0.05% SDS and 0.1X SSC, centrifuged to remove remaining liquid with unbound cDNA, and dried.

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47301;; 3.55693 Temperature: 26.9982

data_processing:
BRB Data Processing Protocol
Calculation Method: Data from 4 independent experiments/treatmentand 6 untreated controls were used for all statistical analyses. Reproducibility was established by comparing gene expression profiles among similarly treated mice from independent experiments in mAdb (referenced above). Expression analyses were performed using BRB ArrayTools (Biometric Research Branch, NCI). Data were background corrected, flagged values were removed, spots in which both signals were <110 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes Yang, 2002 3036 /id}] Analysis was restricted to genes present on >70% of the arrays after filtering. In toto, 30,722 features were reproducily tracked in all microarrays. The gene expression profile of all treatment groups was compared to that of the control groups. The genes differentially regulated by each treatment were categorized using Ingenuity Pathway Analysis (IPA, Ingenuity Systems Inc). Regulators of gene expression were identified and pathways were analyzed and generated using IPA and were supplemented with information from PubMed (http://www.ncbi.nlm.nih.gov/entrez).

source_name: Universal Mouse Reference RNA

label_protocol:
Cy3 Sample Labeling Protocol
Other: 20 ìg of total RNA was reverse-transcribed using 3 ìl of 10X first strand buffer (Stratagene), 2 ìl (5 ìg) of anchored Oligo(dT) (Invitrogen), 150 U of reverse transcriptase (StrataScript HC RT, Stratagene), 2 ìl 20X aminoallyl-dUTP/dNTP mix, and 3 ìl of 0.1 M DTT in a final volume of 30 ìl at 42 oC for 90 min. A reference mouse RNA sample (Stratagene) was processed in parallel. Both cDNA were purified using a MinElute PCR Purification Kit (Qiagen). 10 ìl of cDNA was labeled with Cy3 (universal reference cDNA) reactive dyes (Amersham Biosciences) diluted in 5 ìl of DMSO plus 1.7 ìl of 1M NaHCO3 for 90 min in the dark. Labeled cDNA was purified using MinElute PCR Purification Kits (Qiagen).

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: A151 (TTAGGG) ODN - 3 hours

label_protocol:
Cy5 Sample Labeling Protocol
Other: 20 ìg of total RNA was reverse-transcribed using 3 ìl of 10X first strand buffer (Stratagene), 2 ìl (5 ìg) of anchored Oligo(dT) (Invitrogen), 150 U of reverse transcriptase (StrataScript HC RT, Stratagene), 2 ìl 20X aminoallyl-dUTP/dNTP mix, and 3 ìl of 0.1 M DTT in a final volume of 30 ìl at 42 oC for 90 min. A reference mouse RNA sample (Stratagene) was processed in parallel. Both cDNA were purified using a MinElute PCR Purification Kit (Qiagen). 10 ìl of cDNA was labeled with Cy5 (sample cDNA) reactive dyes (Amersham Biosciences) diluted in 5 ìl of DMSO plus 1.7 ìl of 1M NaHCO3 for 90 min in the dark. Labeled cDNA was purified using MinElute PCR Purification Kits (Qiagen).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted from spleens using TRIzol reagent (Invitrogen) as specified by the manufacturer. 20 ìg of total RNA was reverse-transcribed using 3 ìl of 10X first strand buffer (Stratagene), 2 ìl (5 ìg) of anchored Oligo(dT) (Invitrogen), 150 U of reverse transcriptase (StrataScript HC RT, Stratagene), 2 ìl 20X aminoallyl-dUTP/dNTP mix, and 3 ìl of 0.1 M DTT in a final volume of 30 ìl at 42 oC for 90 min. A reference mouse RNA sample (Stratagene) was processed in parallel. Both cDNA were purified using a MinElute PCR Purification Kit (Qiagen).

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: A151 ODN (TTAGGG suppressive motifs) + equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400ug for A151 ODN and 400 ug CpG ODN
Treatment time: 3 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of A151 ODN (TTAGGG suppressive motifs) and an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0 hr and 3 hr.

value: BALB/c

tag: gender

value: female

value: spleen


title: A151 (TTAGGG) ODN + CpG ODN 3hr - repeat 4 - mAdbID:95544

description: mAdb experiment ID: 95544

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4315;; 3.51543 Temperature: 22.1152


title: CpG ODN 3hr - repeat 2 - mAdbID:88224

description: mAdb experiment ID: 88224

hyb_protocol: Hybridization Protocol Other: Cy-labeled reference and sample cDNAs (10 microliter each) were combined, de-naturated by heating for 2' at 98 C and mixed with 36 microliter of hybridization solution at 42 C (Ambion, Austin, TX). A low volume active mixing chamber was applied to the microarray via an adhesive gasket (MAUI mixer FL, BioMicro Systems, Salt Lake City, Utah), the hybridization solution containing the sample was added to the array, and was placed for 18 h at 42 C in the base unit of the actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah). Post hybridization, the arrays were washed in 1X SSC/0.05X SDS and 0.1X SSC, centrifuged to remove remaining liquid with unbound cDNA, and dried.

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.56;; 4.13 Temperature: 34.44

data_processing:
Data Processing Protocol
Calculation Method: Data were background corrected, flagged values were removed, spots with both signals less than 100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes. Only genes present on >70% of the arrays were included in the subsequent analysis.

label_protocol:
Cy3 Labeling Protocol
Other: 20 microgram of total RNA (universal reference mouse RNA, Stratagene, La Jolla, CA) was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy3 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

source_name: CpG ODN - 3 hrs BALB/c WT

label_protocol:
Cy5 Labeling Protocol
Other: 20 microgram of total RNA was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy5 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

extract_protocol:
RNA Extraction Protocol
Other: Total RNA was extracted from mice spleens using TRIzol reagent (Invitrogen, Carlsbad, CA) as specified by the manufacturer.

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 3 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: Pca_PCS-000286

description: Prostate Cancer

value: Prostate Cancer

tag: time bcr

tag: time clinical recurrence


title: Pca_PCS-000285

description: Prostate Cancer

value: Prostate cancer tumor

tag: time metastatic recurrence

tag: psa


title: A151 (TTAGGG) ODN + CpG ODN 3hr - repeat 2 - mAdbID:94852

description: mAdb experiment ID: 94852

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48613;; 3.52336 Temperature: 25.5638


title: Untreated Control - repeat 2 - mAdbID:88207

description: mAdb experiment ID: 88207

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.36;; 4.05 Temperature: 27.91

source_name: Untreated BALB/c WT


title: Pca_PCS-000284

description: Prostate Cancer

tag: gleason score

tag: tumor stage


title: A151 (TTAGGG) ODN + CpG ODN 3hr - repeat 1 - mAdbID:94866

description: mAdb experiment ID: 94866

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48308;; 3.56059 Temperature: 27.2118

tag: cell type


title: control vs MEHP 1uM

tag: agent


title: Pca_PCS-000283

description: Prostate Cancer

tag: patient number


title: Untreated Control - repeat 6 - mAdbID:88176

description: mAdb experiment ID: 88176

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.23;; 3.6 Temperature: 27.79

tag: strain


title: CpG ODN 3hr - repeat 3 - mAdbID:88205

description: mAdb experiment ID: 88205

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.36;; 4.05 Temperature: 25.69


title: Pca_PCS-000281

description: Prostate Cancer

tag: disease state


title: Pca_PCS-000282

description: Prostate Cancer

tag: tissue


title: Untreated Control - repeat 5 - mAdbID:88175

description: mAdb experiment ID: 88175

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.16;; 3.64 Temperature: 25.32


title: Pca_PCS-000280

description: Prostate Cancer

tag: group


title: Pca_PCS-000278

description: Prostate Cancer

tag: biochemical recurrence


title: Pca_PCS-000276

description: Prostate Cancer

tag: time f/u


title: CpG ODN 3hr - repeat 4 - mAdbID:88206

description: mAdb experiment ID: 88206

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.3;; 3.59 Temperature: 29.35


title: Untreated Control - repeat 3 - mAdbID:88174

description: mAdb experiment ID: 88174

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.66;; 4.15 Temperature: 35.09


title: Pca_PCS-000269

description: Prostate Cancer

tag: time no bcr


title: Untreated Control - repeat 4 - mAdbID:88163

description: mAdb experiment ID: 88163

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.67;; 4.15 Temperature: 35.15

tag: gender


title: Pca_PCS-000273

description: Prostate Cancer

tag: time bcr


title: Pca_PCS-000267

description: Prostate Cancer

tag: time clinical recurrence


title: Pca_PCS-000266

description: Prostate Cancer

tag: time metastatic recurrence


title: Pca_PCS-000265

description: Prostate Cancer

tag: psa


title: BC1-09 control

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

description: This research was approved by Ethic Committee of the Medical and Research Center - Hospital A. C. Camargo number 764/06. Twenty-six sporadic and favorable histology advanced (Stage III or IV) Wilms tumor (WT) samples from Children Oncology Group (NWTSG) were were used to isolate blastemal histological component as described in Maschietto et al. (2008). All patients had presented at least 5 years of follow-up. Total RNA was isolated using TRIzol (Sigma) according to manufacturer´s instructions. A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Alexa-3 or 5-labeled dCTP. A pool of RNAs obtained from 15 distinct human cell lines) was amplified following the same protocol and used as reference for microarray hybridizations. Dye-swap was performed for each sample as control for dye bias and used as replicate.

hyb_protocol: Hybridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Esperma de salmao,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: SSC2X / Temperature:42 / Time:10 / Washing Number: 1 Washing - Round 2 - Solution: SSC0,1X-SDS0,1% / Temperature:42 / Time:10 / Washing Number: 2 Washing - Round 3 - Solution: SSC0,1X-SDS0,1% / Temperature:42 / Time:10 / Washing Number: 3 Washing - Round 4 - Solution: SSC0,1X / Temperature:42 / Time:10 / Washing Number: 4

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowess-normalized log2(Cy3/Cy5) ratios

label: Alexa 555

label_protocol: Labeled cDNA was generated in a reverse transcriptase reaction using 4ug of amplified RNA (aRNA), random hexamer primer (Invitrogen Life Technologies, Carlsbad, CA), Alexa-3 or 5-labeled dCTP (Amersham, Biosciences) and IMPROM (PROMEGA) using oligo-dT7(24), following manufacture recommendations.

extract_protocol: kit Pico Pure RNA Isolation Kit

tag: wilms tumor sample

value: relapse tumor

tag: stage

value: III

label: Alexa 647

source_name: Reference

extract_protocol: Trizol

tag: sample

value: pool of 15 human cell lines


title: Pca_PCS-000264

description: Prostate Cancer

tag: gleason score

tag: tumor stage


title: BC1-05 swap


title: Pca_PCS-000263

description: Prostate Cancer

tag: patient number


title: BC1-08 swap


title: BC1-05 control


title: BC1-09 swap


title: BC1-30 swap

value: no-relapse tumor

value: IV


title: Untreated Control - repeat 1 - mAdbID:88172

description: mAdb experiment ID: 88172

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.29;; 4.06 Temperature: 26.94

tag: cell type

tag: strain


title: BC1-30 control


title: Pca_PCS-000260

description: Prostate Cancer

tag: disease state

tag: tissue

tag: group

value: Unknown


title: Pca_PCS-000261

description: Prostate Cancer

tag: biochemical recurrence

tag: time f/u

tag: time no bcr


title: Pca_PCS-000258

description: Prostate Cancer

tag: time bcr

tag: time clinical recurrence


title: BC1-04 control

tag: gender

value: male


title: BC1-04 swap

tag: wilms tumor sample


title: Pca_PCS-000257

description: Prostate Cancer

tag: time metastatic recurrence

tag: psa


title: Pca_PCS-000250

description: Prostate Cancer

tag: gleason score


title: Pca_PCS-000256

description: Prostate Cancer

tag: tumor stage


title: BC1-08 control

tag: stage

tag: sample


title: BC1-29 control


title: Pca_PCS-000252

description: Prostate Cancer

tag: patient number


title: BC1-27 swap


title: BC1-28 swap


title: Pca_PCS-000247

description: Prostate Cancer

tag: disease state


title: Pca_PCS-000249

description: Prostate Cancer

tag: tissue


title: BC1-29 swap


title: Pca_PCS-000245

description: Prostate Cancer

tag: group


title: Pca_PCS-000246

description: Prostate Cancer

tag: biochemical recurrence


title: BC1-25 control


title: Pca_PCS-000241

description: Prostate Cancer

tag: time f/u


title: BC1-26 swap


title: BC1-25 swap


title: BC1-28 control


title: BC1-24 swap


title: BC1-24 control


title: BC1-27 control


title: BC1-23 control


title: Pca_PCS-000237

description: Prostate Cancer

tag: time no bcr


title: BC1-23 swap


title: BC1-26 control


title: Pca_PCS-000235

description: Prostate Cancer

tag: time bcr


title: BC1-22 swap


title: Pca_PCS-000239

description: Prostate Cancer

tag: time clinical recurrence


title: Pca_PCS-000248

description: Prostate Cancer


title: Pca_PCS-000233

description: Prostate Cancer


title: Pca_PCS-000232

description: Prostate Cancer


title: BC1-21 control

tag: gender


title: BC1-22 control

tag: wilms tumor sample


title: BC1-20 swap


title: N_PCS-000230

description: Normal

value: Normal

value: normal prostate

tag: time metastatic recurrence


title: Pca_PCS-000228

description: Prostate Cancer

tag: psa


title: Pca_PCS-000234

description: Prostate Cancer

tag: gleason score


title: Pca_PCS-000225

description: Prostate Cancer

tag: tumor stage


title: Pca_PCS-000224

description: Prostate Cancer


title: Pca_PCS-000223

description: Prostate Cancer


title: BC1-02 control

tag: stage


title: BC1-21 swap

tag: sample


title: Pca_PCS-000221

description: Prostate Cancer

tag: patient number


title: Pca_PCS-000222

description: Prostate Cancer

tag: disease state


title: BC1-02 swap


title: Pca_PCS-000218

description: Prostate Cancer

tag: tissue


title: Pca_PCS-000214

description: Prostate Cancer

tag: group


title: Pca_PCS-000215

description: Prostate Cancer

tag: biochemical recurrence


title: Pca_PCS-000217

description: Prostate Cancer

tag: time f/u


title: BC1-19 control


title: BC1-18 control


title: Pca_PCS-000211

description: Prostate Cancer

tag: time no bcr


title: BC1-18 swap


title: BC1-19 swap


title: BC1-15 swap


title: Pca_PCS-000210

description: Prostate Cancer

tag: time bcr


title: BC1-20 control


title: Pca_PCS-000209

description: Prostate Cancer

tag: time clinical recurrence


title: BC1-17 control

tag: gender


title: BC1-15 control

tag: wilms tumor sample


title: BC1-17 swap


title: Pca_PCS-000208

description: Prostate Cancer

tag: time metastatic recurrence


title: Pca_PCS-000205

description: Prostate Cancer

tag: psa


title: N_PCS-000204

description: Normal

tag: gleason score


title: Pca_PCS-000203

description: Prostate Cancer

tag: tumor stage


title: BC1-14 control

tag: stage


title: Pca_PCS-000200

description: Prostate Cancer


title: Pca_PCS-000199

description: Prostate Cancer


title: BC1-13 control

tag: sample


title: BC1-01 swap


title: BC1-14 swap


title: BC1-10 control


title: BC1-10 swap


title: BC1-13 swap


title: Pca_PCS-000198

description: Prostate Cancer

tag: patient number


title: BC1-07 swap


title: BC1-01 control


title: Pca_PCS-000192

description: Prostate Cancer

tag: disease state


title: Pca_PCS-000193

description: Prostate Cancer

tag: tissue


title: Pca_PCS-000196

description: Prostate Cancer

tag: group


title: Pca_PCS-000191

description: Prostate Cancer

tag: biochemical recurrence


title: Pca_PCS-000194

description: Prostate Cancer

tag: time f/u


title: BC1-12 swap


title: BC1-12 control


title: Pca_PCS-000189

description: Prostate Cancer

tag: time no bcr


title: CpG ODN 3hr - repeat 1 - mAdbID:88222

description: mAdb experiment ID: 88222

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.42;; 4.08 Temperature: 30.26

tag: cell type

tag: strain


title: bcmo1 ko male under BC diet 5

city: Cleveland

first: Jaume

last: Amengual

state: Ohio

address: 2109 Aderbert Rd

department: Pharmacology

institute: case western reserve university

description: biological replicate 5 of 6. BCMO1 KO male under BC diet

hyb_protocol: Individual 825 ng Cy5-labeled cRNA and 825 ng pooled Cy3-labeled cRNA were fragmentated in 1x fragmentation and 1x blocking agent (Agilent Technologies) at 60 °C  for 30 minutes and thereafter mixed with Gex Hybridization Buffer HI-RPM (Agilent Technologies) and hybridized in a 1:1 ratio at 65 °C for 17 h in an Agilent Microarray hybridization chamber rotating at 4 rpm. After hybridization slides were washed according to the wash protocol with Stabilization and Drying solution (Agilent Technologies).

scan_protocol: Arrays were scanned at an Agilent scanner (G2505B) with 10% and 100% laser power intensities.

data_processing: Signal intensities for each spot were quantifed using feature extraction 9.1 (Agilent Technologies). Quality control for every microarray was performed visually by using ‘Quality’ control graphs from ‘Feature’extraction and M-A plots and boxplots, which were made using limmaGUI in R (Bioconductor).

source_name: inguinal adipose tissue

label_protocol: cDNA was synthesized from 1 µg of inguinal adipose tissue total RNA using the Agilent Low RNA Input Fluorescent Linear Amplification Kit for each animal without addition of spikes. Thereafter samples were split in 2 equal amounts, to synthesize Cyanine 3-CTP (Cy3) and Cyanine 5-CTP (Cy5) labeled cRNA using half the amounts as indicated by the manufacturer per dye (Agilent Technologies). Labelled cRNA was purified using RNeasy columns (Qiagen). 1200 ng of every Cy3 labeled cRNA sample was pooled and used as a common reference pool.

growth_protocol: Mice experiment was conducted according to accepted standard and humane care and use of laboratory animals, and was approved by the bioethical committee of the University of Freiburg (Germany). During the weaning period up to 5 weeks of age all mice were maintained on breeder chow containing 14000 IU of vitamin A/kg diet (Provima kliva AG, Switzerland).

extract_protocol: On the day of euthanization, blood was taken from the vena cava under unesthesia. The animals were then killed and tissues (including inguinal adipose tissue) were dissected.

treatment_protocol: five-week-old WT and BCMO1 KO male and female mice were fed a defined, pelletized diet containing 1500 IU vitamin A/kg and 10% energy as fat, without or with 150 mg BC/kg diet for 14 weeks prior euthanasia.

value: C57/BL6;129Svj background

tag: gender

tag: genotype/variation

value: bcmo1 knockout

tag: diet

value: BC

tag: diet intervention started

value: 5 weeks old

tag: age at sacrifice

value: 19 weeks old

value: inguinal adipose tissue

tag: sample type

value: common reference pool (representing every Cy3 labeled cRNA sample)


title: N_PCS-000188

description: Normal

scan_protocol: SAMs were scanned using Illumina BeadArray Scanner

tag: time bcr

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa

tag: gleason score

tag: tumor stage


title: BC1-07 control

tag: wilms tumor sample

tag: stage

tag: sample


title: Pca_PCS-000185

description: Prostate Cancer

tag: disease state

value: Prostate Cancer

tag: tissue

value: Prostate cancer tumor

tag: group

tag: biochemical recurrence

tag: time f/u

tag: time no bcr

tag: patient number


title: Pca_PCS-000184

description: Prostate Cancer


title: Pca_PCS-000186

description: Prostate Cancer


title: Pca_PCS-000182

description: Prostate Cancer


title: Pca_PCS-000187

description: Prostate Cancer


title: bcmo1 ko male under BC diet 2

description: biological replicate 2 of 6. BCMO1 KO male under BC diet

tag: strain

tag: gender

tag: genotype/variation

tag: diet

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: bcmo1 ko male under BC diet 1

description: biological replicate 1 of 6. BCMO1 KO male under BC diet


title: bcmo1 ko male under BC diet 3

description: biological replicate 3 of 6. BCMO1 KO male under BC diet


title: Pca_PCS-000178

description: Prostate Cancer

tag: time bcr

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa

tag: gleason score

tag: tumor stage


title: Pca_PCS-000180

description: Prostate Cancer

tag: disease state

tag: tissue

tag: group

tag: biochemical recurrence


title: S_PCS-000181

description: Stroma

value: Stroma

tag: time f/u

tag: time no bcr

tag: patient number


title: bcmo1 ko male under control diet 2

description: biological replicate 2 of 6. BCMO1 KO male under control diet

tag: strain

tag: gender

tag: genotype/variation

tag: diet

value: control


title: bcmo1 ko male under control diet 6

description: biological replicate 6 of 6. BCMO1 KO male under control diet

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: Pca_PCS-000179

description: Prostate Cancer

tag: time bcr

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa


title: bcmo1 ko male under BC diet 6

description: biological replicate 6 of 6. BCMO1 KO male under BC diet

tag: tissue


title: Pca_PCS-000176

description: Prostate Cancer

tag: disease state

tag: group

tag: gleason score

tag: tumor stage


title: Pca_PCS-000183

description: Prostate Cancer

tag: biochemical recurrence

tag: time f/u

tag: time no bcr

tag: patient number


title: bcmo1 ko male under control diet 4

description: biological replicate 4 of 6. BCMO1 KO male under control diet

tag: strain

tag: gender

tag: genotype/variation

tag: diet


title: bcmo1 ko male under control diet 5

description: biological replicate 5 of 6. BCMO1 KO male under control diet

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: bcmo1 ko male under BC diet 4

description: biological replicate 4 of 6. BCMO1 KO  male under BC diet


title: Pca_PCS-000170

description: Prostate Cancer

tag: time bcr

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa


title: bcmo1 ko male under control diet 3

description: biological replicate 3 of 6. BCMO1 KO male under control diet

tag: tissue


title: Pca_PCS-000173

description: Prostate Cancer

tag: disease state

tag: group

tag: gleason score

tag: tumor stage


title: bcmo1 ko male under control diet 1

description: biological replicate 1 of 6. BCMO1 KO male under control diet


title: Pca_PCS-000166

description: Prostate Cancer

tag: biochemical recurrence

tag: time f/u

tag: time no bcr

tag: patient number


title: Pca_PCS-000164

description: Prostate Cancer


title: wild-type male under BC diet 2

description: biological replicate 2 of 5. wild-type male under BC diet

tag: strain

tag: gender

tag: genotype/variation

value: wild-type

tag: diet


title: wild-type male under BC diet 5

description: biological replicate 5 of 5. wild-type male under BC diet

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: Pca_PCS-000161

description: Prostate Cancer

tag: time bcr

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa


title: Pca_PCS-000162

description: Prostate Cancer

tag: disease state

tag: tissue

tag: group

tag: gleason score


title: Pca_PCS-000159

description: Prostate Cancer

tag: biochemical recurrence

tag: time f/u

tag: time no bcr

tag: tumor stage


title: wild-type male under BC diet 3

description: biological replicate 3 of 5. wild-type male under BC diet

tag: strain

tag: gender

tag: genotype/variation


title: Pca_PCS-000139

description: Prostate Cancer

tag: patient number


title: Pca_PCS-000136

description: Prostate Cancer

value: Non-Recurrence


title: Pca_PCS-000135

description: Prostate Cancer


title: bcmo1 ko female under BC diet 6

description: biological replicate 6 of 6. BCMO1 KO female under BC diet

value: female

tag: diet

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: wild-type male under control diet 3

description: biological replicate 3 of 6. wild-type male under control diet

value: male


title: wild-type male under control diet 6

description: biological replicate 6 of 6. wild-type male under control diet


title: wild-type male under BC diet 4

description: biological replicate 4 of 5. wild-type male under BC diet


title: wild-type male under BC diet 1

description: biological replicate 1 of 5. wild-type male under BC diet


title: wild-type male under control diet 2

description: biological replicate 2 of 6. wild-type male under control diet


title: bcmo1 ko female under BC diet 3

description: biological replicate 3 of 6. BCMO1 KO female under BC diet


title: Pca_PCS-000130

description: Prostate Cancer

value: Recurrence

value: Unknown

tag: time bcr

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa


title: bcmo1 ko female under BC diet 4

description: biological replicate 4 of 6. BCMO1 KO  female under BC diet

value: C57/BL6;129Svj background

tag: tissue


title: Pca_PCS-000129

description: Prostate Cancer

tag: disease state

tag: group

tag: biochemical recurrence

tag: gleason score


title: wild-type male under control diet 4

description: biological replicate 4 of 6. wild-type male under control diet

tag: strain


title: wild-type male under control diet 5

description: biological replicate 5 of 6. wild-type male under control diet

tag: gender


title: Pca_PCS-000128

description: Prostate Cancer

tag: time f/u

tag: time no bcr

tag: tumor stage


title: bcmo1 ko female under BC diet 5

description: biological replicate 5 of 6. BCMO1 KO female under BC diet

tag: genotype/variation

value: bcmo1 knockout

tag: diet

tag: diet intervention started


title: Pca_PCS-000133

description: Prostate Cancer

tag: time bcr

tag: patient number


title: bcmo1 ko female under BC diet 1

description: biological replicate 1 of 6. BCMO1 KO female under BC diet

value: BC

tag: age at sacrifice

tag: sample type


title: bcmo1 ko female under control diet 6

description: biological replicate 6 of 6. BCMO1 KO female under control diet

value: 5 weeks old

tag: tissue


title: Pca_PCS-000125

description: Prostate Cancer

tag: disease state

tag: time clinical recurrence

tag: time metastatic recurrence

tag: psa


title: wild-type male under control diet 1

description: biological replicate 1 of 6. wild-type male under control diet

tag: strain

value: 19 weeks old


title: Pca_PCS-000120_2

description: Prostate Cancer

tag: group

tag: biochemical recurrence

tag: gleason score


title: bcmo1 ko female under control diet 5

description: biological replicate 5 of 6. BCMO1 KO female under control diet

tag: gender

value: inguinal adipose tissue


title: bcmo1 ko female under BC diet 2

description: biological replicate 2 of 6. BCMO1 KO female under BC diet

tag: genotype/variation

value: common reference pool (representing every Cy3 labeled cRNA sample)


title: Pca_PCS-000123

description: Prostate Cancer

value: Prostate Cancer

tag: time f/u

tag: time no bcr

tag: tumor stage


title: Pca_PCS-000119

description: Prostate Cancer

value: Prostate cancer tumor

tag: time bcr

tag: patient number


title: N_PCS-000120_1

description: Normal

value: Normal

value: normal prostate


title: bcmo1 ko female under control diet 2

description: biological replicate 2 of 6. BCMO1 KO female under control diet

tag: diet

value: control

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: Pca_PCS-000116

description: Prostate Cancer

tag: disease state

tag: tissue

tag: time clinical recurrence

tag: time metastatic recurrence


title: Pca_PCS-000115

description: Prostate Cancer

tag: group

tag: biochemical recurrence

tag: psa


title: Pca_PCS-000095

description: Prostate Cancer

tag: gleason score


title: Pca_PCS-000086

description: Prostate Cancer

tag: time f/u


title: bcmo1 ko female under control diet 3

description: biological replicate 3 of 6. BCMO1 KO female under control diet

tag: strain

tag: gender

tag: genotype/variation


title: wild-type female under BC diet 5

description: biological replicate 5 of 6. wild-type female under BC diet

value: wild-type


title: bcmo1 ko female under control diet 1

description: biological replicate 1 of 6. BCMO1 KO female under control diet

value: female


title: bcmo1 ko female under control diet 4

description: biological replicate 4 of 6. BCMO1 KO  female under control diet


title: Pca_PCS-000081

description: Prostate Cancer

value: Non-Recurrence

tag: time no bcr

tag: time bcr

tag: tumor stage

tag: patient number


title: Pca_PCS-000077

description: Prostate Cancer


title: Pca_PCS-000074

description: Prostate Cancer


title: Pca_PCS-000064

description: Prostate Cancer


title: wild-type female under BC diet 2

description: biological replicate 2 of 6. wild-type female under BC diet

tag: diet

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: Pca_PCS-000072

description: Prostate Cancer

tag: disease state

tag: tissue

tag: time clinical recurrence

tag: time metastatic recurrence


title: wild-type female under BC diet 3

description: biological replicate 3 of 6. wild-type female under BC diet


title: wild-type female under BC diet 1

description: biological replicate 1 of 6. wild-type female under BC diet


title: wild-type female under BC diet 6

description: biological replicate 6 of 6. wild-type female under BC diet


title: wild-type female under control diet 6

description: biological replicate 6 of 6. wild-type female under control diet


title: Pca_PCS-000080

description: Prostate Cancer

tag: group

tag: biochemical recurrence

tag: psa

tag: gleason score


title: wild-type female under BC diet 4

description: biological replicate 4 of 6. wild-type female under BC diet

tag: strain

tag: gender

tag: genotype/variation


title: Pca_PCS-000063

description: Prostate Cancer

value: Recurrence

tag: time f/u

tag: time no bcr

tag: time bcr

tag: tumor stage


title: Pca_PCS-000083

description: Prostate Cancer

value: Unknown

tag: patient number


title: Pca_PCS-000066

description: Prostate Cancer


title: wild-type female under control diet 4

description: biological replicate 4 of 6. wild-type female under control diet

value: C57/BL6;129Svj background

tag: diet

tag: diet intervention started

tag: age at sacrifice

tag: sample type


title: KO-coc-P6-Technical-rep2-b

city: Boston

first: Zheng-Yi

last: Chen

state: MA

address: 243 Charles Street

department: Otolaryngology

institute: MEEI

description:
Gene expression data from P6 Rb1 cKO cochleas
rb-ko-coc-2b

hyb_protocol: Following the Affymetrix gene chip standard protocol of hybridization Wash and stain. 15 ug of fragmented cRNA were hybridized on GeneChip MOE430 A or B Genome Array. The arrays were placed in Affymetrix Genechip Hybridization Oven 640, incubated for 16 hours at 45C, 60rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene chip Scanner 3000 7G.

data_processing: The data were analyzed with dChip, normalized using Invariant set normalization method. The expression values of Model-based expression indexes (MBEI) were created with PM/MM difference model using the default settings. The data were also analyzed with MAS 5.0 to obtain Present/Absent calls.

source_name: Rb1 cKO cochleas at P6, Pooled, Technical rep2

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Small Sample Target Labeling Assay Version II protocol from 0.3-2 ug total RNA.

growth_protocol: Mice were maintained in MGH animal facility.

extract_protocol: Total RNA was extracted with Qiagen Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: P6 or 2-month control and Rb1 cKO littermates were euthanized and the inner ear tissues were dissected in DMEM-F12 medium. Dissected tissues were collected in RNAlater solution for RNA extraction.

tag: tissue

value: dissected cochlea

value: Pou4f3-Cre:Rb1 cKO

tag: age


title: wild-type female under control diet 3

description: biological replicate 3 of 6. wild-type female under control diet

value: 5 weeks old


title: Pca_PCS-000062

description: Prostate Cancer

tag: disease state

tag: group

tag: biochemical recurrence

tag: time clinical recurrence

tag: time metastatic recurrence


title: wild-type female under control diet 5

description: biological replicate 5 of 6. wild-type female under control diet

tag: strain

tag: gender

tag: genotype/variation

value: 19 weeks old


title: wild-type female under control diet 2

description: biological replicate 2 of 6. wild-type female under control diet

value: inguinal adipose tissue


title: Pca_PCS-000057

description: Prostate Cancer

tag: time f/u

tag: time no bcr

tag: time bcr

tag: psa

tag: gleason score


title: Ctrl-coc-P6-Technical-rep1-b

description:
Gene expression data from P6 Rb1 control cochleas
rb-ctrl-coc-1b

source_name: Rb1 control cochleas at P6, Pooled, Technical rep1

value: wild type


title: Ctrl-coc-P6-Technical-rep2-b

description:
Gene expression data from P6 Rb1 control cochleas
rb-ctrl-coc-2b

source_name: Rb1 control cochleas at P6, Pooled, Technical rep2


title: Pca_PCS-000055

description: Prostate Cancer

source_name: Prostate

value: Prostate Cancer

tag: tumor stage

tag: patient number


title: KO-utr-P6-Technical-rep1-b

description:
Gene expression data from P6 Rb1 cKO utricles
rb-ko-utr-1b

source_name: Rb1 cKO utricles at P6, Pooled, Technical rep1

tag: tissue

value: dissected utricle


title: Pca_PCS-000038

description: Prostate Cancer

value: Prostate cancer tumor


title: Pca_PCS-000037

description: Prostate Cancer


title: Pca_PCS-000042

description: Prostate Cancer


title: Pca_PCS-000019

description: Prostate Cancer


title: KO-coc-P6-Technical-rep1-b

description:
Gene expression data from P6 Rb1 cKO cochleas
rb-ko-coc-1b

source_name: Rb1 cKO cochleas at P6, Pooled, Technical rep1

tag: age


title: Ctrl-utr-P6-Technical-rep1-b

description:
Gene expression data from P6 Rb1 control utricles
rb-ctrl-utr-1b

source_name: Rb1 control utricles at P6, Pooled, Technical rep1


title: Pca_PCS-000013

description: Prostate Cancer

tag: disease state


title: KO-utr-2month-Technical-rep2-b

description:
Gene expression data from 2-month Rb1 cKO utricles
BrnRb-2m-KO-2b

source_name: Rb1 cKO utricles at 2 months, Pooled, Technical rep2

value: 2 months


title: Ctrl-utr-P6-Technical-rep2-b

description:
Gene expression data from P6 Rb1 control utricles
rb-ctrl-utr-2b

source_name: Rb1 control utricles at P6, Pooled, Technical rep2


title: KO-utr-2month-Technical-rep1-b

description:
Gene expression data from 2-month Rb1 cKO utricles
BrnRb-2m-KO-1b

source_name: Rb1 cKO utricles at 2 months, Pooled, Technical rep1


title: Pca_PCS-000005

description: Prostate Cancer

tag: group


title: Pca_PCS-000053

description: Prostate Cancer

tag: biochemical recurrence


title: wild-type female under control diet 1

description: biological replicate 1 of 6. wild-type female under control diet

tag: diet

value: control

tag: diet intervention started

tag: age at sacrifice

tag: sample type

value: common reference pool (representing every Cy3 labeled cRNA sample)


title: KO-utr-P6-Technical-rep2-b

description:
Gene expression data from P6 Rb1 cKO utricles
rb-ko-utr-2b

source_name: Rb1 cKO utricles at P6, Pooled, Technical rep2

tag: genotype/variation


title: Ctrl-utr-2month-Technical-rep1-b

description:
Gene expression data from 2-month Rb1 control utricles
BrnRb-2m-Ctrl-1b

source_name: Rb1 control utricles at 2 months, Pooled, Technical rep1


title: Male_gDNA_1

type: genomic

molecule: genomic DNA

source_name: Commercial

tag: time f/u

tag: time clinical recurrence

tag: time metastatic recurrence


title: Ctrl-utr-2month-Technical-rep2-b

description:
Gene expression data from 2-month Rb1 control utricles
BrnRb-2m-Ctrl-2b

source_name: Rb1 control utricles at 2 months, Pooled, Technical rep2


title: Pca_PCS-000017

description: Prostate Cancer

tag: time no bcr

tag: time bcr

tag: psa


title: Pca_PCS-000051

description: Prostate Cancer

tag: gleason score

tag: tumor stage

tag: patient number


title: Male_gDNA_2

tag: disease state


title: ref RNA2 Val Set

description: ref RNA_Ctrl

tag: group

value: ref RNA

tag: time clin rec

tag: time met rec


title: ref RNA3 Val Set

description: ref RNA_Ctrl

tag: biochemical recurrence


title: KO-coc-P6-Technical-rep2-a

description:
Gene expression data from P6 Rb1 cKO cochleas
rb-ko-coc-2a

tag: tissue

tag: age


title: Ctrl-coc-P6-Technical-rep1-a

description:
Gene expression data from P6 Rb1 control cochleas
rb-ctrl-coc-1a

tag: genotype/variation


title: Pca_PCS-000478 Val Set

description: Prostate Cancer

tag: time f/u


title: KO-utr-P6-Technical-rep1-a

description:
Gene expression data from P6 Rb1 cKO utricles
rb-ko-utr-1a


title: Pca_PCS-000473 Val Set

description: Prostate Cancer


title: KO-coc-P6-Technical-rep1-a

description:
Gene expression data from P6 Rb1 cKO cochleas
rb-ko-coc-1a


title: Pca_PCS-000472.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000472.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000472 Val Set

description: Prostate Cancer


title: KO-utr-P6-Technical-rep2-a

description:
Gene expression data from P6 Rb1 cKO utricles
rb-ko-utr-2a


title: Ctrl-utr-P6-Technical-rep2-a

description:
Gene expression data from P6 Rb1 control utricles
rb-ctrl-utr-2a


title: Ctrl-coc-P6-Technical-rep2-a

description:
Gene expression data from P6 Rb1 control cochleas
rb-ctrl-coc-2a


title: Pca_PCS-000293.2 Val Set

description: Prostate Cancer


title: KO-utr-2month-Technical-rep2-a

description:
Gene expression data from 2-month Rb1 cKO utricles
BrnRb-2m-KO-2a


title: Ctrl-utr-P6-Technical-rep1-a

description:
Gene expression data from P6 Rb1 control utricles
rb-ctrl-utr-1a


title: Ctrl-utr-2month-Technical-rep2-a

description:
Gene expression data from 2-month Rb1 control utricles
BrnRb-2m-Ctrl-2a


title: Ctrl-utr-2month-Technical-rep1-a

description:
Gene expression data from 2-month Rb1 control utricles
BrnRb-2m-Ctrl-1a


title: KO-utr-2month-Technical-rep1-a

description:
Gene expression data from 2-month Rb1 cKO utricles
BrnRb-2m-KO-1a


title: Pca_PCS-000293 Val Set

description: Prostate Cancer


title: ref RNA1 Val Set

description: ref RNA_Ctrl


title: Pca_PCS-000289 Val Set

description: Prostate Cancer

value: Non-Recurrence


title: Pca_PCS-000282 Val Set

description: Prostate Cancer


title: Pca_PCS-000273 Val Set

description: Prostate Cancer


title: Pca_PCS-000278 Val Set

description: Prostate Cancer

value: Recurrence


title: Pca_PCS-000280 Val Set

description: Prostate Cancer


title: Pca_PCS-000273.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000269 Val Set

description: Prostate Cancer


title: Pca_PCS-000265 Val Set

description: Prostate Cancer


title: Pca_PCS-000252 Val Set

description: Prostate Cancer


title: Pca_PCS-000257 Val Set

description: Prostate Cancer


title: villus_NWD2_rep3

city: Bronx

first: DONGHAI

last: WANG

state: NY

institute: Montefiore Medical Center

description: Gene expression data from small intestine villi of mice fed with NWD2.

hyb_protocol: Fragmented cRNA was hybridized on the Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CHP files generated by GCOS were imported into BRB-ArrayTools. The spots and probesets with absent calls were filtered. Signal intensities were log transformed (base 2) and global median normalization was performed.

source_name: villus from mice fed with NWD2 for 1 year

label_protocol: Biotinylated cRNA were prepared from 5 ug total RNA following the procedures in the Affymetrix Expression Analysis Technical Manual.

growth_protocol: All of the mice were housed in cages in a conventional animal room and had continuous access to tap water and food.

extract_protocol: Total RNA from the tissues was isolated and purified with the Qiagen RNeasy Mini Kit.

treatment_protocol: Upon weaning, mice used for the dietary study were randomized into 3 groups and fed with different diets (Ain76A, NWD1 and NWD2) for 1 year; mice for the genetic study were fed with Ain76A for 3 months.

tag: strain

tag: genotype

value: villus

tag: food

value: 1 year


title: villus_NWD2_rep1


title: villus_NWD1_rep4

description: Gene expression data from small intestine villi of mice fed with NWD1.

source_name: villus from mice fed with NWD1 for 1 year


title: Pca_PCS-000246 Val Set

description: Prostate Cancer

tag: time no bcr

tag: time bcr


title: Pca_PCS-000248 Val Set

description: Prostate Cancer

tag: psa

tag: gleason score


title: Pca_PCS-000239 Val Set

description: Prostate Cancer

value: Unknown

tag: tumor stage

tag: patient number


title: villus_NWD2_rep2


title: villus_NWD1_rep2


title: Pca_PCS-000237 Val Set

description: Prostate Cancer

tag: group


title: villus_Ain76A_rep4

description: Gene expression data from small intestine villi of mice fed with Ain76A.

source_name: villus from mice fed with Ain76A for 1 year


title: villus_Ain76A_rep3


title: villus_Ain76A_rep2


title: villus_NWD1_rep3


title: crypt_NWD2_rep4

description: Gene expression data from small intestine crypts of mice fed with NWD2.

source_name: crypt from mice fed with NWD2 for 1 year

value: crypt


title: villus_NWD1_rep1


title: crypt_NWD2_rep1


title: crypt_NWD1_rep4

description: Gene expression data from small intestine crypts of mice fed with NWD1.

source_name: crypt from mice fed with NWD1 for 1 year


title: villus_Ain76A_rep1


title: crypt_NWD1_rep3


title: Pca_PCS-000233.2 Val Set

description: Prostate Cancer

tag: time clin rec


title: Pca_PCS-000233 Val Set

description: Prostate Cancer

tag: time met rec


title: Pca_PCS-000233.3 Val Set

description: Prostate Cancer

tag: biochemical recurrence


title: crypt_NWD2_rep2

tag: tissue


title: crypt_NWD1_rep2

tag: age


title: crypt_NWD1_rep1


title: Pca_PCS-000225.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000230 Val Set

description: Prostate Cancer


title: Pca_PCS-000225 Val Set

description: Prostate Cancer


title: Pca_PCS-000222.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000222.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000218 Val Set

description: Prostate Cancer


title: Pca_PCS-000222 Val Set

description: Prostate Cancer


title: Pca_PCS-000215 Val Set

description: Prostate Cancer


title: Pca_PCS-000200 Val Set

description: Prostate Cancer


title: Pca_PCS-000209 Val Set

description: Prostate Cancer


title: crypt_Ain76A_rep2

description: Gene expression data from small intestine crypts of mice fed with Ain76A.

source_name: crypt from mice fed with Ain76A for 1 year


title: Pca_PCS-000196.2 Val Set

description: Prostate Cancer

source_name: Prostate


title: Pca_PCS-000196.3 Val Set

description: Prostate Cancer


title: villus_p21-/-_rep3

description: Gene expression data from small intestine villi of p21-/- mice.

source_name: villus from 3-month-old p21-/- mice

value: 3 months


title: Pca_PCS-000196 Val Set

description: Prostate Cancer


title: crypt_NWD2_rep3


title: Pca_PCS-000193 Val Set

description: Prostate Cancer


title: villus_p21-/-_rep4


title: Pca_PCS-000186.3 Val Set

description: Prostate Cancer


title: villus_Apc1638N/+_rep4

description: Gene expression data from small intestine villi of Apc1638N/+ mice.

source_name: villus from 3-month-old Apc1638N/+ mice


title: villus_p21-/-_rep2


title: crypt_Ain76A_rep4


title: villus_Apc1638N/+_rep3


title: crypt_Ain76A_rep3


title: villus_p21-/-_rep1


title: villus_Apc1638N/+_rep1


title: Pca_PCS-000186.2 Val Set

description: Prostate Cancer


title: villus_wild type_rep4

description: Gene expression data from small intestine villi of wild type mice.

source_name: villus from 3-month-old wild type mice


title: crypt_Ain76A_rep1


title: villus_Apc1638N/+_rep2


title: villus_wild type_rep2


title: villus_wild type_rep3


title: villus_wild type_rep1


title: Pca_PCS-000186 Val Set

description: Prostate Cancer


title: Pca_PCS-000185 Val Set

description: Prostate Cancer


title: Pca_PCS-000184 Val Set

description: Prostate Cancer


title: Pca_PCS-000180 Val Set

description: Prostate Cancer


title: Pca_PCS-000180.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000170 Val Set

description: Prostate Cancer


title: Pca_PCS-000180.2 Val Set

description: Prostate Cancer


title: crypt_p21-/-_rep3

description: Gene expression data from small intestine crypts of p21-/- mice.

source_name: crypt from 3-month-old p21-/- mice


title: Pca_PCS-000139 Val Set

description: Prostate Cancer


title: Pca_PCS-000166 Val Set

description: Prostate Cancer


title: Pca_PCS-000135 Val Set

description: Prostate Cancer


title: Pca_PCS-000136 Val Set

description: Prostate Cancer


title: crypt_p21-/-_rep2


title: Pca_PCS-000130 Val Set

description: Prostate Cancer


title: Pca_PCS-000133 Val Set

description: Prostate Cancer


title: Pca_PCS-000129 Val Set

description: Prostate Cancer


title: Pca_PCS-000176 Val Set

description: Prostate Cancer


title: crypt_Apc1638N/+_rep4

description: Gene expression data from small intestine crypts of Apc1638N/+ mice.

source_name: crypt from 3-month-old Apc1638N/+ mice


title: crypt_Apc1638N/+_rep2


title: crypt_wild type_rep4

description: Gene expression data from small intestine crypts of wild type mice.

source_name: crypt from 3-month-old wild type mice


title: Pca_PCS-000125 Val Set

description: Prostate Cancer


title: crypt_p21-/-_rep1


title: crypt_Apc1638N/+_rep3


title: crypt_wild type_rep2


title: crypt_Apc1638N/+_rep1


title: Pca_PCS-000120 Val Set

description: Prostate Cancer


title: crypt_wild type_rep3


title: crypt_wild type_rep1


title: Pca_PCS-000119 Val Set

description: Prostate Cancer


title: Experimental 2

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

description: AE2 Diab

hyb_protocol: GeneChip arrays were hybridized overnight in the Affymetrix hybridization oven at 42oC. Washing and scanning was performed using the Affymetrix GeneChip Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0; Affymetrix GCOS software) using Affymetrix default analysis settings and global scaling as normalization method. Statistical evaluation was done with Cyber-T and GeneSpring.

source_name: mouse placenta including decidua, diabetic

label_protocol: Biotin-labeled samples were generated using the Affymetrix Eukaryotic One-Cycle Target Labeling Assay.

extract_protocol: Placentae were dissected at E10.5, weighted and stored in Trizol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Diabetes was induced in femal FVB mice by two intraperitoneal injections of 100mg/kg body weight Streptozotocin in 50mM sodium citrate buffer within a one week interval. Mice with a blood glucose level higher than 250mg/dL were considered diabetic and used for mating. The morning with the presence of a vaginal plug was counted as day 0.5.

value: FVB

tag: gender

value: female

value: placenta including decidua

tag: phenotype

value: diabetic


title: Experimental 5

description: AE5 Diab

tag: strain


title: Experimental 3

description: AE3 Diab


title: Experimental 1

description: AE1 Diab


title: Experimental 4

description: AE4 Diab


title: Pca_PCS-000116.3 Val Set

description: Prostate Cancer

value: Prostate Cancer

tag: time f/u


title: Pca_PCS-000060

description: Prostate Cancer

tag: disease state

value: Prostate cancer tumor

tag: time clinical recurrence

tag: time metastatic recurrence


title: Pca_PCS-000116.2 Val Set

description: Prostate Cancer

tag: time no bcr

tag: time bcr

tag: psa


title: Pca_PCS-000123 Val Set

description: Prostate Cancer

tag: gleason score

tag: tumor stage

tag: patient number


title: Pca_PCS-000116 Val Set

description: Prostate Cancer

tag: group

tag: time clin rec

tag: time met rec


title: Pca_PCS-000115 Val Set

description: Prostate Cancer

tag: biochemical recurrence


title: Pca_PCS-000095 Val Set

description: Prostate Cancer


title: Pca_PCS-000083.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000081.3 Val Set

description: Prostate Cancer


title: Control 5

description: FVB C5

source_name: mouse placenta including decidua, control

tag: age

tag: gender

tag: tissue


title: OPC-Rev_1

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku,

department: Institute for Genetic Medicine

institute: Hokkaido University

hyb_protocol: Labeled probes were used for the GeneChip Mouse Genome 430 2.0 array (Affymetrix) according to the manufacturer’s instructions.

data_processing: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix) to generate CEL data. The CEL data were then analyzed with dChip software, which can normalize and process multiple datasets simultaneously.

source_name: mouse OPC

label_protocol: Five micrograms of total RNA were labeled with biotin by in vitro transcription (IVT) using the One-Cycle Target Labeling procedure for biotin labeling by in vitro transcription (Affymetrix), according to the manufacturer’s instruction.

growth_protocol: Oligodendrocyte precursor cells were prepared from postnatal day 0 mouse brain and expanded in serum-free Dulbecco's Modified Eagle's medium (DMEM) medium containing bovine insulin (10 μg/ml), human transferrin (100 μg/ml), BSA (100 μg/ml), progesterone (60 ng/ml), putrescine (16 μg/ml), sodium selenite (40 ng/ml), N-acetylcysteine (60 μg/ml), forskolin (5 μM), PDGF (10 ng/ml), penicillin, streptomycin.

extract_protocol: Total RNA was prepared using a RNeasy Mini Kit (QIAGEN).

tag: cell type

value: oligodendrocyte precursor cells

tag: strain

value: brain

value: postnatal day 0


title: Pca_PCS-000081.2 Val Set

description: Prostate Cancer

tag: time f/u


title: Pca_PCS-000086 Val Set

description: Prostate Cancer


title: Control 2

description: FVB C2

tag: phenotype

value: control


title: Pca_PCS-000081 Val Set

description: Prostate Cancer

value: Non-Recurrence

tag: time no bcr


title: ASTL61-2

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix) to generate CEL data.

data_processing: The CEL data were then analyzed with dChip software, which can normalize and process multiple datasets simultaneously.

source_name: mouse AST

growth_protocol: NSCs were prepared from embryonic day 14.5 mouse telencephalon and expanded in serum-free Dulbecco's Modified Eagle's medium (DMEM) /F12 medium containing bovine insulin (10 μg/ml), human transferrin (100 μg/ml), BSA (100 μg/ml), progesterone (60 ng/ml), putrescine (16 μg/ml), sodium selenite (40 ng/ml), N-acetylcysteine (60 μg/ml), forskolin (5 μM), PDGF (10 ng/ml), penicillin, streptomycin, and bFGF as floating spheres. Astrocytes were induced in NSC cultures by changing the medium to DMEM with 10% FCS for 3 wks. OPCs were induced by culturing NSCs in DMEM containing PDGFAA (10 ng/ml), bFGF (2 ng/ml), and 0.25% FCS and purified by sequential immunopanning.

value: astrocytes

tag: genotype

value: E14.5 embryo


title: Pca_PCS-000074 Val Set

description: Prostate Cancer

tag: time bcr

tag: psa


title: Pca_PCS-000077 Val Set

description: Prostate Cancer

tag: gleason score

tag: tumor stage


title: Control 3

description: FVB C3


title: OPC-CG4_1


title: Control 1

description: FVB C1


title: OPC-CG4_2


title: OPC-FCS_2


title: Control 4

description: FVB C4


title: OPC-Rev_2


title: OPC-FCS_1


title: AST-1


title: ASTL61-1


title: Pca_PCS-000066 Val Set

description: Prostate Cancer

tag: group

tag: patient number


title: Pca_PCS-000083 Val Set

description: Prostate Cancer

tag: time clin rec

tag: time met rec


title: Pca_PCS-000064 Val Set

description: Prostate Cancer

tag: biochemical recurrence


title: Pca_PCS-000063 Val Set

description: Prostate Cancer

value: Recurrence


title: OPCL61-1

tag: age


title: OPC-2

tag: tissue


title: OPCL61-2

tag: cell type


title: AST-2

tag: strain


title: OPC-1


title: Pca_PCS-000060 Val Set

description: Prostate Cancer

tag: time f/u


title: Pca_PCS-000060.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000057.3 Val Set

description: Prostate Cancer


title: NSCL61-2-2

source_name: mouse NSC

value: neural stem cells


title: Pca_PCS-000062 Val Set

description: Prostate Cancer

value: Unknown


title: Pca_PCS-000057 Val Set

description: Prostate Cancer


title: Pca_PCS-000057.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000055 Val Set

description: Prostate Cancer


title: Pca_PCS-000053.2 Val Set

description: Prostate Cancer


title: Pca_PCS-000060.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000053.3 Val Set

description: Prostate Cancer


title: Pca_PCS-000051 Val Set

description: Prostate Cancer


title: Pca_PCS-000038 Val Set

description: Prostate Cancer


title: Pca_PCS-000017 Val Set

description: Prostate Cancer


title: Pca_PCS-000053 Val Set

description: Prostate Cancer


title: Pca_PCS-000005 Val Set

description: Prostate Cancer


title: Pca_PCS-000013 Val Set

description: Prostate Cancer


title: Pca_PCS-000037 Val Set

description: Prostate Cancer


title: Pca_PCS-000042 Val Set

description: Prostate Cancer


title: NSC-2


title: Gene profiling of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice; 7 days post-injury. Biological Replicate 1.

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: Analysis of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice Killed 7 days post-injury

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Images were extracted with the GeneChip Operating Software (Affymetrix GCOS v1.4). Quality control of microarrays was performed using the AffyQCReport software. Background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA).The data were Analyzed using the AffylmGUI Graphical User Interface for the LIMMA microarray package (Wettenhall et al., 2006), and Partek Genomics Suite (Partek Incorporated, St-Louis, MO).

label: Biotin

source_name: Sciatic nerve distal stump of C57BL/6 OlaHsd-Wlds mice at 7 days post-injury

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

extract_protocol: Mice were anesthetized by inhalation of isoflurane and killed by cervical dislocation. Then, sciatic nerves were collected and conective tissue removed. A 4 mm long segment was taken. Tissue was then rapidly frozen in liquid nitrogen and kept at -80C until RNA extraction. Total RNA isolation was performed from pooled tissues by TRI Reagent and purified with the GenElute mammalian total RNA miniprep kit, according to the manufacturer's instructions (Sigma-Aldrich Canada Ltd).

tag: genotype/variation

value: WldS mutant

value: C57BL/6 OlaHsd-Wlds

value: 8-12 weeks old

value: sciatic nerve

tag: stress

value: injured (microcrush lesion)

tag: time

value: 7 days (post-injury)


title: crypt_p21-/-_rep4

tag: genotype

value: crypt

tag: food

value: 3 months


title: Gene profiling of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice; 3 days post-injury. Biological Replicate 2.

description: Analysis of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice Killed 3 days post-injury

source_name: Sciatic nerve distal stump of C57BL/6 OlaHsd-Wlds mice at 3 days post-injury

value: 3 days (post-injury)


title: Gene profiling of the injuried sciatic nerve of C57BL/6 mice; 3 days post-injury. Biological Replicate 2.

description: Analysis of the injuried sciatic nerve of C57BL/6 mice Killed 3 days post-injury

source_name: Sciatic nerve distal stump of C57BL/6 mice at 3 days post-injury

value: wild type


title: N_WCIPC-000186

description: Normal

value: Normal

tag: biochemical recurrence:

tag: time no bcr

tag: time bcr

tag: psa

tag: gleason score


title: N_WCIPC-000184

description: Normal

tag: group

tag: time clin rec

tag: time met rec

tag: tumor stage

tag: patient number


title: N_WCIPC-000182

description: Normal


title: Gene profiling of the injuried sciatic nerve of C57BL/6 mice; 7 days post-injury. Biological Replicate 2.

description: Analysis of the injuried sciatic nerve of C57BL/6 mice Killed 7 days post-injury

source_name: Sciatic nerve distal stump of C57BL/6 mice at 7 days post-injury

tag: strain

tag: age

tag: tissue


title: N_WCIPC-000185

description: Normal

tag: time f/u


title: NSCL61-1-2

tag: cell type

value: brain


title: N_WCIPC-000180

description: Normal


title: Gene profiling of the injuried sciatic nerve of C57BL/6 mice; 7 days post-injury. Biological Replicate 1.

tag: genotype/variation

tag: stress

tag: time


title: Gene profiling of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice; 14 days post-injury. Biological Replicate 2.

description: Analysis of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice Killed 14 days post-injury

source_name: Sciatic nerve distal stump of C57BL/6 OlaHsd-Wlds mice at 14 days post-injury

value: 14 days (post-injury)


title: Gene profiling of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice; 7 days post-injury. Biological Replicate 2.


title: Gene profiling of uninjured C57BL/6 OlaHsd-Wlds mouse sciatic nerve. Biological Replicate 1.

description: Analysis of uninjured C57BL/6 OlaHsd-Wlds mouse sciatic nerve.

source_name: Sciatic nerve of naive C57BL/6 OlaHsd-Wlds mice

value: uninjured (naive)

value: 0 days


title: Gene profiling of the injuried sciatic nerve of C57BL/6 mice; 14 days post-injury. Biological Replicate 1.

description: Analysis of the injuried sciatic nerve of C57BL/6 mice Killed 14 days post-injury

source_name: Sciatic nerve distal stump of C57BL/6 mice at 14 days post-injury


title: Gene profiling of uninjured C57BL/6 mouse sciatic nerve. Biological Replicate 2.

description: Analysis of uninjured C57BL/6 mouse sciatic nerve.

source_name: Sciatic nerve of naive C57BL/6 mice


title: N_WCIPC-000179

description: Normal

source_name: Prostate

tag: biochemical recurrence:

tag: time no bcr


title: Gene profiling of uninjured C57BL/6 OlaHsd-Wlds mouse sciatic nerve. Biological Replicate 2.


title: N_WCIPC-000178

description: Normal

tag: time bcr

tag: psa


title: Pca_WCIPC-000176

description: Prostate Cancer

tag: group

value: Prostate Cancer

tag: biochemical recurrence

value: Recurrence

tag: gleason score


title: Gene profiling of the injuried sciatic nerve of C57BL/6 mice; 3 days post-injury. Biological Replicate 1.


title: Gene profiling of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice; 14 days post-injury. Biological Replicate 1.

value: WldS mutant


title: Gene profiling of the injuried sciatic nerve of C57BL/6 mice; 14 days post-injury. Biological Replicate 2.


title: Xenopus laevis_ClutchC_Stage23_rep

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: Xenopus laevis_ClutchC_Stage23_rep

hyb_protocol: The hybridization and washing of the microarrays were performed following the Agilent protocol for single-channel arrays.

scan_protocol: Agilent Microarray Scanner was used to scan the slides

data_processing: Feature Extraction was used for data processing with protocol GE1_105_Jan09

organism: Xenopus laevis

source_name: Xenopus laevis_ClutchC_Stage23_rep

label_protocol: 7μg of RNA was labeled with Cy-3 and 1.65μg of labeled aRNA was incubated on each microarray. Each embryonic stage was measured in biological triplicates (independent clutches).

growth_protocol: Standard Xenopus techniques were followed to induce ovulation , perform in vitro fertilization, and dejelly the eggs (Sive, Grainger et al. 2000). For the embryo collection of both Xenopus  tropicalis and Xenopus  laevis, the sperm of four individual males was used to individually fertilize clutches of eggs obtained from three females. These 12 clutches were then incubated at 22°C in the case of Xenopus  laevis and 28°C in the case of Xenopus  tropicalis, to provide each species with the optimal temperature for development (see Supplementary Materials). Embryos were staged according to Nieuwkoop and Faber (Nieuwkoop and Faber 1994) and 3 embryos were collected from each clutch at 14 developmental stages spanning the blastula (stages 2, 8, 9), gastrula (stages 10, 12, and 13), neurula (stages 14, 16, 18, and 20), and tailbud stages (stages 23, 25, 30 and 33). After collection, the three clutches with the highest rates of survival and normal development were selected for microarray analysis.

extract_protocol: RNA was extracted from eggs using the RNaqueous kit (Ambion). In the case of Xenopus  laevis each sample comprised a single egg while in Xenopus  tropicalis three eggs were combined to generate RNA amounts comparable to Xenopus  laevis levels. 1μg of total RNA was amplified by one round of in vitro transcription (IVT) using the MessageAmpII kit (Ambion). We also added to this reaction RNA from a Spike-in kit (Agilent) that included 10 different species of RNA at various concentrations.

tag: developmental stage


title: Gene profiling of uninjured C57BL/6 mouse sciatic nerve. Biological Replicate 1.


title: Pca_WCIPC-000172

description: Prostate Cancer

tag: time clin rec

tag: time met rec

tag: tumor stage

value: Unknown

tag: patient number


title: NSC-1

value: neural stem cells

tag: genotype

tag: strain

tag: tissue

tag: age

value: E14.5 embryo


title: Gene profiling of the injuried sciatic nerve of C57BL/6 OlaHsd-Wlds mice; 3 days post-injury. Biological Replicate 1.

tag: genotype/variation

value: C57BL/6 OlaHsd-Wlds

value: 8-12 weeks old

value: sciatic nerve

tag: stress

value: injured (microcrush lesion)

tag: time


title: Pca_WCIPC-000175

description: Prostate Cancer

value: Non-Recurrence

tag: time f/u

tag: time no bcr

tag: time bcr


title: Pca_WCIPC-000161

description: Prostate Cancer

tag: group

tag: biochemical recurrence

tag: psa


title: Pca_WCIPC-000163

description: Prostate Cancer

tag: time clin rec

tag: gleason score


title: Pca_WCIPC-000166

description: Prostate Cancer

tag: time met rec

tag: tumor stage


title: Pca_WCIPC-000167

description: Prostate Cancer

tag: patient number


title: Pca_WCIPC-000159

description: Prostate Cancer


title: Xenopus laevis_ClutchC_Stage10

description: Xenopus laevis_ClutchC_Stage10

source_name: Xenopus laevis_ClutchC_Stage10

tag: developmental stage


title: Pca_WCIPC-000150

description: Prostate Cancer


title: Xenopus laevis_ClutchC_Stage25

description: Xenopus laevis_ClutchC_Stage25

source_name: Xenopus laevis_ClutchC_Stage25


title: Xenopus laevis_ClutchC_Stage9

description: Xenopus laevis_ClutchC_Stage9

source_name: Xenopus laevis_ClutchC_Stage9


title: Xenopus laevis_ClutchC_Stage13

description: Xenopus laevis_ClutchC_Stage13

source_name: Xenopus laevis_ClutchC_Stage13


title: Xenopus laevis_ClutchC_Stage20

description: Xenopus laevis_ClutchC_Stage20

source_name: Xenopus laevis_ClutchC_Stage20


title: Xenopus laevis_ClutchC_Stage40

description: Xenopus laevis_ClutchC_Stage40

source_name: Xenopus laevis_ClutchC_Stage40


title: Xenopus laevis_ClutchC_Stage8

description: Xenopus laevis_ClutchC_Stage8

source_name: Xenopus laevis_ClutchC_Stage8


title: Pca_WCIPC-000147

description: Prostate Cancer


title: Xenopus laevis_ClutchC_Stage23

description: Xenopus laevis_ClutchC_Stage23

source_name: Xenopus laevis_ClutchC_Stage23


title: Xenopus laevis_ClutchC_Stage16

description: Xenopus laevis_ClutchC_Stage16

source_name: Xenopus laevis_ClutchC_Stage16


title: Xenopus laevis_ClutchC_Stage33

description: Xenopus laevis_ClutchC_Stage33

source_name: Xenopus laevis_ClutchC_Stage33


title: Xenopus laevis_ClutchC_Stage14

description: Xenopus laevis_ClutchC_Stage14

source_name: Xenopus laevis_ClutchC_Stage14


title: Xenopus laevis_ClutchC_Stage30

description: Xenopus laevis_ClutchC_Stage30

source_name: Xenopus laevis_ClutchC_Stage30


title: Pca_WCIPC-000154

description: Prostate Cancer


title: Pca_WCIPC-000138

description: Prostate Cancer


title: Pca_WCIPC-000134

description: Prostate Cancer


title: Pca_WCIPC-000145

description: Prostate Cancer


title: Pca_WCIPC-000141

description: Prostate Cancer


title: Pca_WCIPC-000133

description: Prostate Cancer


title: Pca_WCIPC-000144

description: Prostate Cancer


title: Pca_WCIPC-000129

description: Prostate Cancer


title: Pca_WCIPC-000136

description: Prostate Cancer


title: Pca_WCIPC-000126

description: Prostate Cancer


title: Pca_WCIPC-000124

description: Prostate Cancer


title: Xenopus laevis_ClutchC_Stage18

description: Xenopus laevis_ClutchC_Stage18

source_name: Xenopus laevis_ClutchC_Stage18


title: Xenopus laevis_ClutchC_Stage12

description: Xenopus laevis_ClutchC_Stage12

source_name: Xenopus laevis_ClutchC_Stage12


title: Pca_WCIPC-000125

description: Prostate Cancer


title: Pca_WCIPC-000127

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage18

description: Xenopus laevis_ClutchB_Stage18

source_name: Xenopus laevis_ClutchB_Stage18


title: Pca_WCIPC-000117

description: Prostate Cancer

source_name: Prostate


title: Xenopus laevis_ClutchC_Stage2

description: Xenopus laevis_ClutchC_Stage2

source_name: Xenopus laevis_ClutchC_Stage2


title: Xenopus laevis_ClutchB_Stage13

description: Xenopus laevis_ClutchB_Stage13

source_name: Xenopus laevis_ClutchB_Stage13


title: Xenopus laevis_ClutchB_Stage30

description: Xenopus laevis_ClutchB_Stage30

source_name: Xenopus laevis_ClutchB_Stage30


title: Xenopus laevis_ClutchB_Stage20

description: Xenopus laevis_ClutchB_Stage20

source_name: Xenopus laevis_ClutchB_Stage20


title: Xenopus laevis_ClutchB_Stage2

description: Xenopus laevis_ClutchB_Stage2

source_name: Xenopus laevis_ClutchB_Stage2


title: Xenopus laevis_ClutchB_Stage33

description: Xenopus laevis_ClutchB_Stage33

source_name: Xenopus laevis_ClutchB_Stage33


title: Xenopus laevis_ClutchB_Stage14

description: Xenopus laevis_ClutchB_Stage14

source_name: Xenopus laevis_ClutchB_Stage14


title: Pca_WCIPC-000115

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage23

description: Xenopus laevis_ClutchB_Stage23

source_name: Xenopus laevis_ClutchB_Stage23


title: Pca_WCIPC-000114

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage40

description: Xenopus laevis_ClutchB_Stage40

source_name: Xenopus laevis_ClutchB_Stage40


title: Pca_WCIPC-000121

description: Prostate Cancer


title: Pca_WCIPC-000112

description: Prostate Cancer


title: Pca_WCIPC-000113

description: Prostate Cancer


title: Pca_WCIPC-000108

description: Prostate Cancer


title: Pca_WCIPC-000111

description: Prostate Cancer


title: Pca_WCIPC-000107

description: Prostate Cancer


title: Pca_WCIPC-000101

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage12

description: Xenopus laevis_ClutchB_Stage12

source_name: Xenopus laevis_ClutchB_Stage12


title: Xenopus laevis_ClutchB_Stage10

description: Xenopus laevis_ClutchB_Stage10

source_name: Xenopus laevis_ClutchB_Stage10


title: Pca_WCIPC-000096

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage16

description: Xenopus laevis_ClutchB_Stage16

source_name: Xenopus laevis_ClutchB_Stage16


title: Pca_WCIPC-000100

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage9

description: Xenopus laevis_ClutchB_Stage9

source_name: Xenopus laevis_ClutchB_Stage9


title: Pca_WCIPC-000089

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage40_rep

description: Xenopus laevis_ClutchB_Stage40_rep

source_name: Xenopus laevis_ClutchB_Stage40_rep


title: Pca_WCIPC-000087

description: Prostate Cancer


title: Xenopus laevis_ClutchA_Stage40_rep

description: Xenopus laevis_ClutchA_Stage40_rep

source_name: Xenopus laevis_ClutchA_Stage40_rep


title: Xenopus laevis_ClutchA_Stage30

description: Xenopus laevis_ClutchA_Stage30

source_name: Xenopus laevis_ClutchA_Stage30


title: Pca_WCIPC-000081

description: Prostate Cancer

source_name: Prostate


title: Pca_WCIPC-000073

description: Prostate Cancer


title: Xenopus laevis_ClutchA_Stage33

description: Xenopus laevis_ClutchA_Stage33

source_name: Xenopus laevis_ClutchA_Stage33


title: Pca_WCIPC-000079

description: Prostate Cancer


title: Pca_WCIPC-000084

description: Prostate Cancer


title: Xenopus laevis_ClutchA_Stage20

description: Xenopus laevis_ClutchA_Stage20

source_name: Xenopus laevis_ClutchA_Stage20


title: Pca_WCIPC-000043

description: Prostate Cancer


title: Pca_WCIPC-000033

description: Prostate Cancer


title: Pca_WCIPC-000063

description: Prostate Cancer


title: Xenopus laevis_ClutchA_Stage23

description: Xenopus laevis_ClutchA_Stage23

source_name: Xenopus laevis_ClutchA_Stage23


title: Pca_WCIPC-000032

description: Prostate Cancer


title: Xenopus laevis_ClutchA_Stage16

description: Xenopus laevis_ClutchA_Stage16

source_name: Xenopus laevis_ClutchA_Stage16


title: Pca_WCIPC-000058

description: Prostate Cancer


title: Xenopus laevis_ClutchB_Stage25

description: Xenopus laevis_ClutchB_Stage25

source_name: Xenopus laevis_ClutchB_Stage25


title: Xenopus laevis_ClutchA_Stage40

description: Xenopus laevis_ClutchA_Stage40

source_name: Xenopus laevis_ClutchA_Stage40


title: Pca_WCIPC-000064

description: Prostate Cancer


title: Xenopus laevis_ClutchA_Stage25

description: Xenopus laevis_ClutchA_Stage25

source_name: Xenopus laevis_ClutchA_Stage25


title: Pca_WCIPC-000001

description: Prostate Cancer


title: Xenopus laevis_ClutchA_Stage8

description: Xenopus laevis_ClutchA_Stage8

source_name: Xenopus laevis_ClutchA_Stage8


title: Xenopus laevis_ClutchA_Stage18

description: Xenopus laevis_ClutchA_Stage18

source_name: Xenopus laevis_ClutchA_Stage18


title: Xenopus laevis_ClutchA_Stage13

description: Xenopus laevis_ClutchA_Stage13

source_name: Xenopus laevis_ClutchA_Stage13


title: Xenopus tropicalis_ClutchC_Stage2

description: Xenopus tropicalis_ClutchC_Stage2

organism: Xenopus tropicalis

source_name: Xenopus tropicalis_ClutchC_Stage2


title: Xenopus laevis_ClutchA_Stage10

description: Xenopus laevis_ClutchA_Stage10

source_name: Xenopus laevis_ClutchA_Stage10


title: Xenopus laevis_ClutchA_Stage14

description: Xenopus laevis_ClutchA_Stage14

source_name: Xenopus laevis_ClutchA_Stage14


title: Xenopus tropicalis_ClutchC_Stage13

description: Xenopus tropicalis_ClutchC_Stage13

source_name: Xenopus tropicalis_ClutchC_Stage13


title: Xenopus laevis_ClutchA_Stage12

description: Xenopus laevis_ClutchA_Stage12

source_name: Xenopus laevis_ClutchA_Stage12


title: Xenopus laevis_ClutchA_Stage2

description: Xenopus laevis_ClutchA_Stage2

source_name: Xenopus laevis_ClutchA_Stage2


title: RR5b

description: RefRNA

source_name: Commercial

value: RefRNA

tag: biochemical recurrence:

tag: time f/u:

tag: time no bcr:

tag: time bcr:

tag: time clin rec:

tag: time met rec:

tag: psa:

tag: gleason score:

tag: tumor stage:

tag: patient number:


title: RR5a

description: RefRNA

tag: group


title: RR5c

description: RefRNA


title: Pca_PCS-000139

description: Prostate Cancer

source_name: Prostate

tag: biochemical recurrence

tag: time f/u

tag: time no bcr

tag: time bcr

tag: time clin rec

tag: psa


title: N_PCS-000472_1

description: Normal

value: Normal

tag: biochemical recurrence:

tag: time met rec

tag: gleason score

tag: tumor stage

tag: patient number


title: N_PCS-000478_1

description: Normal


title: RDb

description: RefDNA

value: RefDNA

tag: time f/u:

tag: time no bcr:

tag: time bcr:

tag: time clin rec:

tag: time met rec:


title: N_PCS-000473_1

description: Normal

tag: group


title: Xenopus laevis_ClutchB_Stage8

description: Xenopus laevis_ClutchB_Stage8

source_name: Xenopus laevis_ClutchB_Stage8

tag: developmental stage


title: RDa

description: RefDNA

tag: psa:

tag: gleason score:

tag: tumor stage:

tag: patient number:


title: Xenopus tropicalis_ClutchC_Stage33

description: Xenopus tropicalis_ClutchC_Stage33

source_name: Xenopus tropicalis_ClutchC_Stage33


title: Xenopus tropicalis_ClutchC_Stage12

description: Xenopus tropicalis_ClutchC_Stage12

source_name: Xenopus tropicalis_ClutchC_Stage12


title: Xenopus tropicalis_ClutchC_Stage25

description: Xenopus tropicalis_ClutchC_Stage25

source_name: Xenopus tropicalis_ClutchC_Stage25


title: Xenopus laevis_ClutchA_Stage9

description: Xenopus laevis_ClutchA_Stage9

source_name: Xenopus laevis_ClutchA_Stage9


title: Xenopus tropicalis_ClutchC_Stage9

description: Xenopus tropicalis_ClutchC_Stage9

source_name: Xenopus tropicalis_ClutchC_Stage9


title: Pca_PCS-000133

description: Prostate Cancer

tag: biochemical recurrence

tag: time f/u

tag: time no bcr

tag: time bcr

tag: time clin rec

tag: psa


title: Pca_PCS-000135

description: Prostate Cancer

tag: time met rec

tag: gleason score

tag: tumor stage

tag: patient number


title: Xenopus tropicalis_ClutchC_Stage23

description: Xenopus tropicalis_ClutchC_Stage23

source_name: Xenopus tropicalis_ClutchC_Stage23


title: Xenopus tropicalis_ClutchC_Stage14

description: Xenopus tropicalis_ClutchC_Stage14

source_name: Xenopus tropicalis_ClutchC_Stage14


title: Xenopus tropicalis_ClutchC_Stage20

description: Xenopus tropicalis_ClutchC_Stage20

source_name: Xenopus tropicalis_ClutchC_Stage20


title: Pca_PCS-000130

description: Prostate Cancer


title: Xenopus tropicalis_ClutchC_Stage16

description: Xenopus tropicalis_ClutchC_Stage16

source_name: Xenopus tropicalis_ClutchC_Stage16


title: Pca_PCS-000129

description: Prostate Cancer


title: Pca_PCS-000125

description: Prostate Cancer


title: Xenopus tropicalis_ClutchC_Stage8

description: Xenopus tropicalis_ClutchC_Stage8

source_name: Xenopus tropicalis_ClutchC_Stage8


title: N_PCS-000120_1

description: Normal

tag: biochemical recurrence:


title: Pca_PCS-000123

description: Prostate Cancer

tag: group


title: Pca_PCS-000136

description: Prostate Cancer


title: Pca_PCS-000119

description: Prostate Cancer


title: Xenopus tropicalis_ClutchC_Stage10

description: Xenopus tropicalis_ClutchC_Stage10

source_name: Xenopus tropicalis_ClutchC_Stage10

tag: developmental stage


title: Pca_PCS-000116

description: Prostate Cancer


title: Xenopus tropicalis_ClutchC_Stage18

description: Xenopus tropicalis_ClutchC_Stage18

source_name: Xenopus tropicalis_ClutchC_Stage18


title: Pca_PCS-000115

description: Prostate Cancer


title: Xenopus tropicalis_ClutchC_Stage30

description: Xenopus tropicalis_ClutchC_Stage30

source_name: Xenopus tropicalis_ClutchC_Stage30


title: Xenopus tropicalis_ClutchB_Stage13

description: Xenopus tropicalis_ClutchB_Stage13

source_name: Xenopus tropicalis_ClutchB_Stage13


title: Xenopus tropicalis_ClutchB_Stage14

description: Xenopus tropicalis_ClutchB_Stage14

source_name: Xenopus tropicalis_ClutchB_Stage14


title: Pca_PCS-000086

description: Prostate Cancer

source_name: Prostate


title: Pca_PCS-000083

description: Prostate Cancer


title: Pca_PCS-000081

description: Prostate Cancer


title: Xenopus tropicalis_ClutchB_Stage33

description: Xenopus tropicalis_ClutchB_Stage33

source_name: Xenopus tropicalis_ClutchB_Stage33


title: Pca_PCS-000074

description: Prostate Cancer


title: Xenopus tropicalis_ClutchB_Stage10

description: Xenopus tropicalis_ClutchB_Stage10

source_name: Xenopus tropicalis_ClutchB_Stage10


title: Pca_PCS-000066

description: Prostate Cancer


title: Xenopus tropicalis_ClutchB_Stage18

description: Xenopus tropicalis_ClutchB_Stage18

source_name: Xenopus tropicalis_ClutchB_Stage18


title: Xenopus tropicalis_ClutchB_Stage20

description: Xenopus tropicalis_ClutchB_Stage20

source_name: Xenopus tropicalis_ClutchB_Stage20


title: Xenopus tropicalis_ClutchB_Stage12

description: Xenopus tropicalis_ClutchB_Stage12

source_name: Xenopus tropicalis_ClutchB_Stage12


title: Pca_PCS-000095

description: Prostate Cancer


title: Pca_PCS-000077

description: Prostate Cancer


title: Xenopus tropicalis_ClutchB_Stage23

description: Xenopus tropicalis_ClutchB_Stage23

source_name: Xenopus tropicalis_ClutchB_Stage23


title: Xenopus tropicalis_ClutchB_Stage2

description: Xenopus tropicalis_ClutchB_Stage2

source_name: Xenopus tropicalis_ClutchB_Stage2


title: Xenopus tropicalis_ClutchB_Stage9

description: Xenopus tropicalis_ClutchB_Stage9

source_name: Xenopus tropicalis_ClutchB_Stage9


title: Xenopus tropicalis_ClutchB_Stage30

description: Xenopus tropicalis_ClutchB_Stage30

source_name: Xenopus tropicalis_ClutchB_Stage30


title: Xenopus tropicalis_ClutchB_Stage8

description: Xenopus tropicalis_ClutchB_Stage8

source_name: Xenopus tropicalis_ClutchB_Stage8


title: Pca_PCS-000063

description: Prostate Cancer


title: Pca_PCS-000064

description: Prostate Cancer


title: Pca_PCS-000060

description: Prostate Cancer


title: Xenopus tropicalis_ClutchB_Stage16

description: Xenopus tropicalis_ClutchB_Stage16

source_name: Xenopus tropicalis_ClutchB_Stage16


title: Xenopus tropicalis_ClutchB_Stage10_env_control


title: Pca_PCS-000062

description: Prostate Cancer


title: Xenopus tropicalis_ClutchB_Stage25

description: Xenopus tropicalis_ClutchB_Stage25

source_name: Xenopus tropicalis_ClutchB_Stage25


title: Xenopus tropicalis_ClutchB_Stage40

description: Xenopus tropicalis_ClutchB_Stage40

source_name: Xenopus tropicalis_ClutchB_Stage40


title: Pca_PCS-000055

description: Prostate Cancer


title: Xenopus tropicalis_ClutchA_Stage8_repeat


title: Pca_PCS-000053

description: Prostate Cancer


title: Pca_PCS-000057

description: Prostate Cancer


title: Xenopus tropicalis_ClutchA_Stage12_repeat


title: Xenopus tropicalis_ClutchA_Stage10

description: Xenopus tropicalis_ClutchA_Stage10

source_name: Xenopus tropicalis_ClutchA_Stage10


title: Pca_PCS-000051

description: Prostate Cancer


title: Pca_PCS-000038

description: Prostate Cancer


title: Pca_PCS-000042

description: Prostate Cancer


title: Pca_PCS-000037

description: Prostate Cancer


title: Xenopus tropicalis_ClutchA_Stage33

description: Xenopus tropicalis_ClutchA_Stage33

source_name: Xenopus tropicalis_ClutchA_Stage33


title: Pca_PCS-000017

description: Prostate Cancer


title: Pca_PCS-000013

description: Prostate Cancer


title: Xenopus tropicalis_ClutchA_Stage40

description: Xenopus tropicalis_ClutchA_Stage40

source_name: Xenopus tropicalis_ClutchA_Stage40


title: Pca_PCS-000005

description: Prostate Cancer

source_name: Prostate


title: Xenopus tropicalis_ClutchA_Stage14

description: Xenopus tropicalis_ClutchA_Stage14

source_name: Xenopus tropicalis_ClutchA_Stage14


title: Xenopus tropicalis_ClutchA_Stage13

description: Xenopus tropicalis_ClutchA_Stage13

source_name: Xenopus tropicalis_ClutchA_Stage13


title: Xenopus tropicalis_ClutchA_Stage25

description: Xenopus tropicalis_ClutchA_Stage25

source_name: Xenopus tropicalis_ClutchA_Stage25


title: Xenopus tropicalis_ClutchA_Stage18

description: Xenopus tropicalis_ClutchA_Stage18

source_name: Xenopus tropicalis_ClutchA_Stage18


title: Xenopus tropicalis_ClutchA_Stage30

description: Xenopus tropicalis_ClutchA_Stage30

source_name: Xenopus tropicalis_ClutchA_Stage30


title: Xenopus tropicalis_ClutchA_Stage8

description: Xenopus tropicalis_ClutchA_Stage8

source_name: Xenopus tropicalis_ClutchA_Stage8


title: Xenopus tropicalis_ClutchA_Stage20

description: Xenopus tropicalis_ClutchA_Stage20

source_name: Xenopus tropicalis_ClutchA_Stage20


title: Xenopus tropicalis_ClutchA_Stage2

description: Xenopus tropicalis_ClutchA_Stage2

source_name: Xenopus tropicalis_ClutchA_Stage2


title: Xenopus tropicalis_ClutchA_Stage12

description: Xenopus tropicalis_ClutchA_Stage12

source_name: Xenopus tropicalis_ClutchA_Stage12


title: Xenopus tropicalis_ClutchA_Stage16

description: Xenopus tropicalis_ClutchA_Stage16

source_name: Xenopus tropicalis_ClutchA_Stage16


title: MCF10A-3D-16days-5

city: Nashville

first: David

last: Simpson

state: TN

address: Suite 4140 Medical Research Building III

institute: Vanderbilt University Medical Center

description: Gene expression data from cells cultured in 3D for 16 days

hyb_protocol: The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.

scan_protocol: The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.

data_processing: The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.

source_name: cells cultured in 3D for 16 days

label_protocol: 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

growth_protocol: MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).

extract_protocol: The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.

tag: cell type

value: mammary epithelial cells

tag: cell line

value: MCF10A cells

tag: culture condition

value: Matrigel (3D)

tag: time

value: 16 days


title: MCF10A-3D-16days-4


title: MCF10A-3D-16days-3


title: Xenopus tropicalis_ClutchA_Stage9

description: Xenopus tropicalis_ClutchA_Stage9

source_name: Xenopus tropicalis_ClutchA_Stage9


title: MCF10A-3D-16days-2


title: Xenopus tropicalis_ClutchA_Stage23

description: Xenopus tropicalis_ClutchA_Stage23

source_name: Xenopus tropicalis_ClutchA_Stage23


title: MCF10A-3D-16days-1


title: MCF7-CARM1#13-DOX+E2-b

city: Madison

first: Wei

last: Xu

state: WI

address: 1400 University Ave

institute: UW-Madison

description:
Dox and E2
SOM01X75
Sample barcode: 6562602

hyb_protocol: Hybridization was performed at 42C for 20hrs, according to NimbleGen gene expression arrays user’s guide (2010).

scan_protocol: One-color NimbleGen arrays were scanned with the MS 200 Microarray Scanner and the data were extract using the MS 200 Data Collection Software.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: breast cancer cell line

label_protocol: Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit was used to synthesize double-stranded cDNA that was going to be labeled using a NimbleGen One-Color DNA Labeling Kit.

growth_protocol: MCF7-tet-on-CARM1 cells were grown in DMEM in 10% FBS. Two days before E2 treatment, the cells were switched to phenol-red free DMEM with 5% 6X charcoal stripped FBS.

extract_protocol: mRNA were extracted from cells using Qiagen Rneasy Kit

treatment_protocol: When the cells were treated with Dox, they were treated with 1ug/ml Dox for 4 days to induce CARM1 expression. The medium were changed to phenol-red free DMEM+charcoal stripped FBS for 2 days before treating with E2 (10nM)

value: breast cancer cell line

value: MCF7-tet-on-CARM1 clone 13

tag: treatment

value: Dox and D2


title: MCF10A-2D-5days-1

description: Gene expression data from cells cultured in 2D for 5 days

source_name: cells cultured in 2D for 5 days

value: traditional monolayer cell culture setting (2D)

value: 5 days


title: MCF10A-3D-8days-3

description: Gene expression data from cells cultured in 3D for 8 days

source_name: cells cultured in 3D for 8 days

value: 8 days


title: MCF10A-2D-2days-3

description: Gene expression data from cells cultured in 2D for 2 days

source_name: cells cultured in 2D for 2 days

value: 2 days


title: Xenopus tropicalis_ClutchA_Stage10_env_control


title: MCF10A-3D-8days-2


title: MCF10A-2D-5days-3


title: MCF10A-3D-8days-1


title: Control Individual 8

city: Burnaby

first: Nicole

middle: Lisa

last: Quinn

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

hyb_protocol: Details of the microarray hybridization process can be found at the University of Victoria cGRASP website (http://web.uvic.ca/grasp/microarray/array.html) within the .pdf document entitled Invitrogen Indirect cDNA Labeling System version 3.

scan_protocol: Images were scanned on a ScanArray™ Express Microarray Scanner (Packard BioScience BioChip Technologies, model #ASCEX00). Slides were scanned at 74 and 72 PMT for Cy3 and Cy5, respectively, and spot intensity was calculated with ImaGene ver. 6.5.1.

data_processing: All statistical analyses of the microarray data were conducted using Genespring ver. 7.3.1. Signals were normalized per spot and per chip using an intensity-dependent (LOWESS) normalization, then per gene to normalize to the median. Spots were filtered on flags present, and only spots with signals greater or equal to the average base/proportional value of the raw channel were retained.

organism: Salvelinus alpinus

source_name: Arctic charr gill tissue whole RNA reverse transcribed to cDNA, control

label_protocol: cDNA (300 ng) and aRNA (500 ng) were labeled with Cy5 and Cy3 (Amersham Biosciences), respectively, using Invitrogen’s SuperScript Indirect cDNA Labeling System following the manufacturer's instructions.

extract_protocol: Total RNA was isolated from gill tissues disrupted and homogenized in 1 ml TRIzol reagent using a Mixer-mill (Retch® MM 301) with tungsten carbide beads. Phase separation was conducted using 200 µl chloroform, and RNA was purified using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 200 Arctic charr were exposed to heat stress. 10 fish were sampled before the stress (control). Six randomly sampled fish in this group were used for microarray analysis.

tag: tissue

value: gill

tag: condition

value: before temperature stress

value: control

tag: individual

organism: Salmo salar

source_name: reference aRNA

value: gonad, brain, spleen


title: MCF10A-2D-5days-2


title: Control Individual 6


title: Control Individual 1


title: Control Individual 10


title: MCF7-CARM1#13-DOX-a

description:
Dox alone
SOM01VSE
Sample barcode: 6958502

value: Dox


title: MCF7-CARM1#13-E2-b

description:
E2 alone
SOM01X73
Sample barcode: 6543902


title: Training70-2

city: Bethesda

first: Jeffrey

middle: E

last: Green

address: Rm 4054, 37 Convent Drive

institute: NCI

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355244

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

scan_protocol: GeneChips were scanned using the Affymetrix G3000 GeneArray Scanner

data_processing: The data were processed with R (v 2.6.1) and BRB-ArrayTools (v 3.6).

source_name: Pretreatment sample_Training set

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

extract_protocol: Total RNA was extracted from tumor-rich area using Trizol, according to the manufacturer's instructions.

tag: Pretreatment endoscopic biopsy samples collected from CF-treated metastatic gastric cancer patients


title: MCF10A-2D-2days-1


title: Control Individual 2


title: MCF7-CARM1#13-DOX+E2-c

description:
Dox and E2
SOM01X79
Sample barcode: 5954602


title: Training64-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355238


title: Control Individual 7


title: Training77-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355251


title: Training71-2

description:
Training set to identify the signature for the intrinsic resistance to CF
This sample uses the same CEL data as GSM355245


title: MCF10A-2D-2days-2