title: A2780_oxa_IC90_16h_4

status: Public on Jul 01 2007

city: Buffalo

first: Yseult

middle: F

last: Brun

address: Elm and Carlton St

department: Cancer prevention and epidemiology

institute: Roswell Park Cancer Institute

hyb_protocol: polyA RNA was hybridized to Affymetrix U95Av2 GeneChip arrays according to the standard Affymetrix protocol

scan_protocol: Gene chips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Probe level analysis was performed using Robust Multiarray Average (RMA) method using the Bioconductor package

molecule: polyA RNA

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC90 , 16h.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: A2780 is a human ovarian carcinoma cell line generously provided by Dr. Ozols (Fox Chase Cancer Center, Philadelphia, PA). Cells were mycoplasma-free and maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% L-glutamine at 37ºC in humidified 5% CO2 atmosphere.

extract_protocol: Total RNA from log phase cells (10-15 x 106 cells) was isolated using Qiagen RNeasy kit (Qiagen, Inc.) according to specifications. Poly-A RNA was then isolated using Qiagen Oligotex kit (Qiagen, Inc.) from ~50 ìg total RNA and processed according to Affymetrix specifications (Affymetrix GeneChip Expression Analysis Manual, Affymetrix Inc, Santa Clara, CA).  Briefly, double stranded cDNA was synthesized from ~2.5 mg poly-A RNA using the Superscript Choice System (Invitrogen, Grand Island, NY)  followed by amplification and biotinylation by in vitro transcription reaction (BioArray High Yield Transcription Labeling Kit, Enzo Diagnostics, Farmingdale, NY).

treatment_protocol: samples were treated with specific growth-inhibitory concentrations of cisplatin or oxaliplatin for 2 hours, then washed three times in PBS and incubated in drug-free media. Cells were harvested and processed at various time.

tag: A2780 human ovarian carcinoma cells


title: A2780_oxa_IC90_16h_1

type: RNA

state: NY

country: USA

label: biotin

organism: Homo sapiens


title: A2780_oxa_IC50_16h_1

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC50 , 16h.


title: A2780_oxa_IC75_16h_1

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC75 , 16h.


title: A2780_oxa_IC10_16h_1

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC10 , 16h.


title: HMEC_control A1

status: Public on Aug 08 2007

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

country: Germany

institute: Hannover Medical School

description: standard culture conditions, no treatment

molecule: total RNA

source_name: HMEC-1 cell line

tag: cell culture


title: HMEC_control A2


title: A2780_oxa_IC90_16h_2


title: A2780_oxa_IC50_16h_2


title: A2780_oxa_IC90_16h_3


title: A2780_oxa_IC10_16h_2


title: A2780_oxa_IC75_16h_2


title: A2780_oxa_IC25_16h_1

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC25 , 16h.


title: A2780_oxa_IC25_16h_2


title: A2780_cis_IC90_16h_4

source_name: A2780 cells, exposed 2 h to cisplatin at IC90 , 16h.


title: A2780_cis_IC90_16h_2


title: E+ diet, tn treatment vs. E- diet, HS treatment (21 cy3 ----4 Cy 5)

status: Public on Jul 07 2007

city: Columbia

first: Raja

middle: S

last: Settivari

state: MO

address: 920 E Campus Drive

department: ASRC

institute: University of Missouri

description: Rats (n=24) were fed ad libitum diets containing either ground endophyte-free (E-) seed or endophyte–infected (E+) seed for five days at thermoneutrality (21°C) followed by a 3 day heat stress. Rats (n=24) with intraperitonial transmitters were used with core temperature (Tc) and general activity measured every 5 minutes during the study. At treatment end, the liver was removed, weighed and frozen in liquid nitrogen.  RNA was extracted from liver samples, converted to cDNA, and hybridized with the printed oligonucleotide slides.

hyb_protocol: Custom protocol

scan_protocol: Genepix 6

data_processing: Data was analyzed using Genepix, JMAANOVA softwares

organism: Rattus norvegicus

label_protocol: Cy5 dye protocol

extract_protocol: Qiagen kit protocol

tag: MALE RAT LIVER TISSUE, E- DIET, HS TREATMENT

label_protocol: Cy3 dye kit protocol (Amersham)

extract_protocol: Qiagen RNA extraction protocol

tag: MALE RAT LIVER TISSUE, E+ TREATMENT


title: A2780_cis_IC90_16h_5


title: A2780_cis_IC90_16h_3


title: A2780_cis_IC50_16h_1

source_name: A2780 cells, exposed 2 h to cisplatin at IC50 , 16h.


title: A2780_cis_IC25_16h_2

source_name: A2780 cells, exposed 2 h to cisplatin at IC25 , 16h.


title: A2780_cis_IC75_16h_1

source_name: A2780 cells, exposed 2 h to cisplatin at IC75 , 16h.


title: A2780_control_16h_4

source_name: A2780 cells, control , 16h.


title: A2780_cis_IC50_16h_2


title: A2780_control_16h_3


title: A2780_cis_IC90_16h_1


title: A2780_control_16h_2


title: A2780_cis_IC10_16h_2

source_name: A2780 cells, exposed 2 h to cisplatin at IC10 , 16h.


title: A2780_oxa_IC90_24h

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC90 , 24h.


title: A2780_control_2h

source_name: A2780 cells, control , 2h.


title: A2780_cis_IC75_16h_2


title: A2780_control_6h

source_name: A2780 cells, control , 6h.


title: A2780_cis_IC10_16h_1


title: A2780_control_16h_1


title: A2780_oxa_IC90_6h_1

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC90 , 6h.


title: A2780_cis_IC25_16h_1


title: A2780_oxa_IC90_6h_2


title: A2780_oxa_IC90_0h_2

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC90 , 0h.


title: A2780_control_0h

source_name: A2780 cells, control , 0h.


title: A2780_oxa_IC90_2h_2

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC90 , 2h.


title: A2780_oxa_IC90_2h_1


title: A2780_cis_IC90_24h

source_name: A2780 cells, exposed 2 h to cisplatin at IC90 , 24h.


title: A2780_cis_IC90_6h_2

source_name: A2780 cells, exposed 2 h to cisplatin at IC90 , 6h.


title: A2780_cis_IC90_2h_1

source_name: A2780 cells, exposed 2 h to cisplatin at IC90 , 2h.


title: A2780_cis_IC90_6h_1


title: A2780_cis_IC90_2h_2


title: A2780_oxa_IC90_pre_2

source_name: A2780 cells, exposed 2 h to oxaliplatin at IC90 , pre.


title: A2780_cis_IC90_0h_2

source_name: A2780 cells, exposed 2 h to cisplatin at IC90 , 0h.


title: A2780_oxa_IC90_0h_1


title: A2780_cis_IC90_pre_1

source_name: A2780 cells, exposed 2 h to cisplatin at IC90 , pre.


title: A2780_cis_IC90_0h_1


title: A2780_cis_IC90_pre_2


title: B10.BR day 7 rep3

status: Public on Jun 20 2007

city: La Jolla

first: Michael

last: McHeyzer-Williams

state: CA

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

description: Gene expression data from B10.BR immunized mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: genechips were scanned using GSI Lumonics scanner

data_processing: GC-RMA normalized data via Genespring GX software

organism: Mus musculus

source_name: lymph node

label_protocol: Biotinylated cRNA were prepared according to Ambion protocol from 10 ug total RNA.

extract_protocol: Qiagen column as described by the manufacturer's protocol

tag: B10.BR-D7 immunized mouse-CD4 cells


title: B10.BR day 7 rep2


title: A2780_control_pre

source_name: A2780 cells, control , pre.


title: B10.BR day 28 rep2

tag: B10.BR-D28 immunized mouse-CD4 cells


title: A2780_oxa_IC90_pre_1


title: B10.BR day 28 rep1


title: B10.BR day 7 rep1


title: B10.BR naive rep3

description: Gene expression data from B10.BR naive mouse

tag: B10.BR-CD4 naive


title: B10.BR naive rep2


title: B10.BR naive rep1

treatment_protocol: lymph node was extracted and single cell suspension made sorted by flow cytometry


title: PANC-1_Treated_BiolRep2

status: Public on Jun 05 2007

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

description: RNA extracted from the first biological replicate was derived from 3 culture dishes producing enough sample for three technical replicates, whereas RNA from the second and third biological replicates were derived from one culture dish each.

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: HP Gene Array Scanner

data_processing: The data were analyzed using RMA (with quantile normalization) followed by batch effect removal using 2-way mixed model Anova (Partek Genomics Suite)

label: phycoerytrin

source_name: PANC-1 cell line grown in serum-containing media

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

growth_protocol: PANC-1 cells (American Type Culture Collection, Manassas, VA) were started as passage 1 (passages 3–6 were used for all experiments). Cells were cultured in serum-containing media (SCM), a mixture of DMEM (Cellgro, Mediatech, Herndon, VA) containing 10% FBS.

extract_protocol: TRIzol to isolate total RNA, followed by cleanup using QIAGEN RNeasy Mini Kit.

treatment_protocol: To induce ICA formation, Serum-containing medium (SCM) was removed, cells were exposed for 60–120 s to 0.05% trypsin (CellgroMediatech) at 25°C, to loosen but not detach the cells from their extracellular matrix (ECM) and then cultured in Serum Free Medium (SFM). SFM was DME/F12 medium containing 17.5 mM glucose, 1% BSA (no. 152401, ICN) and insulin— transferrin—selenium (GIBCO).

tag: Human pancreatic carcinoma, epithelial-like cell line, Gender

value: Male


title: PANC-1_Treated_BiolRep1_TechRep3


title: PANC-1_Treated_BiolRep1_TechRep2


title: PANC-1_BiolRep3


title: PANC-1_BiolRep2


title: PANC-1_Treated_BiolRep1_TechRep1


title: Cancer Chemo patient 94

status: Public on May 31 2007

city: Atlanta

first: Nathan

middle: J.

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

description: Gene expression data from ovarian cancer patient pre-treated with cancer chemotherapy.

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

scan_protocol: GeneChips were scanned using GeneArray Scanner Model G2500

data_processing: The data were analyzed using GCRMA normalization with GeneTraffic Software (Iobion, La Jolla, CA).

source_name: Cancer Chemo patient 94

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

growth_protocol: A set of 43 ovarian tumors was obtained from the Ovarian Cancer Institute (Atlanta).  Tissue was collected at the time of surgery and preserved in RNAlater (Ambion, Austin, TX) within one minute of collection.

extract_protocol: RNA was isolated from crude homogenate according to the manufacturer’s protocols (Trizol) and further enriched using an RNEasy column (Qiagen, Valencia, CA).

treatment_protocol: Tissue was collected at the time of surgery and preserved in RNAlater (Ambion, Austin, TX) within one minute of collection. Linear polyacrylamide (5 ul) was added to ~50 mg of tumor sample and homogenization was carried out on ice in 1.5 ml Trizol (Invitrogen, Carlsbad, CA) with a polytron homogenizer for 30 seconds.

tag: invasive malignant

tag: Age at surgery:55


title: Cancer Chemo patient 76

source_name: Cancer Chemo patient 76

tag: Age at surgery:49


title: Cancer Chemo patient 36

source_name: Cancer Chemo patient 36

tag: Age at surgery:66


title: Cancer Chemo patient 326

source_name: Cancer Chemo patient 326

tag: Age at surgery


title: Cancer Chemo patient 9

source_name: Cancer Chemo patient 9

tag: Age at surgery:51


title: PANC-1_BiolRep1_TechRep1


title: Cancer Chemo patient 338

source_name: Cancer Chemo patient 338


title: Cancer Chemo patient 325

source_name: Cancer Chemo patient 325


title: Cancer Chemo patient 314

source_name: Cancer Chemo patient 314


title: Cancer Chemo patient 312

source_name: Cancer Chemo patient 312


title: PANC-1_BiolRep1_TechRep3


title: PANC-1_BiolRep1_TechRep2


title: PANC-1_Treated_BiolRep3


title: Cancer Chemo patient 310

source_name: Cancer Chemo patient 310


title: Cancer Chemo patient 303

source_name: Cancer Chemo patient 303


title: Cancer Chemo patient 311

source_name: Cancer Chemo patient 311


title: Cancer Chemo patient 29

source_name: Cancer Chemo patient 29


title: Cancer Chemo patient 259

source_name: Cancer Chemo patient 259


title: Cancer Chemo patient 150

source_name: Cancer Chemo patient 150


title: Cancer Chemo patient 286

source_name: Cancer Chemo patient 286


title: Cancer Chemo patient 279

source_name: Cancer Chemo patient 279


title: Cancer Chemo patient 269

source_name: Cancer Chemo patient 269


title: Cancer Chemo patient 272

source_name: Cancer Chemo patient 272


title: Carcinoma patient 99

description: Gene expression data from ovarian carcinoma.

source_name: Carcinoma patient 99


title: Cancer Chemo patient 184

source_name: Cancer Chemo patient 184


title: Carcinoma patient 66

source_name: Carcinoma patient 66


title: Cancer Chemo patient 253

source_name: Cancer Chemo patient 253

tag: Histology:Endometriod adenocarcinoma


title: Cancer Chemo patient 187

source_name: Cancer Chemo patient 187


title: Carcinoma patient 212

source_name: Carcinoma patient 212


title: Carcinoma patient 4

source_name: Carcinoma patient 4


title: Carcinoma patient 23

source_name: Carcinoma patient 23


title: Carcinoma patient 204

source_name: Carcinoma patient 204


title: Cancer Chemo patient 199

source_name: Cancer Chemo patient 199


title: Carcinoma patient 2

source_name: Carcinoma patient 2


title: Carcinoma patient 196

source_name: Carcinoma patient 196


title: Cancer Chemo patient 255

source_name: Cancer Chemo patient 255

tag: Histology:Undifferentiated carcinoma


title: Carcinoma patient 183

source_name: Carcinoma patient 183


title: Adenoma patient 146

description: Gene expression data from ovarian adenoma.

source_name: Adenoma patient 146

tag: benign

tag: Histology:Simple cystadenoma


title: Adenoma patient 300

source_name: Adenoma patient 300

tag: Histology:Serous cystadenofibroma


title: Adenoma patient 125

source_name: Adenoma patient 125

tag: Histology:Serous cystadenoma


title: Adenoma patient 97

source_name: Adenoma patient 97


title: Adenoma patient 159

source_name: Adenoma patient 159


title: Adenoma patient 172

source_name: Adenoma patient 172


title: Adenoma patient 221

source_name: Adenoma patient 221


title: Adenoma patient 132

source_name: Adenoma patient 132


title: Tumor samples from patient No.16 PT16U95Av2

status: Public on May 08 2007

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

institute: The Methodist Hospital

description: Gene expression data from primary prostate cancer

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95Av2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: PT16, tumor samples from patient No.16

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

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.

tag: Tissue:primary prostate tumor

tag: Tumor stage

tag: Gleason Grade


title: Tumor samples from patient No.20 PT20U95Av2

source_name: PT20, tumor samples from patient No.20


title: Adenoma patient 64

source_name: Adenoma patient 64


title: Tumor samples from patient No.10 PT10U95Av2

source_name: PT10, tumor samples from patient No.10


title: Tumor samples from patient No.13 PT13U95Av2

source_name: PT13, tumor samples from patient No.13


title: Chimp 86A005 (Pt4) Visual Cortex

status: Public on Apr 26 2007

city: Barcelona

first: Mario

last: Cáceres

state: Barcelona

address: Dr. Aiguader 88

department: Genes and Disease Program

country: Spain

institute: Center for Genomic Regulation

description: Gene expression data from brain visual cortex of chimpanzee 86A005 (Pt4).

hyb_protocol: Following fragmentation, hybridizations were performed on Affymetrix HG_U95Av2 GeneChips for 16 hr at 50C at a final cRNA concentration of 0.06 ug/ul. After hybridization, GeneChips were washed in the Affymetrix Fluidics Station and stained manually following the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner with default parameters. Two scans were performed for each array.

organism: Pan troglodytes

source_name: Chimpanzee brain visual cortex from the left hemisphere

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

growth_protocol: Brain tissue samples were dissected during autopsy or surgical procedures.

extract_protocol: Around 100 mg of each tissue sample were isolated on ice, placed on a tube containing 1 ml of Trizol, and homogenized with a 7-mm polytron for 2 min. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissue samples (1-5 g) were immediately frozen after dissection in liquid nitrogen and kept at –80°C until used for RNA extraction. Around 100 mg of each tissue sample were then separated on ice, placed on a tube containing 1 ml of Trizol, and homogenized with a 7-mm polytron for 2 min.

tag: Gender

value: Female

tag: Age

value: 15 years

tag: Tissue

value: Visual cortex

tag: Origin

value: Autopsy (PMI = 3.5 hours)


title: Adenoma patient 77A

source_name: Adenoma patient 77A


title: Chimp 86A005 (Pt4) Cerebellum

description: Gene expression data from brain cerebellum vermis of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain cerebellum vermis from the left hemisphere

value: Cerebellum vermis


title: PLN_4w_3

status: Public on Mar 10 2009

city: Stanford

first: Keiichi

last: Kodama

address: 269 Campus Drive, Room 2225

department: Department of Medicine, Division of Immunology & Rheumatology

institute: Stanford Univeristy School of Medicine

description: PLN_4w_3; VALUE=LOG10(NOD/NOD.B10)

hyb_protocol: as described in In situ Hybridization kit-plus

scan_protocol: Agilent scanner, manufacturer's protocol

data_processing: Agilent Feature Extraction software 8.5

source_name: NOD

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit

extract_protocol: Qiagen RNeasy

tag: tissue type

value: pancreatic lymph nodes

tag: age

value: 4 weeks

tag: disease state

value: diabetic

value: control


title: Chimp 86A005 (Pt4) Hippocampus

description: Gene expression data from brain hippocampus of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain hippocampus from the left hemisphere

value: Hippocampus


title: Chimp 86A005 (Pt4) Temporal Pole

description: Gene expression data from brain temporal pole cortex of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain temporal pole cortex from the left hemisphere

value: Temporal pole


title: Chimp 86A005 (Pt4) Anterior Cingulate Cortex

description: Gene expression data from brain anterior cingulate cortex of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain anterior cingulate cortex from the left hemisphere

value: Anterior cingulate cortex


title: Chimp N98-45 (Pt2) Inferior Parietal Lobule, technical rep2

description: Gene expression data from brain inferior parietal lobule cortex of chimpanzee N98-45 (Pt2).

source_name: Chimpanzee brain inferior parietal lobule cortex from the left hemisphere

value: 1 years

value: Inferior parietal lobule

value: Autopsy (PMI = 3 hours)


title: Chimp 86A005 (Pt4) Anterior Inferior Parietal Lobule

description: Gene expression data from brain anterior inferior parietal lobule cortex of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain anterior inferior parietal lobule from the left hemisphere

value: Anterior inferior parietal lobule


title: Chimp 86A005 (Pt4) Middle Frontal Gyrus

description: Gene expression data from brain middle frontal gyrus cortex of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain middle frontal gyrus cortex from the left hemisphere

value: Middle frontal gyrus


title: Chimp 86A005 (Pt4) Anterior Inferior Temporal Cortex

description: Gene expression data from brain anterior inferior temporal cortex of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain anterior inferior temporal cortex from the left hemisphere

value: Female

value: Anterior inferior temporal cortex


title: Chimp A242B (Pt3) Superior Temporal Gyrus, technical rep1

description: Gene expression data from brain superior temporal gyrus cortex of chimpanzee X035 (Pt1).

source_name: Chimpanzee brain superior temporal gyrus cortex from the left hemisphere

value: 24 years

value: Superior temporal gyrus

value: Autopsy (PMI < 5.5 hours)


title: Chimp N98-45 (Pt2) Inferior Parietal Lobule, technical rep1


title: Chimp X035 (Pt1) Superior Temporal Gyrus, technical rep1

value: Male

value: est. 34 years

value: Autopsy (PMI < 12 hours)


title: Human 303 Cerebellum, technical rep2

description: Gene expression data from brain cerebellum tonsils of human 303.

source_name: Human brain cerebellum tonsils

value: 49 years

value: Cerebellum tonsils

value: Surgery


title: Chimp X035 (Pt1) Superior Temporal Gyrus, technical rep2


title: Chimp 86A005 (Pt4) Frontal Pole

description: Gene expression data from brain frontal pole cortex of chimpanzee 86A005 (Pt4).

source_name: Chimpanzee brain frontal pole cortex from the left hemisphere

value: 15 years

value: Frontal pole

value: Autopsy (PMI = 3.5 hours)


title: Chimp A242B (Pt3) Superior Temporal Gyrus, technical rep2


title: Human 284 (Hs4) Hippocampus

description: Gene expression data from brain hippocampus of human 284 (Hs4).

source_name: Human brain hippocampus

value: 42 years

value: Hippocampus


title: Human 301 Cerebellum, technical rep2

description: Gene expression data from brain cerebellum tonsils of human 301.

value: 21 years


title: Human 285 (Hs5) Hippocampus

description: Gene expression data from brain hippocampus of human 285 (Hs5).

value: Female


title: Human 285 (Hs5) Anterior Inferior Temporal Cortex

description: Gene expression data from brain anterior inferior temporal cortex of human 285 (Hs5).

source_name: Human brain anterior inferior temporal cortex

value: Anterior inferior temporal cortex


title: Human 303 Cerebellum, technical rep1


title: Human 251 (Hs3) Hippocampus

description: Gene expression data from brain hippocampus of human 251 (Hs3).

source_name: Human brain hippocampus from the left hemisphere

value: 71 years

value: Autopsy (PMI = 3 hours)


title: Human 301 Cerebellum, technical rep1


title: Human 284 (Hs4) Anterior Inferior Temporal Cortex

description: Gene expression data from brain anterior inferior temporal cortex of human 284 (Hs4).


title: Human 251 (Hs3) Cerebellum

description: Gene expression data from brain cerebellum of human 251 (Hs3).

source_name: Human brain cerebellum from the left hemisphere

value: Cerebellum


title: Human 251 (Hs3) Anterior Cingulate Cortex

description: Gene expression data from brain middle frontal gyrus cortex of human 251 (Hs3).

source_name: Human brain anterior cingulate cortex from the left hemisphere

value: Male

value: Anterior cingulate cortex


title: Human 251 (Hs3) Anterior Inferior Parietal Lobule

description: Gene expression data from brain anterior inferior parietal lobule cortex of human 251 (Hs3).

source_name: Human brain anterior inferior parietal lobule cortex from the left hemisphere

value: Anterior inferior parietal lobule


title: Human 1029 (Hs2) Cerebellum

description: Gene expression data from brain cerebellum of human 1029 (Hs2).

value: 30 years

value: Autopsy (PMI = 12 hours)


title: Human 251 (Hs3) Middle Frontal Gyrus

description: Gene expression data from brain anterior inferior temporal cortex of human 251 (Hs3).

source_name: Human brain middle frontal gyrus cortex from the left hemisphere

value: Middle frontal gyrus


title: Human 251 (Hs3) Anterior Inferior Temporal Cortex

source_name: Human brain anterior inferior temporal cortex from the left hemisphere


title: Human 813 (Hs1) Caudate Nucleus

description: Gene expression data from brain caudate nucleus of human 813 (Hs1).

source_name: Human brain caudate nucleus from the left hemisphere

value: 31 years

value: Caudate nucleus

value: Autopsy (PMI = 14 hours)


title: Human 813 (Hs1) Cerebellum

description: Gene expression data from brain cerebellum of human 813 (Hs1).


title: Hep2_43_rep1

status: Public on Apr 10 2007

city: Boston

first: Jason

middle: Matthew

last: Laramie

state: MA

address: 715 Albany Street

department: Bioinformatics

institute: Boston University

hyb_protocol: affymetrix protocol

scan_protocol: affymetrix protocol

source_name: Hep2 cells heated to 43 degrees rep 1

label_protocol: standard affymetrix labeling protocol

extract_protocol: Standard Affymetrix Protocol

treatment_protocol: Heated to 43 degrees for 1 hour

tag: Cell Culture


title: Human 1029 (Hs2) Frontal Pole

description: Gene expression data from brain frontal pole cortex of human 1029 (Hs2).

source_name: Human brain frontal pole cortex from the left hemisphere

value: Frontal pole


title: Hep2_42_rep3

source_name: Hep2 cells heated to 42 degrees rep 3

treatment_protocol: Heated to 42 degrees for 1 hour


title: Human 1029 (Hs2) Caudate Nucleus

description: Gene expression data from brain caudate nucleus of human 1029 (Hs2).


title: Hep2_42_rep2

source_name: Hep2 cells heated to 42 degrees rep 2


title: Hep2_43_rep2

source_name: Hep2 cells heated to 43 degrees rep 2


title: Human 813 (Hs1) Frontal Pole

description: Gene expression data from brain frontal pole cortex of human 813 (Hs1).


title: Hep2_41_rep3

source_name: Hep2 cells heated to 41 degrees rep 3

treatment_protocol: Heated to 41 degrees for 1 hour


title: Hep2_41_rep2

source_name: Hep2 cells heated to 41 degrees rep 2


title: Human 813 (Hs1) Hippocampus

description: Gene expression data from brain hippocampus of human 813 (Hs1).

value: Hippocampus


title: Hep2_40_rep1

source_name: Hep2 cells heated to 40 degrees rep 1

treatment_protocol: Heated to 40 degrees for 1 hour


title: Hep2_37_rep2

source_name: Hep2 cells heated to 37 degrees rep 2

treatment_protocol: Heated to 37 degrees for 1 hour


title: Hep2_40_rep2

source_name: Hep2 cells heated to 40 degrees rep 2


title: Hep2_41_rep1

source_name: Hep2 cells heated to 41 degrees rep 1


title: Hep2_37_rep3

source_name: Hep2 cells heated to 37 degrees rep 3


title: Hep2_37_rep1

source_name: Hep2 cells heated to 37 degrees rep 1


title: Hep2_43_rep3

source_name: Hep2 cells heated to 43 degrees rep 3

tag: Cell Culture tissure

value: Hep2 Cells


title: Human 1029 (Hs2) Hippocampus

description: Gene expression data from brain hippocampus of human 1029 (Hs2).

source_name: Human brain hippocampus from the left hemisphere


title: P53(-),Ar(+),Rep#3

status: Public on Apr 07 2007

city: Louisville

first: Xiaoqiang

last: Xu

state: KY

address: University of Louisville

department: Department of Pharmacology & Toxicology

institute: University of Louisville

description: p53(-), Arsenite-treated, Replication 3

hyb_protocol: cRNA, 15 µg per sample, was heated at 80ºC for 33 min in fragmentation buffer. Fragmented cRNAs were hybridized to U95Av2 GeneChips (Affymetrix) for 16 hr at 45ºC.

scan_protocol: We scanned stained GeneChips on an Agilent GeneArray Scanner (Agilent Technologies)

data_processing: GCOS, BioConductor/R

label: Biotin-labeled cRNA were stained with streptavidin phycoerythrin stain solution. Signal was amplified with goat anti-streptavidin antibody and biotinylated goat IgG (Affymetrix).

source_name: Fibroblast explant cells from a Li-Fraumeni patient

label_protocol: We synthesized biotin-labeled cRNA with an ENZO RNA transcript labeling kit using 0.7 µg cDNA per reaction. cRNAs were purified with RNeasy purification columns (Qiagen).

extract_protocol: Extracted with oligo-dt cellulose using a Micro FastTrack Kit (Invitrogen)

tag: p53 deficient fibroblasts expressing p53 from a tet-off regulated contruct


title: P53(-),Ar(+),Rep#1

description: p53(-), Arsenite-treated, Replication 1


title: P53(-),Ar(+),Rep#4

description: p53(-), Arsenite-treated, Replication 4


title: P53(+),Ar(+),Rep#1

description: p53(+), Arsenite-treated, Replication 1

tag: Fibroblast explant cells from a Li-Fraumeni patient


title: P53(+),Ar(+),Rep#4

description: p53(+), Arsenite-treated, Replication 4


title: P53(-),Ar(-),Rep#4

description: p53(-), Non arsenite-treated, Replication 4


title: P53(+),Ar(+),Rep#3

description: p53(+), Arsenite-treated, Replication 3


title: P53(+),Ar(+),Rep#2

description: p53(+), Arsenite-treated, Replication 2


title: P53(-),Ar(-),Rep#3

description: p53(-), Non arsenite-treated, Replication 3


title: P53(-),Ar(+),Rep#2

description: p53(-), Arsenite-treated, Replication 2


title: P53(-),Ar(-),Rep#2

description: p53(-), Non arsenite-treated, Replication 2


title: P53(+),Ar(-),Rep#3

description: p53(+), Non arsenite-treated, Replication 3


title: P53(-),Ar(-),Rep#1

description: p53(-), Non arsenite-treated, Replication 1


title: P53(+),Ar(-),Rep#2

description: p53(+), Non arsenite-treated, Replication 2


title: SKM KO5

status: Public on Apr 02 2007

first: Susan

last: Gray

address: 20 Shattuck Street

institute: Brigham and Womens Hospital

description: Gene expression data from quadriceps skeletal muscle of 4-5 month old, 18h fasted, WT versus KLF15-null female mice

hyb_protocol: Hybridization is carried out according to the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station.  Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on an Affymetrix Model 7000 scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 7000 scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility.  All systems are CFR21-11 and HIPPA compliant

data_processing: The GCOS default analysis algorithms and parameters for normalization and transformation were used. There was no scaling done. The default values for the analysis and the details on the algorithms can be found in Appendix F in the Affymetrix GCOS Manual.

source_name: skeletal muscle (quadriceps); fasted 18h

label_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371). In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: Flash frozen samples extracted using Trizol (Invitrogen) as per manufacturer's instructions, further purified using Rneasy Micro Kit (Qiagen) as per manufacturer's instructions

tag: C57BL/6 female, fasted 18h (overnight), age 4-5 months


title: In Vitro Cultured Memory B cells #3

status: Public on Apr 03 2007

city: New York

first: Kathryn

last: Calame

address: 701 W.168th Street, HHSC 1204

institute: Columbia University

description: mAdb experiment ID: 65540

hyb_protocol: protocol_name: NCI cDNA Microarray Hybridization other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual)

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 740;; 760 ScanPower: 100;; 100 LaserPower: 3.39;; 3.47 Temperature: 34.38

data_processing:
mAdb Standard Data Processing Protocol
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: Lymphoma Cell Lines

label_protocol:
Lymphochip Labeling-cy3
Label amount: 4ul
Label method: reverse transcription
Nature. 2000 Feb 3;403(6769):503-11

extract_protocol: All cDNA microarray analyses were performed using poly-(A)+ mRNA (Fast Track, Invitrogen).

tag: Raji, Jurkat, L428, OCI-Ly3, OCI-Ly8, OCI-Ly1, SUDHL5, SUDHL6 and WSU1

source_name: In Vitro Cultured Memory B cells #3

label_protocol:
Lymphochip Labeling-cy5
Label amount: 4ul
Label method: reverse transcription
Nature. 2000 Feb 3;403(6769):503-11

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: In vitro cultured tonsillar germinal center B cells treated with CD40L, IL-2, and IL-4 for 7 days.


title: P53(+),Ar(-),Rep#1

description: p53(+), Non arsenite-treated, Replication 1


title: P53(+),Ar(-),Rep#4

description: p53(+), Non arsenite-treated, Replication 4


title: In Vitro Cultured Centrocytes #3

description: mAdb experiment ID: 60939

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 670;; 680 ScanPower: 100;; 100 LaserPower: 3.17;; 6 Temperature: 40.67

source_name: In Vitro Cultured Centrocytes Sample #3

tag: In vitro cultured tonsillar germinal center B cells with CD40L and IL-2 for 3 days.


title: SKM KO8


title: SKM KO7


title: SKM WT2


title: SKM WT4


title: SKM KO6


title: Liver KO7

description: Gene expression data from liver of 4-5 month old, 18h fasted, WT versus KLF15-null female mice

source_name: liver; fasted 18h


title: SKM WT1


title: Liver KO6


title: SKM WT3


title: Liver KO8


title: Liver WT2


title: Liver KO5


title: Liver WT4


title: Liver WT1


title: macrophage_IFN-beta knock out_unstimulated

status: Public on Mar 08 2007

city: Baltimore

first: Stefaine

last: Vogel

address: 660 W. Redwood Street

department: Dept. of Microbiology and Immunology

institute: Univ. of Maryland

description: unstimulated macrophage from IFN-beta knock out mouse

hyb_protocol: The Affymetrix arrays were hybridized and washed using the manufacturer's protocol. The arrays were then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol (GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA).

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner at 488 nm and 3-micron resolution.

data_processing: The images were analyzed using Microarray Suite 5.0 software (MAS5; Affymetrix Inc., Santa Clara, CA). Expression ratios were computed by comparative analysis of MAS5 values. The data were filtered using MAS5's signal detection and change calls generated at recommended default settings. The ratios included were those that had present calls for signal detection or an increase or decrease call associated with the ratio

label: SAPE

label_protocol: cRNA targets for the Affymetrix arrays were synthesized, labeled, and purified according to vendor's (Affymetrix) instructions. Briefly, 10 μg of total RNA was used to make double-stranded cDNA using reagents and protocols obtained from Invitrogen (Carlsbad, CA). Linear amplification was carried out by a modification of the Eberwine T7 method [56], and biotin was incorporated into the cRNA using the Enzo High Yield RNA Transcript labeling Kit (EnzoDiagnostics, Farmingdale, NY).

extract_protocol: RNA was isolated from the cells using TriReagent following the manufacturer's protocol (Molecular Research Center, Inc., Cincinnati, OH). Integrity of the RNA was confirmed by analysis with the Agilent 2100 Bioanalyzer (Palo Alto, CA) using the RNA 6000 LabChip® kit.

treatment_protocol: Thioglycollate-elicited murine peritoneal macrophages from IFN-beta knock out grown in media alone.

tag: Strain;>N8 on a C57BL/6 background


title: Macrophage_Ifnbeta knock out_DMXAA_3h

description: Macrophage_Ifnbeta knock out

source_name: Macrophage_Ifnbeta knock out

tag: Strain;N8 on a C57BL/6 background


title: 585pos3 tumor

status: Public on Mar 10 2007

city: Berlin

first: Andreas

last: Klein

address: Charitéplatz 1

department: Institute of Biochemistry

institute: Charité (CCO)

description: see: Comparison of gene expression data from human and mouse breast cancers: Identification of a conserved breast tumor gene set. International Journal of Cancer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430A 2.0 Array. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.

data_processing: The raw experimental microarray data were normalized with the Affymetrix GeneChip operating software based on the housekeeping gene method. Further analyses were performed with the software “CorrXpression”.

source_name: mammary gland

label_protocol: The doublestranded DNA was transcribed in vitro into biotinylated cRNA

growth_protocol: breast cancer

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

treatment_protocol: breast cancer

tag: mouse breast cancer

tag: This animal synthesizes the SV40 T/t- antigens selectively in the mammary gland epithelial cells. Strain

value: NMRI, female, breast cancer.


title: 585pos5 tumor


title: Liver WT3


title: Wildtype_DMXAA_Macrophage

description: Wild type stimulated with DMXAA for 3 h

source_name: macrophage stimulated with DMXAA for 3 h

treatment_protocol: Thioglycollate-elicited murine peritoneal macrophages were stimulated with DMXAA (100 micrograms/ml) for 3h.

tag: Strain; C57BL/6J


title: 597pos9 tumor


title: Wild type unstimulated

description: Wild type unstimulated macrophages

source_name: macrophages


title: UC-38-un

status: Public on Mar 01 2007

first: Shukti

last: Chakravarti

address: 720 Rutland Ave

department: Medicine

institute: Johns Hopkins University School of Medicine

description: Colonic biopsy was collected during endoscopy from unaffected area of a patient with ulcerative colitis (UC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on GeneChip U95Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Affymetrix).

data_processing: The DNA-Chip Analyzer (dChip) software (Li, C. and Wong, W.H. 2001) was used to normalize the image data and calculate the expression value.

source_name: colonoscopic biopsy from adult with unaffected colon from adult with UC

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.

treatment_protocol: Fresh biopsy was placed on ice in the Trizol solution (Invitrogen).

tag: disease unaffected colon of a adult with ulcerative colitis (UC).


title: INF-157

description: Colonic biopsy was collected during endoscopy from affected area of a patient with bacterial infectious colitis (INF). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

source_name: colonoscopic biopsy from adult with affected colon from adult with INF

tag: disease affected colon of an adult with bacterial infectious colitis (INF).


title: INF-156


title: IC-44-Aff

description: Colonic biopsy was collected during endoscopy from affected area of a patient with indeterminate colitis (IC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

source_name: colonoscopic biopsy from adult with affected colon from adult with IC

tag: disease affected colon of an adult with indeterminate colitis (IC).


title: UC-55-un


title: UC-32-un


title: IC-44-un

description: Colonic biopsy was collected during endoscopy from unaffected area of a patient with indeterminate colitis (IC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

source_name: colonoscopic biopsy from adult with unaffected colon from adult with IC

tag: disease unaffected colon of an adult with indeterminate colitis (IC).


title: UC-33-un


title: UC-71-Aff

description: Colonic biopsy was collected during endoscopy from affected area of a patient with ulcerative colitis (UC). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

source_name: colonoscopic biopsy from adult with affected colon from adult with UC

tag: disease affected colon of an adult with ulcerative colitis (UC).


title: UC-55-Aff


title: CD-58-un

description: Colonic biopsy was collected during endoscopy from unaffected area of a patient with Crohn's disease (CD). The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

source_name: colonoscopic biopsy from adult with unaffected colon with Crohn's disease

tag: disease unaffected colon of a adult with Crohn's disease (CD)


title: UC-32-Aff


title: CD-76-un


title: CD-51-un


title: CD-59-un


title: CD-53-un


title: CD-59-un2


title: UC-35-Aff


title: UC-38-Aff


title: CD-76-Aff2

description: Colonic biopsy was collected during endoscopy from affected area of a patient with Crohn's disease. The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

source_name: colonoscopic biopsy from adult with affected colon with Crohn's disease

tag: disease affected colon of an adult with Crohn's disease (CD). Replicate-2


title: CD-48-un


title: CD-76-Aff1

tag: disease affected colon of an adult with Crohn's disease (CD). Replicate-1


title: CD-45-un


title: CD-48-un2


title: CD-33-un


title: CD-49-un1


title: CD-58-Aff

tag: disease affected colon of an adult with Crohn's disease (CD).


title: CD-51-Aff


title: CD-53-Aff


title: CD-45-un2


title: N66s1

description: Colonic biopsy was collected during endoscopy from normal control individual. The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.

source_name: colonoscopic biopsy from normal adult

tag: normal sigmoid colon of adult


title: CD-33-Aff


title: CD-49-Aff1


title: N69s


title: N79s


title: N65s2


title: ID_63_TimePt_14

status: Public on Feb 27 2007

city: Bloomington

first: Milton

middle: W

last: Taylor

state: IN

address: 343 Jordan Hall

department: Biology

institute: Indiana University

description: Gene Expression for human subject. Human PBMC collected from whole blood. PBMC were collected in sodium heparin-CPT tubes at day 0 (before treatment) and days 1, 2, 7, 14 and 28 after initiation of treatment. Whole blood was diluted with an equal volume (8 ml) of phosphate buffered saline (PBS), carefully layered over a 10 ml Ficoll-Hypaque gradient (Amersham/Pharmacia, Piscataway, NJ) and centrifuged at 800 rpm for 20 minutes at room temperature. The buffy coat layer was transferred to a 15ml RNAse-free tube, diluted with PBS, and centrifuged at 100 x g for 15 minutes at room temperature. The supernatants were discarded and the PBMC were retained.

hyb_protocol: Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

scan_protocol: The microarrays were scanned using a dedicated Model 3000 scanner controlled by GCOS software.

data_processing:
GCOS was used for data processing. The average intensity on each array was normalized by global scaling to a target intensity of 1000. Data were extracted using the Affymetrix Microarray Suite 5 (MAS5) algorithm

CEL file unavailable due to computer disk failure

source_name: Human PBMC collected from whole blood.

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out according to the protocols recommended by Affymetrix in the GeneChip® Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA)

extract_protocol: Samples were shipped overnight by express courier at 4 degrees C to a central repository where RNA was isolated on arrival  The PBMC were lysed in 1 ml of TRI reagent (Molecular Research Center Inc: Cincinnati, OH). The PBMC lysate was mixed with 1-Bromo-3-chloropropane (BCP)-phase separation agent for 1 minute, and incubated at room temperature for 15 minutes. After centrifugation for 15 minutes at 12,000 rpm and 4 degrees C, RNA was precipitated from the supernatant overnight at -20 degrees C with an equal volume of isopropanol and 1/10 volume of 7.5 M-ammonium acetate. The precipitate was washed twice with 75% ethanol, and then with 95% ethanol. RNA was briefly air-dried and then further purified using RNeasy columns (Qiagen: Valencia, CA).

treatment_protocol: The clinical protocol called for participants to be treated for up to 48 weeks with peginterferon alpha-2a (Pegasys™, Roche Pharmaceuticals Nutley, NJ) in a dose of 180 µg weekly by self-administered subcutaneous injection and ribavirin (Copegus™, Roche) orally in a dose of 1000 or 1200 mg daily based on body weight of less than 75 kg or equal to or greater than 75 kg.


title: ID_63_TimePt_7


title: ID_63_TimePt_2


title: ID_63_TimePt_1


title: ID_61_TimePt_7


title: ID_61_TimePt_2


title: ID_61_TimePt_0


title: ID_63_TimePt_0


title: ID_63_TimePt_28


title: ID_51_TimePt_28


title: ID_61_TimePt_1


title: ID_61_TimePt_14


title: ID_51_TimePt_14


title: ID_50_TimePt_28


title: ID_51_TimePt_7


title: ID_50_TimePt_14


title: ID_51_TimePt_2


title: ID_51_TimePt_0


title: ID_33_TimePt_0


title: ID_33_TimePt_28


title: ID_33_TimePt_14


title: ID_50_TimePt_0


title: ID_33_TimePt_1


title: ID_31_TimePt_14


title: ID_50_TimePt_1


title: ID_51_TimePt_1


title: ID_31_TimePt_2


title: ID_50_TimePt_2


title: ID_33_TimePt_7


title: ID_31_TimePt_7


title: ID_33_TimePt_2


title: ID_31_TimePt_1


title: ID_50_TimePt_7


title: ID_31_TimePt_28


title: ID_30_TimePt_14


title: ID_26_TimePt_28


title: ID_31_TimePt_0


title: ID_26_TimePt_0


title: ID_22_TimePt_14


title: ID_30_TimePt_2


title: ID_22_TimePt_7


title: Resistant Replicate 4

status: Public on Feb 24 2007

city: Shreveport

first: Reinhold

last: Munker

state: LA

address: 1501 Kings Highway

institute: LSU Health Sciences Center

description: See manuscript (Leukemia Research, 2007).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U95A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the HP GeneArray Scanner .

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

source_name: cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: grown in tissue culture medium

tag: KBM-7/B5 cloe 1803


title: ID_26_TimePt_7


title: ID_26_TimePt_14


title: ID_30_TimePt_28


title: ID_30_TimePt_0


title: Resistant Replicate 5


title: ID_30_TimePt_1


title: ID_26_TimePt_1


title: ID_22_TimePt_28


title: ID_22_TimePt_2


title: ID_26_TimePt_2


title: ID_24_TimePt_0


title: ID_22_TimePt_0


title: ID_22_TimePt_1


title: Superior Frontal Gyrus_10y_normal

status: Public on Feb 05 2007

city: Beaverton

first: Valerie

last: Matagne

state: OR

address: 505 nw 185th Ave

department: Neuroscience

institute: OHSU

description: gene expression data from the Superior Frontal Gyrus of 10year-old normal girl, RNA labeled and hybridized Dec. 2001

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001) Standard Affymetrix external spikes added to hybridization mixture: BioB, BioD, and CreX at 5.0pm, 25pm and 100pm respectively.

scan_protocol: Software – Affymetrix Microarray Suite 4.0 Scanning Hardware = HP GeneArray Scanner.

data_processing: Probe level measurements produced by Affymetrix Microarray Suite 4.0. Analysis performed at level of raw average difference. A GCOS absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of 200.  The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters ALPHA 1 and ALPHA 2 are set to 0.1 and 0.15 respectively.  These parameters set the point at which a probe set is called present (P), marginal (M), or   undetectable (A).  This call is based on the Detection p-value of the probe set.

label: see Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).

source_name: Superior Frontal Gyrus from 10 year-old normal girl

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel

tag: Superior Frontal Gyrus from a 10 year-old girl not suffering from Rett Syndrome and therefore considered as a normal subject.


title: Resistant Replicate 2


title: Superior Frontal Gyrus_2y_normal

description: gene expression data from the Superior Frontal Gyrus of 2y-old normal girl, RNA labeled and hybridized Dec. 2001

source_name: Superior Frontal Gyrus from 2year-old normal girl

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

extract_protocol: Total RNA was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications.  RNA quality was assessed by OD reading and 1% formaldehyde agarose gel

tag: Superior Frontal Gyrus from a 2year-old girl not suffering from Rett Syndrome and therefore considered as a normal subject.


title: Resistant Replicate 1


title: Brain area 8/9_8yp_RTT

description: gene expression data from the Brain area 8/9 of two 8 year-old girls suffering from from Rett Syndrome (RTT), RNA labeled and hybridized Dec. 2001

source_name: Superior Frontal Gyrus from two 8 year-old RTT girls

extract_protocol: Total RNA from each sample was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel. Because there was not enough RNA material, samples from the two 8-year-old brains were pooled and used as a single sample.

tag: Brain area 8/9 from two 8 year-old girls suffering from Rett Syndrome.


title: Resistant Replicate 3


title: Sensitive Replicate 3


title: Sensitive Replicate 4


title: Superior Frontal Gyrus_5y_normal

description: gene expression data from the Superior Frontal Gyrus of 5 year-old normal girl, RNA labeled and hybridized Nov. 2001

source_name: Superior Frontal Gyrus from 5 year-old normal girl

tag: Superior Frontal Gyrus from a 5 year-old girl not suffering from Rett Syndrome and therefore considered as a normal subject.


title: Sensitive Replicate 2


title: Superior Frontal Gyrus_2-4y_RTT

description: gene expression data from the Superior Frontal Gyrus of pooled RNA from a 2 and a 4 year-old girl both suffering from Rett Syndrome (RTT) and labeled and hybridized Dec. 2001

source_name: Superior Frontal Gyrus from a 2 and 4 year-old RTT girl

extract_protocol: Total RNA from each sample was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel. Because there was not enough RNA material, samples from the 2 and 4 year-old brains were pooled and used as a single sample.

tag: Superior Frontal Gyrus from 2 and 4 year-old girls suffering from Rett Syndrome.


title: Sensitive Replicate 5


title: mouse_urothelium_IBC-proximal, biological rep2

status: Public on Feb 02 2007

city: Saint Louis

first: Christopher

middle: Swanson

last: Reigstad

address: 4444 Forest Park Blvd.

department: Center for Genome Sciences

institute: Washington University in St. Louis

description: Gene expression data from laser-capture microdissected urothelium residing <10 cell diameters from intracellular communities of UPEC (strain UTI89) in the section plane from 8-10 week old female C3H/HeJ mice.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Array 430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0); scaling = 1500

source_name: Mouse urothelium (IBC-distal, rep2)

label_protocol: cRNA were amplified (Arcturus) and biotinylated (Enzo) according to standard protocols from a 1 nanogram aliquot of total RNA representing a pool of >25,000 urothelial cell sections (~5000 from each of 5 mice).

extract_protocol: PicoPure (Arcturus) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mouse urothelial cells residing <10 cell diameters from intracellular communities of UPEC (strain UTI89) in the section plane were harvested by laser capture microdissection (Arcturus). RNA was isolated and linearly amplified 2x using the PicoPure and RiboAmp HS kits (Arcturus) and Bioarray High Yield RNA transcript kit (Enzo).

tag: Genotype

tag: Age

value: 8-10 weeks old


title: Brain area 8/9_6y_RTT

description: gene expression data from brain area 8/9 of a 6 year-old girl suffering from from Rett Syndrome (RTT) 6yr, RNA labeled and hybridized Aug. 2001

source_name: Brain area 8/9 from 6 year-old RTT girl

extract_protocol: Total RNA from each sample was isolated and purified using RNeasy Mini Columns and DNase On-Column digestion (Qiagen, Valencia, CA) according to the manufacturer’s specifications. RNA quality was assessed by OD reading and 1% formaldehyde agarose gel.

tag: Superior Frontal Gyrus from a 6 year-old girl suffering from Rett Syndrome.


title: mouse_urothelium_IBC-distal, biological rep2

description: Gene expression data from laser-capture microdissected urothelium residing >10 cell diameters from intracellular communities of UPEC (strain UTI89) in the section plane from 8-10 week old female C3H/HeJ mice.

treatment_protocol: Mouse urothelial cells residing >10 cell diameters from intracellular communities of UPEC (strain UTI89) in the section plane were harvested by laser capture microdissection (Arcturus). RNA was isolated and linearly amplified 2x using the PicoPure and RiboAmp HS kits (Arcturus) and Bioarray High Yield RNA transcript kit (Enzo).


title: mouse_urothelium_IBC-proximal, biological rep1

source_name: Mouse urothelium (IBC-distal, rep1)


title: mouse_urothelium_mock-infected, biological rep2

description: Gene expression data from laser-capture microdissected mock-infected (sterile 1x PBS) urothelium from 8-10 week old female C3H/HeJ mice.

source_name: Mouse urothelium (mock-infected, rep2)

treatment_protocol: Mock-infected (sterile 1x PBS) mouse urothelial cells were harvested by laser capture microdissection (Arcturus). RNA was isolated and linearly amplified 2x using the PicoPure and RiboAmp HS kits (Arcturus) and Bioarray High Yield RNA transcript kit (Enzo).


title: mouse_urothelium_IBC-distal, biological rep1


title: mouse_urothelium_mock-infected, biological rep1

source_name: Mouse urothelium (mock-infected, rep1)


title: Cancer 22

status: Public on Jan 20 2007

first: Fang-An

last: Chen

address: 345E 24th Street

department: Oral and Maxillifacial surgery

institute: New York Univ. College of Dentistry

description: Gene expression data of human normal head and neck mucosa.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  Affymetrix human U95A.v2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized with RMA and signal intensity of probe sets were computed with GeneTraffic v3.2 (Iobion Informatics).

source_name: human head and neck cancer

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

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

treatment_protocol: normal tissue collected during removal of head and neck cancer, snap frozen with lq N2 in operating room, stored at -80 until RNA isolation

tag: tissue sample from Bellevue Hospital, NY


title: Cancer 21


title: Normal mucosa 20

source_name: human head and neck normal mucosa


title: Cancer 18


title: Normal mucosa 19


title: Normal mucosa 22


title: Cancer 17


title: Cancer 16


title: mouse_urothelium_uninfected, biological rep2

description: Gene expression data from laser-capture microdissected uninfected urothelium from 8-10 week old female C3H/HeJ mice.

source_name: Mouse urothelium (uninfected, rep2)

treatment_protocol: Uninfected mouse urothelial cells were harvested by laser capture microdissection (Arcturus). RNA was isolated and linearly amplified 2x using the PicoPure and RiboAmp HS kits (Arcturus) and Bioarray High Yield RNA transcript kit (Enzo).


title: mouse_urothelium_uninfected, biological rep1

source_name: Mouse urothelium (uninfected, rep1)


title: Cancer 15


title: Normal mucosa 16


title: Normal mucosa 18


title: Cancer 20


title: Normal mucosa 15


title: Normal mucosa 21


title: Cancer 14


title: Normal mucosa 17


title: Cancer 19


title: Cancer 13


title: Normal mucosa 14


title: Cancer 12


title: Cancer 8


title: Cancer 10


title: Normal mucosa 10


title: Cancer 11


title: Normal mucosa 12


title: Normal mucosa 13


title: Cancer 7


title: Normal mucosa 7


title: Liver, Male WT Chow Diet Control Pool (n=9) vs. Liver, Male wt, Chow Diet  -8

status: Public on Mar 08 2009

city: Seattle

first: Xia

last: Yang

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description: Liver gene expression profiling of 8 lipoprotein lipase (Lpl) heterozygous knockout mice and 8 littermate control mice.

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver? system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Liver

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Liver, Male wt, Chow Diet  -8


title: Normal mucosa 8


title: Cancer 9


title: Normal mucosa 6


title: Normal mucosa 11


title: Cancer 5


title: Cancer 6


title: Normal mucosa 3


title: Normal mucosa 9


title: Normal mucosa 4


title: Normal mucosa 5


title: Cancer 3


title: Normal mucosa 2


title: Cancer 2


title: Normal mucosa 1


title: Cancer 4


title: C2C12 Myotubes treated with Palmitate, rep3

status: Public on Jan 18 2007

city: boston

first: Sarah

last: Crunkhorn

address: 1 Joslin Place

department: CMP

institute: Joslin Diabetes Center

description: Gene expression data from Mouse C2C12 Myoblasts differentiated into Myotubes and treated for 16 hrs.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse M430A version 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Mouse C2C12 Myotubes treated with Palmitate for 16 hours

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

growth_protocol: Grown in DMEM + 20% FBS to confluence.  Then, media is changed to differentiation media (see above).

extract_protocol: Qiagen Rneasy kit protocol

treatment_protocol: C2C12 myoblasts differentiated with 2% horse serum for 5 days.  Treated for 16 hrs with 500 micromolar Palmitate.  RNA collected using Rneasy (Qiagen) protocol.

tag: fully differentiated (day 6) myotubes


title: Cancer 1


title: C2C12 Myotubes treated with Palmitate, rep1


title: C2C12 Myotubes treated with Palmitate, rep2


title: C2C12 Myotubes treated with BSA, rep3

source_name: Mouse C2C12 Myotubes treated with BSA for 16 hours

treatment_protocol: C2C12 myoblasts differentiated with 2% horse serum for 5 days.  Treated for 16 hrs with 1% BSA.  RNA collected using Rneasy (Qiagen) protocol.


title: Normal prostate tissue adjacent to tumor from patient No.105 PN105U95Av2

status: Public on Jan 16 2007

first: Federico

last: Monzon

address: 6565 Fannin St, MS205

institute: The Methodist Hospital

description: Gene expression data from normal prostate tissue adjacent to tumor

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95Av2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: PN105, normal prostate tissue adjacent to tumor from patient No.105

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

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

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 minutes of excision and stored in -80C until RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. For prostate tissues adjacent to tumor, samples free of cancer cells, high-grade prostatic neoplasia, or any obvious neoplastic alterations, containing at least 60% glandular cells were selected.

tag: Tissue:normal prostate tissue adjacent to tumor


title: Normal prostate tissue adjacent to tumor from patient No.107 PN107U95Av2

source_name: PN107, normal prostate tissue adjacent to tumor from patient No.107


title: Normal prostate tissue adjacent to tumor from patient No.96 PN96U95Av2

source_name: PN96, normal prostate tissue adjacent to tumor from patient No.96


title: Normal prostate tissue adjacent to tumor from patient No.99 PN99U95Av2

source_name: PN99, normal prostate tissue adjacent to tumor from patient No.99


title: Normal prostate tissue adjacent to tumor from patient No.101 PN101U95Av2

source_name: PN101, normal prostate tissue adjacent to tumor from patient No.101


title: Normal prostate tissue adjacent to tumor from patient No.94 PN94U95Av2

source_name: PN94, normal prostate tissue adjacent to tumor from patient No.94


title: Normal prostate tissue adjacent to tumor from patient No.97 PN97U95Av2

source_name: PN97, normal prostate tissue adjacent to tumor from patient No.97


title: C2C12 Myotubes treated with BSA, rep1


title: C2C12 Myotubes treated with BSA, rep2


title: Gyk-7BC

city: Los Angeles

first: Josh

last: Deignan

address: 675 Charles E Young Dr South, MRL 3220

department: Cardiology

institute: UCLA

hyb_protocol: 800 ng of labeled cRNA product is hybridized to prepared whole genome arrays and allowed to incubate overnight ( 16 –20 hrs) at 55 degrees C.  Arrays are washed then stained with Cy3 labeled streptavadin. Excess stain is removed by washing and the arrays are dried and scanned on an Illumina BeadScan con-focal laser scanner.

scan_protocol: Scanning was performed using Illumina BeadScan con-focal laser scanner.

data_processing: Data were scaled and normalized using the rank invariant method in the Beadstudio software v. 1.5.1.3. (Illumina Inc.)

source_name: Strain: Gyk wildtype gender:female, age: 23 weeks, tissue: liver

label_protocol: RNA samples queued for whole genome analysis using Illumina gene expression chips are first quanted using the ribogreen RNA quantitation kit. Samples are normalized to 11 ng per ul. 100 ng of normalized total RNA is used as a template for the synthesis of cDNA using Ambion cDNA synthesis kit AMIL1791. Newly synthesized  cDNA becomes the template for the amplification and biotinylation of cRNA . Labeled cRNA is quanted (ribogreen) and normalized to 77 ng per ul.

growth_protocol: These mice were fed a 4% fat chow diet until 11 weeks of age.

extract_protocol: Liver tissues were homogenized and total RNA extracted using Trizol reagent (Invitrogen, CA) according to the manufacturer’s instructions.  RNA samples were isolated from liver tissues using a Qiagen RNeasy Kit and quality-checked with an Agilent 2100 Bioanalyzer (Foster City, CA).

treatment_protocol: Mice were fed a 6% fat chow diet from 11 weeks of age until sacrifice at 23 weeks of age.

tag: Liver, 6% fat diet, 12 weeks


title: Normal prostate tissue adjacent to tumor from patient No.95 PN95U95Av2

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

source_name: PN95, normal prostate tissue adjacent to tumor from patient No.95


title: Normal prostate tissue adjacent to tumor from patient No.93 PN93U95Av2

source_name: PN93, normal prostate tissue adjacent to tumor from patient No.93


title: Normal prostate tissue adjacent to tumor from patient No.100 PN100U95Av2

source_name: PN100, normal prostate tissue adjacent to tumor from patient No.100


title: Normal prostate tissue adjacent to tumor from patient No.91 PN91U95Av2

source_name: PN91, normal prostate tissue adjacent to tumor from patient No.91


title: Normal prostate tissue adjacent to tumor from patient No.88 PN88U95Av2

source_name: PN88, normal prostate tissue adjacent to tumor from patient No.88


title: Normal prostate tissue adjacent to tumor from patient No.90 PN90U95Av2

source_name: PN90, normal prostate tissue adjacent to tumor from patient No.90


title: Normal prostate tissue adjacent to tumor from patient No.83 PN83U95Av2

source_name: PN83, normal prostate tissue adjacent to tumor from patient No.83


title: Normal prostate tissue adjacent to tumor from patient No.81 PN81U95Av2

source_name: PN81, normal prostate tissue adjacent to tumor from patient No.81


title: Normal prostate tissue adjacent to tumor from patient No.84 PN84U95Av2

source_name: PN84, normal prostate tissue adjacent to tumor from patient No.84


title: Normal prostate tissue adjacent to tumor from patient No.82 PN82U95Av2

source_name: PN82, normal prostate tissue adjacent to tumor from patient No.82


title: Normal prostate tissue adjacent to tumor from patient No.80 PN80U95Av2

source_name: PN80, normal prostate tissue adjacent to tumor from patient No.80


title: Normal prostate tissue adjacent to tumor from patient No.70 PN70U95Av2

source_name: PN70, normal prostate tissue adjacent to tumor from patient No.70


title: Normal prostate tissue adjacent to tumor from patient No.71 PN71U95Av2

source_name: PN71, normal prostate tissue adjacent to tumor from patient No.71


title: Normal prostate tissue adjacent to tumor from patient No.87 PN87U95Av2

source_name: PN87, normal prostate tissue adjacent to tumor from patient No.87


title: Normal prostate tissue adjacent to tumor from patient No.85 PN85U95Av2

source_name: PN85, normal prostate tissue adjacent to tumor from patient No.85


title: Normal prostate tissue adjacent to tumor from patient No.63 PN63U95Av2

source_name: PN63, normal prostate tissue adjacent to tumor from patient No.63


title: Normal prostate tissue adjacent to tumor from patient No.72 PN72U95Av2

source_name: PN72, normal prostate tissue adjacent to tumor from patient No.72


title: Normal prostate tissue adjacent to tumor from patient No.65 PN65U95Av2

source_name: PN65, normal prostate tissue adjacent to tumor from patient No.65


title: Normal prostate tissue adjacent to tumor from patient No.62 PN62U95Av2

source_name: PN62, normal prostate tissue adjacent to tumor from patient No.62


title: Normal prostate tissue adjacent to tumor from patient No.79 PN79U95Av2

source_name: PN79, normal prostate tissue adjacent to tumor from patient No.79


title: Normal prostate tissue adjacent to tumor from patient No.60 PN60U95Av2

source_name: PN60, normal prostate tissue adjacent to tumor from patient No.60


title: Normal prostate tissue adjacent to tumor from patient No.66 PN66U95Av2

source_name: PN66, normal prostate tissue adjacent to tumor from patient No.66


title: Normal prostate tissue adjacent to tumor from patient No.64 PN64U95Av2

source_name: PN64, normal prostate tissue adjacent to tumor from patient No.64


title: Normal prostate tissue adjacent to tumor from patient No.56 PN56U95Av2

source_name: PN56, normal prostate tissue adjacent to tumor from patient No.56


title: Normal prostate tissue adjacent to tumor from patient No.51 PN51U95Av2

source_name: PN51, normal prostate tissue adjacent to tumor from patient No.51


title: Normal prostate tissue adjacent to tumor from patient No.76 PN76U95Av2

source_name: PN76, normal prostate tissue adjacent to tumor from patient No.76


title: Normal prostate tissue adjacent to tumor from patient No.75 PN75U95Av2

source_name: PN75, normal prostate tissue adjacent to tumor from patient No.75


title: Normal prostate tissue adjacent to tumor from patient No.45 PN45U95Av2

source_name: PN45, normal prostate tissue adjacent to tumor from patient No.45


title: Normal prostate tissue adjacent to tumor from patient No.73 PN73U95Av2

source_name: PN73, normal prostate tissue adjacent to tumor from patient No.73


title: Normal prostate tissue adjacent to tumor from patient No.77 PN77U95Av2

source_name: PN77, normal prostate tissue adjacent to tumor from patient No.77


title: Normal prostate tissue adjacent to tumor from patient No.67 PN67U95Av2

source_name: PN67, normal prostate tissue adjacent to tumor from patient No.67


title: Normal prostate tissue adjacent to tumor from patient No.92 PN92U95Av2

source_name: PN92, normal prostate tissue adjacent to tumor from patient No.92


title: Normal prostate tissue adjacent to tumor from patient No.40 PN40U95Av2

source_name: PN40, normal prostate tissue adjacent to tumor from patient No.40


title: Normal prostate tissue adjacent to tumor from patient No.54 PN54U95Av2

source_name: PN54, normal prostate tissue adjacent to tumor from patient No.54


title: Normal prostate tissue adjacent to tumor from patient No.39 PN39U95Av2

source_name: PN39, normal prostate tissue adjacent to tumor from patient No.39


title: Normal prostate tissue adjacent to tumor from patient No.50 PN50U95Av2

source_name: PN50, normal prostate tissue adjacent to tumor from patient No.50


title: Normal prostate tissue adjacent to tumor from patient No.61 PN61U95Av2

source_name: PN61, normal prostate tissue adjacent to tumor from patient No.61


title: Normal prostate tissue adjacent to tumor from patient No.53 PN53U95Av2

source_name: PN53, normal prostate tissue adjacent to tumor from patient No.53


title: Normal prostate tissue adjacent to tumor from patient No.36 PN36U95Av2

source_name: PN36, normal prostate tissue adjacent to tumor from patient No.36


title: Normal prostate tissue adjacent to tumor from patient No.34 PN34U95Av2

source_name: PN34, normal prostate tissue adjacent to tumor from patient No.34


title: Normal prostate tissue adjacent to tumor from patient No.46 PN46U95Av2

source_name: PN46, normal prostate tissue adjacent to tumor from patient No.46


title: Normal prostate tissue adjacent to tumor from patient No.35 PN35U95Av2

source_name: PN35, normal prostate tissue adjacent to tumor from patient No.35


title: Normal prostate tissue adjacent to tumor from patient No.74 PN74U95Av2

source_name: PN74, normal prostate tissue adjacent to tumor from patient No.74


title: Normal prostate tissue adjacent to tumor from patient No.30 PN30U95Av2

source_name: PN30, normal prostate tissue adjacent to tumor from patient No.30


title: Normal prostate tissue adjacent to tumor from patient No.43 PN43U95Av2

source_name: PN43, normal prostate tissue adjacent to tumor from patient No.43


title: Tumor samples from patient No.100 PT100U95Av2

description: Gene expression data from primary prostate cancer

source_name: PT100, tumor samples from patient No.100

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.

tag: Tissue

value: primary prostate tumor

tag: Tumor stage

tag: Gleason Grade


title: Tumor samples from patient No.101 PT101U95Av2

source_name: PT101, tumor samples from patient No.101


title: Tumor samples from patient No.99 PT99U95Av2

source_name: PT99, tumor samples from patient No.99


title: Tumor samples from patient No.97 PT97U95Av2

source_name: PT97, tumor samples from patient No.97


title: Normal prostate tissue adjacent to tumor from patient No.41 PN41U95Av2

source_name: PN41, normal prostate tissue adjacent to tumor from patient No.41


title: Normal prostate tissue adjacent to tumor from patient No.42 PN42U95Av2

source_name: PN42, normal prostate tissue adjacent to tumor from patient No.42


title: Tumor samples from patient No.95 PT95U95Av2

source_name: PT95, tumor samples from patient No.95


title: Normal prostate tissue adjacent to tumor from patient No.69 PN69U95Av2

source_name: PN69, normal prostate tissue adjacent to tumor from patient No.69


title: Tumor samples from patient No.88 PT88U95Av2

source_name: PT88, tumor samples from patient No.88


title: Tumor samples from patient No.87 PT87U95Av2

source_name: PT87, tumor samples from patient No.87


title: Tumor samples from patient No.89 PT89U95Av2

source_name: PT89, tumor samples from patient No.89


title: Tumor samples from patient No.86 PT86U95Av2

source_name: PT86, tumor samples from patient No.86


title: Normal prostate tissue adjacent to tumor from patient No.47 PN47U95Av2

source_name: PN47, normal prostate tissue adjacent to tumor from patient No.47


title: Tumor samples from patient No.93 PT93U95Av2

source_name: PT93, tumor samples from patient No.93


title: Tumor samples from patient No.94 PT94U95Av2

source_name: PT94, tumor samples from patient No.94


title: Tumor samples from patient No.91 PT91U95Av2

source_name: PT91, tumor samples from patient No.91


title: GBM xenograft tumor, line 3, generation 11, microarray hybridization batch 1

status: Public on Mar 07 2009

city: San Francisco

first: Graeme

last: Hodgson

department: Neurological Surgery

institute: UCSF

description: Gene expression data from GBM subcutaneous xenograft tumor tissue

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: CEL files were read into R/Bioconductor using the Affy/affyPLM package, and RMA (robust multi-array average) intensity in log2 scale was generated for each probe set (gene). The 11 perfect match (PM) intensities per probe set were (i) background corrected; (ii) quantile-normalized (to make the distribution of intensities the same for all arrays); and (iii) summarized for each probe set using a robust fit of linear models as described.

source_name: GBM xenograft tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted from GBMX tumors and non-neoplastic control brain using the mirVana RNA isolation system (Ambion), further purified using RNeasy columns (Qiagen), and RNA integrity assessed using a bioanalyzer (Aglient).

tag: tissue type

value: Glioblastoma multiforme (GBM) xenograft tumor tissue

tag: tumor grade

value: Grade-IV tumor


title: Tumor samples from patient No.90 PT90U95Av2

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: PT90, tumor samples from patient No.90


title: Tumor samples from patient No.105 PT105U95Av2

source_name: PT105, tumor samples from patient No.105


title: Tumor samples from patient No.75 PT75U95Av2

source_name: PT75, tumor samples from patient No.75


title: Tumor samples from patient No.92 PT92U95Av2

source_name: PT92, tumor samples from patient No.92


title: Tumor samples from patient No.81 PT81U95Av2

source_name: PT81, tumor samples from patient No.81


title: Normal prostate tissue adjacent to tumor from patient No.48 PN48U95Av2

source_name: PN48, normal prostate tissue adjacent to tumor from patient No.48


title: Tumor samples from patient No.96 PT96U95Av2

source_name: PT96, tumor samples from patient No.96


title: Tumor samples from patient No.73 PT73U95Av2

source_name: PT73, tumor samples from patient No.73


title: Tumor samples from patient No.72 PT72U95Av2

source_name: PT72, tumor samples from patient No.72


title: Tumor samples from patient No.85 PT85U95Av2

source_name: PT85, tumor samples from patient No.85


title: Tumor samples from patient No.84 PT84U95Av2

source_name: PT84, tumor samples from patient No.84


title: Tumor samples from patient No.83 PT83U95Av2

source_name: PT83, tumor samples from patient No.83


title: Tumor samples from patient No.82 PT82U95Av2

source_name: PT82, tumor samples from patient No.82


title: Tumor samples from patient No.69 PT69U95Av2

source_name: PT69, tumor samples from patient No.69


title: Tumor samples from patient No.68 PT68U95Av2

source_name: PT68, tumor samples from patient No.68


title: Tumor samples from patient No.80 PT80U95Av2

source_name: PT80, tumor samples from patient No.80


title: Tumor samples from patient No.67 PT67U95Av2

source_name: PT67, tumor samples from patient No.67


title: Tumor samples from patient No.66 PT66U95Av2

source_name: PT66, tumor samples from patient No.66


title: Tumor samples from patient No.76 PT76U95Av2

source_name: PT76, tumor samples from patient No.76


title: Tumor samples from patient No.65 PT65U95Av2

source_name: PT65, tumor samples from patient No.65


title: Tumor samples from patient No.62 PT62U95Av2

source_name: PT62, tumor samples from patient No.62


title: Tumor samples from patient No.60 PT60U95Av2

source_name: PT60, tumor samples from patient No.60


title: Tumor samples from patient No.58 PT58U95Av2

source_name: PT58, tumor samples from patient No.58


title: Tumor samples from patient No.55 PT55U95Av2

source_name: PT55, tumor samples from patient No.55


title: Normal prostate tissue adjacent to tumor from patient No.58 PN58U95Av2

source_name: PN58, normal prostate tissue adjacent to tumor from patient No.58


title: Tumor samples from patient No.74 PT74U95Av2

source_name: PT74, tumor samples from patient No.74


title: Normal prostate tissue adjacent to tumor from patient No.55 PN55U95Av2

source_name: PN55, normal prostate tissue adjacent to tumor from patient No.55


title: Tumor samples from patient No.71 PT71U95Av2

source_name: PT71, tumor samples from patient No.71


title: Tumor samples from patient No.51 PT51U95Av2

source_name: PT51, tumor samples from patient No.51


title: Tumor samples from patient No.50 PT50U95Av2

source_name: PT50, tumor samples from patient No.50

tag: Tissue:primary prostate tumor


title: Tumor samples from patient No.48 PT48U95Av2

source_name: PT48, tumor samples from patient No.48


title: Tumor samples from patient No.64 PT64U95Av2

source_name: PT64, tumor samples from patient No.64


title: Tumor samples from patient No.56 PT56U95Av2

source_name: PT56, tumor samples from patient No.56


title: Tumor samples from patient No.46 PT46U95Av2

source_name: PT46, tumor samples from patient No.46


title: Tumor samples from patient No.61 PT61U95Av2

source_name: PT61, tumor samples from patient No.61


title: Tumor samples from patient No.54 PT54U95Av2

source_name: PT54, tumor samples from patient No.54


title: Tumor samples from patient No.44 PT44U95Av2

source_name: PT44, tumor samples from patient No.44


title: Tumor samples from patient No.53 PT53U95Av2

source_name: PT53, tumor samples from patient No.53


title: Tumor samples from patient No.52 PT52U95Av2

source_name: PT52, tumor samples from patient No.52


title: Tumor samples from patient No.47 PT47U95Av2

source_name: PT47, tumor samples from patient No.47


title: Tumor samples from patient No.35 PT35U95Av2

source_name: PT35, tumor samples from patient No.35


title: Tumor samples from patient No.45 PT45U95Av2

source_name: PT45, tumor samples from patient No.45


title: Tumor samples from patient No.107 PT107U95Av2

source_name: PT107, tumor samples from patient No.107


title: Tumor samples from patient No.41 PT41U95Av2

source_name: PT41, tumor samples from patient No.41


title: Tumor samples from patient No.43 PT43U95Av2

source_name: PT43, tumor samples from patient No.43


title: Normal prostate tissue adjacent to tumor from patient No.86 PN86U95Av2

source_name: PN86, normal prostate tissue adjacent to tumor from patient No.86


title: Tumor samples from patient No.40 PT40U95Av2

source_name: PT40, tumor samples from patient No.40


title: Metastatic prostate tumor samples in para aortic lymph node from patient FB561 FB561_1BU95Av2

description: Gene expression data from metastatic prostate cancer

source_name: FB561_1B, metastatic prostate tumor samples in para aortic lymph node from patient FB561

treatment_protocol: Specimens were received directly from the operating room. Samples (>500 mg) were excised and snap frozen in liquid nitrogen within 30 min of excision and stored at -80°C until extraction of RNA. Metastatic tumor samples were obtained from a warm autopsy program and processed similarly to primary tumors. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Dissection of the frozen tissue block was performed with the guidance of a marked H & E slide to minimize the presence of host tissue in the metastatic samples. All samples used in the study contained >80% tumor. Metastatic tumor samples were minced and divided into two equal portions to be extracted with the sample protocol used for each set of primary tumors.

value: prostate tumor metastases in para aortic lymph node


title: Tumor samples from patient No.36 PT36U95Av2

source_name: PT36, tumor samples from patient No.36


title: Normal prostate tissue adjacent to tumor from patient No.68 PN68U95Av2

source_name: PN68, normal prostate tissue adjacent to tumor from patient No.68


title: Tumor samples from patient No.57 PT57U95Av2

source_name: PT57, tumor samples from patient No.57


title: Tumor samples from patient No.70 PT70U95Av2

source_name: PT70, tumor samples from patient No.70


title: Tumor samples from patient No.42 PT42U95Av2

source_name: PT42, tumor samples from patient No.42


title: Normal prostate tissue adjacent to tumor from patient No.38 PN38U95Av2

source_name: PN38, normal prostate tissue adjacent to tumor from patient No.38


title: Tumor samples from patient No.34 PT34U95Av2

source_name: PT34, tumor samples from patient No.34


title: Normal prostate tissue adjacent to tumor from patient No.44 PN44U95Av2

source_name: PN44, normal prostate tissue adjacent to tumor from patient No.44


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561 FB561_2GU95Av2

source_name: FB561_2G, metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561

value: prostate tumor metastases in retroperitoneal lymph node


title: Metastatic prostate tumor samples in para aortic lymph node from patient FB561 FB561_1CU95Av2

source_name: FB561_1C, metastatic prostate tumor samples in para aortic lymph node from patient FB561


title: Metastatic prostate tumor samples in liver from patient FB561 FB561_5BU95Av2

source_name: FB561_5B, metastatic prostate tumor samples in liver from patient FB561

value: prostate tumor metastases in liver


title: Metastatic prostate tumor samples in para aortic lymph node from patient EB669 EB669_4AU95Av2

source_name: EB669_4A, metastatic prostate tumor samples in para aortic lymph node from patient EB669


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561 FB561_2FU95Av2

source_name: FB561_2F, metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7EU95Av2

source_name: EB667_7E, metastatic prostate tumor samples in para tracheal lymph node from patient EB667

value: prostate tumor metastases in paratracheal lymph node


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_3BU95Av2

source_name: FB561_3B, metastatic prostate tumor samples in para tracheal lymph node from patient FB561


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_6BU95Av2

source_name: FB561_6B, metastatic prostate tumor samples in para tracheal lymph node from patient FB561

value: prostate tumor metastases in para tracheal lymph node


title: Metastatic prostate tumor samples in left inguinal lymph node from patient EB667 EB667_5A+5BU95Av2

source_name: EB667_5A+5B, metastatic prostate tumor samples in left inguinal lymph node from patient EB667

value: prostate tumor metastases in left inguinal lymph node


title: Metastatic prostate tumor samples in para tracheal lymph node from patient FB561 FB561_6CU95Av2

source_name: FB561_6C, metastatic prostate tumor samples in para tracheal lymph node from patient FB561


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7FU95Av2

source_name: EB667_7F, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Metastatic prostate tumor samples in paratracheal lymph node from patient EB667 EB667_7AU95Av2

source_name: EB667_7A, metastatic prostate tumor samples in paratracheal lymph node from patient EB667


title: Metastatic prostate tumor samples in retroperitoneal lymph node from patient EB667 EB667_6AU95Av2

source_name: EB667_6A, metastatic prostate tumor samples in retroperitoneal lymph node from patient EB667


title: Metastatic prostate tumor samples in liver from patient EB669 EB669_7B+7DU95Av2

source_name: EB669_7B+7D, metastatic prostate tumor samples in liver from patient EB669


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7B+7DU95Av2

source_name: EB667_7B+7D, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Metastatic prostate tumor samples in lung from patient FB561 FB561_7BU95Av2

source_name: FB561_7B, metastatic prostate tumor samples in lung from patient FB561

value: prostate tumor metastases in lung


title: Metastatic prostate tumor samples in liver from patient EB669 EB669_7A+7CU95Av2

source_name: EB669_7A+7C, metastatic prostate tumor samples in liver from patient EB669


title: Metastatic prostate tumor samples in adrenal gland from patient EB669 EB669_8CU95Av2

source_name: EB669_8C, metastatic prostate tumor samples in adrenal gland from patient EB669

value: prostate tumor metastases in adrenal gland


title: Metastatic prostate tumor samples in adrenal gland from patient EB669 EB669_8BU95Av2

source_name: EB669_8B, metastatic prostate tumor samples in adrenal gland from patient EB669


title: Metastatic prostate tumor samples in kidney from patient EB667 EB667_2A+2B+2CU95Av2

source_name: EB667_2A+2B+2C, metastatic prostate tumor samples in kidney from patient EB667

value: prostate tumor metastases in kidney


title: Metastatic prostate tumor samples in liver from patient FB561 FB561_5FU95Av2

source_name: FB561_5F, metastatic prostate tumor samples in liver from patient FB561


title: Metastatic prostate tumor samples in liver from patient EB666 EB666_1G+1HU95Av2

source_name: EB666_1G+1H, metastatic prostate tumor samples in liver from patient EB666


title: Metastatic prostate tumor samples recurrent in prostate from patient FB561 FB561_4HU95Av2

source_name: FB561_4H, metastatic prostate tumor samples recurrent in prostate from patient FB561

value: metastases recurrent in prostate


title: Metastatic prostate tumor samples in para tracheal lymph node from patient EB667 EB667_7CU95Av2

source_name: EB667_7C, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Normal prostate tissue free of any pathological alteration from organ donor PD016 PD016U95Av2

description: Gene expression data from normal prostate tissues free of any pathological alteration

source_name: PD016, normal prostate tissue free of any pathological alteration from organ donor PD016

treatment_protocol: Donor prostate tissues were obtained at the time of organ donation in brain-dead men. Samples were collected from peripheral zone of the prostate gland with at least 60% glandular components and free of any pathological alteration.

tag: Tissue:normal prostate tissue free of any pathological alteration from brain-dead organ donor

tag: Race

value: Caucasian


title: Normal prostate tissue free of any pathological alteration from organ donor PD015 PD015U95Av2

source_name: PD015, normal prostate tissue free of any pathological alteration from organ donor PD015


title: Normal prostate tissue free of any pathological alteration from organ donor PD020 PD020U95Av2

source_name: PD020, normal prostate tissue free of any pathological alteration from organ donor PD020


title: Normal prostate tissue free of any pathological alteration from organ donor PD019 PD019U95Av2

source_name: PD019, normal prostate tissue free of any pathological alteration from organ donor PD019


title: Normal prostate tissue free of any pathological alteration from organ donor PD014 PD014U95Av2

source_name: PD014, normal prostate tissue free of any pathological alteration from organ donor PD014


title: Normal prostate tissue free of any pathological alteration from organ donor PD013 PD013U95Av2

source_name: PD013, normal prostate tissue free of any pathological alteration from organ donor PD013


title: Normal prostate tissue free of any pathological alteration from organ donor PD012 PD012U95Av2

source_name: PD012, normal prostate tissue free of any pathological alteration from organ donor PD012


title: Normal prostate tissue free of any pathological alteration from organ donor PD011 PD011U95Av2

source_name: PD011, normal prostate tissue free of any pathological alteration from organ donor PD011


title: Normal prostate tissue free of any pathological alteration from organ donor PD007 PD007U95Av2

source_name: PD007, normal prostate tissue free of any pathological alteration from organ donor PD007


title: Normal prostate tissue free of any pathological alteration from organ donor PD010 PD010U95Av2

source_name: PD010, normal prostate tissue free of any pathological alteration from organ donor PD010


title: Normal prostate tissue free of any pathological alteration from organ donor PD009 PD009U95Av2

source_name: PD009, normal prostate tissue free of any pathological alteration from organ donor PD009


title: Normal prostate tissue free of any pathological alteration from organ donor PD006 PD005U95Av2

source_name: PD006, normal prostate tissue free of any pathological alteration from organ donor PD006

value: African American