title: Young C57-01, chip

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by System Administrator (OGCInfo@ohri.ca; ) for analysis.
Stembase Experiment ID:			E246
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=246
SCGP Sample ID:				S404
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=246#SAMPLE_405
Short description:			Gastrocnemius from normal C57B1/6 mice
Estimated purity:				95-99%
RNA concentration:			0.05 ug/ul
Sample volume:				5 ul

source_name: Total Muscle, Skeletal Muscle Gastrocnemius


title: dexrazoxane control 3

status: Public on Feb 24 2009

type: RNA

city: Mainz

first: Shiwei

last: Deng

address: Obere Zahlbacher Str. 67

country: Germany

institute: Uni Mainz

description:
>99.5% TOP2A expression can be silenced in HTETOP cells by the addition of tetracycline
pooled RNA from three cell passages was used for hybridization

hyb_protocol: Following fragmentation, cRNA were hybridized to Human Genome U133 Plus 2.0 GeneChips from Affymetrix.

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000.

data_processing: The images were processed by GeneChip Operating Software 1.3 and the raw data were normalized by Robust Multiarray Analysis (RMA).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: control HTETOP cells

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

extract_protocol: Total RNA was extracted using peqGOLD Total RNA Kit according to the manufacturer’s instructions.

treatment_protocol: HTETOP cells were treated with 100 µM dexrazoxane or vehicle for 24 hours.

tag: cell line

value: HTETOP


title: Young C57-02, chip

status: Public on Feb 26 2009

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

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

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

label: Biotin

organism: Mus musculus

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

extract_protocol: RNA prep method:				RNeasy

tag: strain

tag: gender

value: Male

tag: karyotype

value: Normal


title: Balb/c WT2 liver

status: Public on Feb 28 2009

city: Hanover

first: Jennifer

middle: L

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

country: USA

institute: Dartmouth Medical School

description: Following RNA preparation, all microarray procedures were carried out at the Dartmouth Genomics and Microarray Laboratory (Lebanon, NH)

hyb_protocol: Standard hybridization protocols as per Affymetrix directions.  Hybe for 16 hours, at 45oC, 60 rpm

scan_protocol: washed, stained and scanned according to standard Affymetrix protocols.

data_processing: Initial data processing and normalizations were carried out at the Dartmouth Genomics and Microarray Laboratory (Lebanon, NH).

source_name: Balb/c wildtype control 2

label_protocol: standard Affymetrix one-cycle labelling protocol

extract_protocol: Trizol extraction

tag: 11 day old balb/c wildtype mouse liver (replicate 2)


title: IFNko TGFB1 KO3 liver

hyb_protocol: Standard hybridization protocols as per Affymetrix directions. Hybe for 16 hours, at 45oC, 60 rpm

source_name: IFNko TGFB1 KO3 (balb/c)

tag: 11 day old balb/c INF knockout, TGFB1 knockout mouse liver (replicate 3)


title: IFNko TGFB1 KO2 liver

source_name: IFNko TGFB1 KO2 (balb/c)

tag: 11 day old balb/c INF knockout, TGFB1 knockout mouse liver (replicate 2)


title: HCT116 stable PCLKC 1

city: Kisarazu

first: Rui

last: Ose

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Human Genome Research

country: Japan

institute: Kazusa DNA Research Institute

description: no additional information

hyb_protocol: Refer to the Affymetrix Expression Analysis Technical Manual

source_name: HCT116 with stable PCLKC

label_protocol: IVT labeling Kit

extract_protocol: Qiagen RNeasy Mini Kit

tag: HCT116 human colon cancer cells with stable PCLKC


title: dexrazoxane 1

source_name: dexrazoxane-treated HTETOP cells


title: HCT116 2

description: no additional information

scan_protocol: Refer to the Affymetrix Expression Analysis Technical Manual

tag: HCT116 human colon cancer cells


title: HCT116 1

description: no additional information


title: dexrazoxane control 2


title: Young C57-03, chip


title: dexrazoxane 3


title: INFko TGFB+ liver

source_name: INFko TGBF+ (balb/c)

tag: 11 day old balb/c INF knock out, TGFB+(wt) mouse liver (replicate 1)


title: HCT116 stable PCLKC B5 1

description: no additional information

source_name: HCT116 with stable PCLKC-GFP

tag: HCT116 human colon cancer cells with stable PCLKC-GFP


title: HCT116 stable GFP 1

description: no additional information

source_name: HCT116 with stable GFP

tag: HCT116 human colon cancer cells with stable GFP


title: HCT116 stable PCLKC 2

description: no additional information

extract_protocol: Qiagen Rneasy Mini Kit


title: Human adult normal kidney control, pool of 5 samples

city: Basel

first: Friedrich

last: Raulf

department: Novartis Institutes for BioMedical Research / ATDA

country: Switzerland

institute: Novartis Pharma AG

description: Gene expression data from human normal adult kidney (commercial pool)

hyb_protocol: Hybridization of arrays was carried out at 45°C for about18 h, then arrays were stained on a GeneChip Fluidics Workstation 450 according to the manufacturer’s technical manual (Affymetrix).

scan_protocol: GeneChips were scanned on a GeneArray Scanner 3000 according to the manufacturer’s technical manual (Affymetrix).

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 150.

source_name: Human control kidney (pool of 5 adult healthy samples)

label_protocol: Labeled probes were prepared either according to the Affymetrix 2-cycle cDNA amplification protocol (Affymetrix, Santa Clara, CA) from 50 ng total RNA of all biopsy samples, or from 5 microg of total RNA of all control kidney samples according to the standard Affymetrix protocol. The cDNA was transcribed in vitro in the presence of biotinylated ribonucleotides (Bioarray high-yield T7 DNA transcription kit; ENZO Life Sciences, Inc.). The biotinylated cRNA was purified on an affinity resin (RNeasy; Qiagen), quantified, and fragmented into strands of 50–200 nucleotides in length.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen, Hilden, Germany).

tag: Pool of 5 normal adult kidney samples, Sex


title: Patient 70-PJ, renal graft bx, diagnosis non-rejecting

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of no rejection.

source_name: Biopsy from non-rejecting human kidney allograft

tag: Patient identifier

value: 70-PJ, Sex:male, Type of donor:deceased, Serum creatinine:128 microMol/L, Renal graft bx:70-PJ, Banff'97:non-rejecting,


title: Patient 281004-L7, control kidney from nephrectomy

description: Gene expression data from human normal adult kidney (from nephrectomy).

source_name: Human control kidney from nephrectomy

value: 281004-L7, Control kidney sample  from nephrectomy


title: Patient 4-MS, renal graft bx, diagnosis CAN I

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of chronic allograft nephropathy grade I.

source_name: Chronic allograft nephropathy biopsy grade I from human transplanted kidney

value: 4-MS, Sex:male, Age of patient:35, Serum creatinine:231 microMol/L, Renal graft bx:4-MS, Banff'97:CAN I,


title: Patient 1-ME, renal graft bx, diagnosis CAN I

value: 1-ME, Sex:male, Age of patient:42, Type of donor:deceased, Serum creatinine:177 microMol/L, Renal graft bx:1-ME, Banff'97:CAN I,


title: Patient 3-AO, renal graft bx, diagnosis CAN I

value: 3-AO, Sex:male, Age of patient:57, Type of donor:deceased, Serum creatinine:131 microMol/L, Renal graft bx:3-AO, Banff'97:CAN I,


title: Patient TX26, renal graft bx 1.32, diagnosis CAN III

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of chronic allograft nephropathy grade III.

source_name: Chronic allograft nephropathy biopsy grade III from human transplanted kidney

value: TX26, Sex:male, Age of patient:33, Serum creatinine:572 microMol/L, Renal graft bx:1.32, Banff'97:CAN III,


title: Patient C06, control kidney from nephrectomy, without clamping

value: C06, Sex:male, Age of patient:44, Serum creatinine:88 microMol/L, Control kidney from nephrectomy sample without clamping


title: Patient C05, control kidney from nephrectomy

value: C05, Sex:female, Age of patient:37, Serum creatinine:36 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX07, renal graft bx 1.08, diagnosis CAN III

value: TX07, Sex:male, Age of patient:39, Type of donor:deceased, Serum creatinine:495 microMol/L, Renal graft bx:1.08, Banff'97:CAN III,


title: Patient TX04, renal graft bx 1.04, diagnosis CAN III

value: TX04, Sex:male, Age of patient:39, Type of donor:deceased, Renal graft bx:1.04, Banff'97:CAN III,


title: Patient C11, control kidney from nephrectomy, cortex

value: C11, Sex:male, Age of patient:82, Serum creatinine:113 microMol/L, Control kidney sample (cortex)  from nephrectomy


title: Patient C15, control kidney from nephrectomy

value: C15, Sex:male, Age of patient:60, Serum creatinine:93 microMol/L, Control kidney sample  from nephrectomy


title: Patient C11, control kidney from nephrectomy, cortex + medulla

value: C11, Sex:male, Age of patient:82, Serum creatinine:113 microMol/L, Control kidney sample (cortex+medulla)  from nephrectomy


title: Patient C13, control kidney from nephrectomy

value: C13, Sex:male, Age of patient:76, Serum creatinine:88 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX34, renal graft bx 1.42, diagnosis CAN III

value: TX34, Sex:male, Age of patient:61, Type of donor:deceased, Serum creatinine:250 microMol/L, Renal graft bx:1.42, Banff'97:CAN III,


title: Patient C14, control kidney from nephrectomy

value: C14, Sex:male, Age of patient:74, Serum creatinine:107 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX24, renal graft bx 1.30, diagnosis CAN III

value: TX24, Sex:male, Age of patient:45, Type of donor:deceased, Serum creatinine:210 microMol/L, Renal graft bx:1.30, Banff'97:CAN III,


title: Patient TX38, renal graft bx 1.46, diagnosis CAN III

value: TX38, Sex:male, Age of patient:55, Type of donor:deceased, Serum creatinine:201 microMol/L, Renal graft bx:1.46, Banff'97:CAN III,


title: Patient TX12, renal graft bx 1.13, diagnosis non-rejecting

value: TX12, Sex:male, Age of patient:33, Serum creatinine:130 microMol/L, Renal graft bx:1.13, Banff'97:non-rejecting,


title: Patient TX41, renal graft bx 1.49, diagnosis non-rejecting

value: TX49, Sex:male, Type of donor:deceased, Serum creatinine:104 microMol/L, Renal graft bx:1.49, Banff'97:non-rejecting,


title: Patient TX21, renal graft bx 1.26, diagnosis non-rejecting

value: TX21, Sex:male, Age of patient:42, Type of donor:deceased, Serum creatinine:118 microMol/L, Renal graft bx:1.26, Banff'97:non-rejecting,


title: Patient TX49, renal graft bx 1.57, diagnosis CAN II

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of chronic allograft nephropathy grade II.

source_name: Chronic allograft nephropathy biopsy grade II from human transplanted kidney

value: TX49, Sex:female, Age of patient:45, Type of donor:deceased, Serum creatinine:298 microMol/L, Renal graft bx:1.57, Banff'97:CAN II,


title: Patient C10, control kidney from nephrectomy

value: C10, Sex:male, Age of patient:64, Serum creatinine:91 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX08, renal graft bx 1.09, diagnosis non-rejecting

value: TX08, Sex:male, Age of patient:33, Type of donor:deceased, Serum creatinine:158 microMol/L, Renal graft bx:1.09, Banff'97:non-rejecting,


title: Patient C01, control kidney from nephrectomy

value: C01, Sex:female, Age of patient:61, Serum creatinine:65 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX27, renal graft bx 1.34, diagnosis non-rejecting

value: TX27, Sex:male, Age of patient:54, Type of donor:living, Serum creatinine:219 microMol/L, Renal graft bx:1.34, Banff'97:non-rejecting,


title: Patient C16, control kidney from nephrectomy

value: C16, Sex:male, Age of patient:71, Serum creatinine:114 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX29, renal graft bx 1.36, diagnosis CAN III

value: TX29, Sex:male, Age of patient:40, Type of donor:living, Serum creatinine:427 microMol/L, Renal graft bx:1.36, Banff'97:CAN III,


title: Patient C03, control kidney from nephrectomy

value: C03, Sex:male, Age of patient:71, Serum creatinine:61 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX25, renal graft bx 1.33, diagnosis non-rejecting

value: TX25, Sex:female, Age of patient:54, Type of donor:deceased, Serum creatinine:192 microMol/L, Renal graft bx:1.33, Banff'97:non-rejecting,


title: Patient TX37, renal graft bx 1.45, diagnosis non-rejecting

value: TX37, Sex:male, Age of patient:43, Type of donor:living, Serum creatinine:199 microMol/L, Renal graft bx:1.45, Banff'97:non-rejecting,


title: Patient C06, control kidney from nephrectomy, with clamping

value: C06, Sex:male, Age of patient:44, Serum creatinine:88 microMol/L, Control kidney from nephrectomy sample with clamping


title: Patient C04, control kidney from nephrectomy

value: C04, Sex:male, Age of patient:28, Serum creatinine:75 microMol/L, Control kidney sample  from nephrectomy


title: Patient TX32, renal graft bx 1.39, diagnosis CAN III

value: TX32, Sex:male, Age of patient:58, Serum creatinine:1000 microMol/L, Renal graft bx:1.39, Banff'97:CAN III,


title: Patient TX23, renal graft bx 1.29, diagnosis CAN II

value: TX23, Sex:female, Age of patient:46, Type of donor:deceased, Serum creatinine:161 microMol/L, Renal graft bx:1.29, Banff'97:CAN II,


title: Patient TX31, renal graft bx 1.38, diagnosis CAN II

value: TX31, Sex:female, Age of patient:47, Type of donor:deceased, Serum creatinine:167 microMol/L, Renal graft bx:1.38, Banff'97:CAN II,


title: Patient TX46, renal graft bx 1.54, diagnosis CAN II

value: TX46, Sex:male, Age of patient:59, Type of donor:deceased, Serum creatinine:200 microMol/L, Renal graft bx:1.54, Banff'97:CAN II,


title: Patient TX13, renal graft bx 1.16, diagnosis CAN II

value: TX13, Sex:female, Age of patient:60, Type of donor:deceased, Serum creatinine:332 microMol/L, Renal graft bx:1.16, Banff'97:CAN II,


title: Patient TX33, renal graft bx 1.40, diagnosis CAN II

value: TX33, Sex:female, Age of patient:24, Type of donor:living, Serum creatinine:175 microMol/L, Renal graft bx:1.40, Banff'97:CAN II,


title: Patient TX11, renal graft bx 1.61, diagnosis AR+CAN

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of acute rejection plus chronic allograft nephropathy.

source_name: Biopsy with acute rejection and chronic allograft nephropathy from human transplanted kidney

value: TX11, Sex:male, Age of patient:53, Type of donor:deceased, Serum creatinine:204 microMol/L, Renal graft bx:1.61, Banff'97:AR+CAN,


title: Patient TX53, renal graft bx 1.62, diagnosis AR+CAN

value: TX53, Sex:female, Age of patient:45, Type of donor:deceased, Serum creatinine:122 microMol/L, Renal graft bx:1.62, Banff'97:AR+CAN,


title: Patient TX52, renal graft bx 1.60, diagnosis CAN I

value: TX52, Sex:female, Age of patient:27, Serum creatinine:121 microMol/L, Renal graft bx:1.60, Banff'97:CAN I,


title: Patient TX44, renal graft bx 1.52, diagnosis CAN II

value: TX44, Sex:male, Age of patient:49, Type of donor:deceased, Serum creatinine:182 microMol/L, Renal graft bx:1.52, Banff'97:CAN II,


title: Patient TX50, renal graft bx 1.58, diagnosis AR IIB

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of acute rejection IIB.

source_name: Acute rejection biopsy type IIB from human kidney allograft

value: TX50, Sex:female, Age of patient:48, Type of donor:deceased, Serum creatinine:328 microMol/L/L, Renal graft bx:1.58, Banff'97:AR IIB,


title: Patient TX48, renal graft bx 1.56, diagnosis CAN II

value: TX48, Sex:male, Age of patient:60, Type of donor:deceased, Serum creatinine:186 microMol/L, Renal graft bx:1.56, Banff'97:CAN II,


title: Patient TX01, renal graft bx 1.01, diagnosis borderline changes

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of borderline changes.

source_name: Biopsy with borderline rejection / suspicious changes from human kidney allograft

value: TX01, Sex:male, Age of patient:46, Type of donor:deceased, Serum creatinine:270 microMol/L, Renal graft bx:1.01, Banff'97:borderline changes,


title: Patient TX54, renal graft bx 1.63, diagnosis AR+CAN

value: TX54, Sex:male, Age of patient:38, Serum creatinine:900 microMol/L, Renal graft bx:1.65, Banff'97:AR+CAN,


title: Patient TX20, renal graft bx 1.25, diagnosis AR IB

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of acute rejection IB.

source_name: Acute rejection biopsy type IB from human kidney allograft

value: TX25, Sex:male, Age of patient:35, Type of donor:deceased, Serum creatinine:171 microMol/L/L, Renal graft bx:1.25, Banff'97:AR IB,


title: Patient TX03, renal graft bx 1.03, diagnosis AR IB

value: TX03, Sex:male, Age of patient:22, Type of donor:deceased, Serum creatinine:161 microMol/L/L, Renal graft bx:1.03, Banff'97:AR IB,


title: Patient TX02, renal graft bx 1.02, diagnosis CAN I

value: TX02, Sex:male, Serum creatinine:120 microMol/L, Renal graft bx:1.02, Banff'97:CAN I,


title: Patient TX56, renal graft bx 1.65, diagnosis AR+CAN

value: TX56, Sex:female, Age of patient:44, Type of donor:deceased, Serum creatinine:806 microMol/L, Renal graft bx:1.65, Banff'97:AR+CAN,


title: Patient TX51, renal graft bx 1.59, diagnosis CAN I

value: TX51, Sex:male, Age of patient:55, Serum creatinine:267 microMol/L, Renal graft bx:1.59, Banff'97:CAN I,


title: Patient TX06, renal graft bx 1.07, diagnosis borderline changes

value: TX06, Sex:female, Age of patient:29, Type of donor:deceased, Serum creatinine:199 microMol/L, Renal graft bx:1.07, Banff'97:borderline changes,


title: Patient TX42, renal graft bx 1.50, diagnosis CAN I

value: TX42, Sex:male, Age of patient:67, Type of donor:deceased, Serum creatinine:110 microMol/L, Renal graft bx:1.50, Banff'97:CAN I,


title: Patient TX58, renal graft bx 1.67, diagnosis AR+CAN

value: TX58, Sex:female, Age of patient:35, Type of donor:deceased, Serum creatinine:200 microMol/L, Renal graft bx:1.67, Banff'97:AR+CAN,


title: Patient TX06, renal graft bx 1.06, diagnosis borderline changes

value: TX06, Sex:female, Age of patient:29, Type of donor:deceased, Serum creatinine:200 microMol/L, Renal graft bx:1.06, Banff'97:borderline changes,


title: Patient TX10, renal graft bx 1.17, diagnosis AR+CAN

value: TX10, Sex:female, Age of patient:34, Type of donor:deceased, Serum creatinine:640 microMol/L, Renal graft bx:1.17, Banff'97:AR+CAN,


title: Patient TX11, renal graft bx 1.12, diagnosis AR IIA

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of acute rejection IIA.

source_name: Acute rejection biopsy type IIA from human kidney allograft

value: TX11, Sex:male, Age of patient:53, Type of donor:deceased, Serum creatinine:228 microMol/L/L, Renal graft bx:1.12, Banff'97:AR IIA,


title: Patient TX10, renal graft bx 1.11, diagnosis AR+CAN

value: TX10, Sex:female, Age of patient:34, Type of donor:deceased, Serum creatinine:356 microMol/L, Renal graft bx:1.11, Banff'97:AR+CAN,


title: Patient TX55, renal graft bx 1.64, diagnosis CAN II

value: TX55, Sex:female, Age of patient:43, Serum creatinine:240 microMol/L, Renal graft bx:1.64, Banff'97:CAN II,


title: KO_EtOH0mM_B

city: Wako

first: Hideki

last: Tatsukawa

state: Saitama

address: Hirosawa 2-1

institute: RIKEN

description: transglutaminase knock out mice, liver, total RNA processed to biotin-labeled cRNA

hyb_protocol: standard Affymetrix procedures (16 hour)

scan_protocol: standard Affymetrix procedures

data_processing: Using GeneSpring GX

label_protocol: Total RNA was processed to produce biotinylated cRNA targets by one-cycle target labeling using IVT labeling Kit

extract_protocol: Total RNA was extracted from the primary hepatocytes using an RNeasy kit (Qiagen).

treatment_protocol: Mouse primary hepatocytes from TG2KO mouse were incubated as a control for 15hr

tag: Stain

tag: Primary hepatocytes

tag: TG2KO mouse (transglutaminase-knockout mouse)


title: KO_EtOH100mM_B


title: Patient TX25, renal graft bx 1.31, diagnosis AR IB

value: TX25, Sex:female, Age of patient:54, Type of donor:deceased, Serum creatinine:466 microMol/L/L, Renal graft bx:1.31, Banff'97:AR IB,


title: Patient TX01, renal graft bx 1.15, diagnosis AR IA

description: Gene expression data from core human renal allograft biopsy (16 gauge) with histological diagnosis of acute rejection IA.

source_name: Acute rejection biopsy type IA from human kidney allograft

value: TX01, Sex:male, Age of patient:47, Type of donor:deceased, Serum creatinine:230 microMol/L/L, Renal graft bx:1.15, Banff'97:AR IA,


title: WT_EtOH100mM_B

description: wild-type mice mice, liver, total RNA processed to biotin-labeled cRNA

treatment_protocol: Mouse primary hepatocytes were incubated as a control for 15hr

tag: Wild-type mouse


title: WT_EtOH0mM_B


title: KO_EtOH100mM_A

treatment_protocol: Mouse primary hepatocytes from TG2KO mouse were treated with EtOH for 15hr


title: Patient TX22, renal graft bx 1.27, diagnosis AR IA

value: TX22, Sex:male, Age of patient:41, Type of donor:deceased, Serum creatinine:187 microMol/L/L, Renal graft bx:1.27, Banff'97:AR IA,


title: SA treated, biological rep3

city: Lucknow

first: Samir

last: Sawant

state: U.P, India

address: Rana Pratap Marg

department: Centre of Plant Molecular Biology

country: India

institute: National Botanical Research Institute

description: Gene expression data from SA treated Arabidopsis seeedlings

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA (Robust Multichip Average) using Affymetrix default analysis settings .

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings Col-0

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

growth_protocol: Arabidopsis seedlings Col-0 were grown for 9 days in controlled environment rooms at 22°C temperature and a photoperiod of 16 h light 100 µm m2 s_1 cool-white fluorescent illumination

extract_protocol: Total RNA was performed according to the Sigma RNA isolation kit (STRN250)

treatment_protocol: Arabidopsis seedlings Col-0 were grown for 9 days and then transferred into water as a mock treatment and with the defense related signaling molecules salicylic acid (SA) for one day

tag: development stage

value: seedling

tag: cultivar


title: Patient TX40, renal graft bx 1.48, diagnosis AR IA

value: TX40, Sex:male, Age of patient:52, Renal graft bx:1.48, Banff'97:AR IA,


title: Water treated, biological rep2

description: Gene expression data from water treated Arabidopsis seeedlings


title: Water treated, biological rep1


title: KO_EtOH0mM_A


title: TBM3 stim

status: Public on Feb 23 2009

city: Ho Chi Minh City

first: Sarah

middle: J

last: Dunstan

address: 190 Ben Ham Tu, Quan 5

department: Hospital for Tropical Diseases

country: Viet Nam

institute: 1.	Oxford University Clinical Research Unit

description: Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours.

hyb_protocol: Following fragmentation, ten micrograms of adjusted cRNA fromeach sample was hybridized for 16 hours at 45 deg C to Affymetrix GeneChip

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor

source_name: macrophage, ex vivio stimulation TB extract for 4 hrs

label_protocol: Standard Affymetrix IVT labeling protocol. See Affymetrix Expression Analysis Technical Manual

growth_protocol: Peripheral Blood Mononuclear Cells (PBMCs) were separated from heparinized whole blood by Lymphoprep (Asix-Shield, Norway) gradient centrifugation according to the manufacturer's protocol. 20 ml of blood was slowly added to the tube containing 20ml of Lymphoprep and spun at 2800 rpm for 24 minutes at room temperature with low brake. The PBMC layer was transferred to a new tube and washed 3 times with cold PBS 3% fetal calf serum (FCS) to remove platelets. To derive monocytes, 1-1.5x107 PBMCs were plated in a well of a 6-well plate (Nunc, Denmark) in RPMI-1640 (Sigma, Germany) with 10% heat-inactivated fetal calf serum (FCS; Sigma, Germany), 2mM L-glutamine and 100 units of penicillin for 2 hours at 370C. Non-adhered cells were washed off 3 times with PBS 3 % FCS. The cells were plated in RPMI media for 5 days at 370C 5% CO2 to make monocyte-derived macrophages (MDMs).

extract_protocol: Cells grown in a monolayer were treated with Trizol (Invitrogen, USA) to extract RNA. 1 ml of Trizol was added to a well of a 6-well plate to disrupt cells, dissolve cell components and release RNA. Cell suspension was transferred to a tube and 0.2 ml of chloroform was added to separate the solution into an aqueous phase and an organic phase by centrifugation at 10,000 rpm for 15 minutes. The aqueous phase which contains RNA was transferred to a new tube. Isopropanol was added next with an equal volume to precipitate the RNA by centrifugation at 12,000 for 10 minutes. Then the supernatant was removed and the RNA pellet was washed with 75% ethanol, dried, dissolved in RNase- free water and stored at -80oC.

treatment_protocol: MDMs were stimulated ex-vivo with either 5 µg/ml of whole cell lysate of M. tuberculosis H37Rv (obtained from the Mycobacteria Research laboratories at Colorado State University, USA) or PBS control for 4 hours.

tag: 5 day monocyte-derived macrophage

tag: meningeal tuberculosis


title: PTB2 unstim

source_name: macrophage, ex vivo stimulation with media (control)

tag: Pulmonary


title: PTB1 stim


title: WT_EtOH100mM_A

treatment_protocol: Mouse primary hepatocytes were treated with 100mM EtOH for 15hr


title: LTB2 stim

tag: Latent


title: LTB4 unstim


title: WT_EtOH0mM_A


title: LTB3 stim


title: LTB4 stim


title: PTB2 stim


title: PTB4 stim


title: TBM1 stim


title: TBM4 stim


title: LTB3 unstim


title: Patient TX45, renal graft bx 1.53, diagnosis CAN II

value: TX45, Sex:male, Age of patient:43, Type of donor:deceased, Serum creatinine:200 microMol/L, Renal graft bx:1.53, Banff'97:CAN II,


title: SA treated, biological rep1


title: TBM3 unstim


title: PTB1 unstim


title: SA treated, biological rep2


title: LTB2 unstim


title: PTB3 stim


title: TBM2 stim


title: PTB4 unstim


title: BMDCs cocultured with tumor

city: Tianjin

first: Rongcun

last: Yang

address: Nankai District, 94 Weijin Lu

department: Department of Immunology

country: China

institute: Nankai University School of Medicine

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

source_name: Bone marrow-derived dendritic cells, 1D8 treated

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

extract_protocol: Total RNA was isolated from DCs using TRIzol Reagent (Invitrogen) followed by RNA clean up with RNeasy Mini kit (QIAGEN).

treatment_protocol: Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days.  BMDCs were cocultured with 1D8 tumor cells and then sorted by staining with FITC labeled anti-CD80 antibody and flow cytometry.

tag: C57BL/6 mice, Gender

value: Male, Age:6~8 weeks.

tag: BMDCs were prepared from bone marrow cells collected by removing the femur bones, cutting off each end and flushing out the bone marrow with RPMI 1640 medium using a syringe. The pooled cells were harvested by centrifugation at 600 g, 10 min and resuspended in 2 ml ACK buffer for 5 min at room temperature to lyse the red blood cells. These cells were washed in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin and the Dendritic Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days. They were cocultured with 1D8 mouse ovarian surface epithelial tumor cells at a ratio 1:5, tumor:BMDC


title: TBM1 unstim


title: PTB3 unstim


title: TBM2 unstim


title: LTB1 unstim


title: BDMCs cultured in tumor-conditioned medium

source_name: Bone marrow-derived dendritic cells, 1D8 tumor cell supernatent treated

treatment_protocol: Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days.  BMDCs were cocultured in 1D8 tumor cell-conditioned medium and sorted by staining with FITC labeled anti-CD80 antibody and flow cytometry.

tag: BMDCs were prepared from bone marrow cells collected by removing the femur bones, cutting off each end and flushing out the bone marrow with RPMI 1640 medium using a syringe. The pooled cells were harvested by centrifugation at 600 g, 10 min and resuspended in 2 ml ACK buffer for 5 min at room temperature to lyse the red blood cells. These cells were washed in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin and the Dendritic Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days. They were cocultured in 1D8 (mouse ovarian surface epithelial cell) tumor cell-conditioned medium at 25% (v/v).


title: BMDCs cocultured with irradiated tumor

source_name: Bone marrow-derived dendritic cells, irradiated 1D8 treated

treatment_protocol: Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days.  BMDCs were cocultured with irradiated  (50Gy) 1D8 tumor cells and then sorted by staining with FITC labeled anti-CD80 antibody and flow cytometry.

tag: BMDCs were prepared from bone marrow cells collected by removing the femur bones, cutting off each end and flushing out the bone marrow with RPMI 1640 medium using a syringe. The pooled cells were harvested by centrifugation at 600 g, 10 min and resuspended in 2 ml ACK buffer for 5 min at room temperature to lyse the red blood cells. These cells were washed in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin and the Dendritic Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days.  They were cocultured with irradiated  (50Gy) 1D8 mouse ovarian surface epithelial tumor cells at a ratio 1:5, tumor:BMDC


title: TBM4 unstim


title: LTB1 stim


title: BMDC control cells

source_name: Bone marrow-derived dendritic cells, not 1D8 treated

treatment_protocol: Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days.  BMDCs were sorted by staining with FITC labeled anti-CD80 antibody and flow cytometry.

tag: BMDCs were prepared from bone marrow cells collected by removing the femur bones, cutting off each end and flushing out the bone marrow with RPMI 1640 medium using a syringe. The pooled cells were harvested by centrifugation at 600 g, 10 min and resuspended in 2 ml ACK buffer for 5 min at room temperature to lyse the red blood cells. These cells were washed in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin and the Dendritic Cells were cultured in medium containing 500 U/ml GM-CSF (R&D systems, MN, USA) for 7days.


title: C57BL/6 CD4+ CD25+ Treg cells #2

status: Public on Feb 22 2009

city: Miami

first: Thomas

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

description: B6 EA33257

hyb_protocol: per Affymetrix technical manual at Expression Analysis (Durhan, NC)

data_processing: GC-RMA normalized through Geneshifter as log2 transformed values

source_name: mouse spleen

extract_protocol: RNA isolated with Trizol reagent and purified with RNAeassy minikit (Qiagen) and amplified 1X IVT as per Affymetrix technical manual.

tag: Genetic background

value: normal C57BL/6 mice

tag: Age

value: 12 weeks

tag: Number of mice per chip

tag: Tissue

value: spleen

tag: Purification

value: Fresh spleen cells were depleted of CD8+ T cells and B cells, CD4+CD25+ T cells were enriched by MACS for CD25+ T cells then sorted for CD4+ CD25hi cells

tag: % CD4+ CD25hi post sort


title: C57BL/6-2Rbeta-WT/thymus transgenic CD4+ CD25+ Treg cells #1

description: C57BL/6-2Rbeta-WT/thymus transgenic  EA33256

scan_protocol: per Affymetrix technical manual at Expression Analysis (Durhan, NC)

value: 33 weeks


title: C57BL/6-2Rbeta-WT/thymus transgenic CD4+ CD25+ Treg cells #3

description: C57BL/6-2Rbeta-WT/thymus transgenic  EA34569

label_protocol: per Affymetrix technical manual at Expression Analysis (Durhan, NC)

value: 7-16 weeks


title: C57BL/6 CD4+ CD25+ Treg cells #1

description: B6  EA33255


title: C57BL/6 CD4+ CD25+ Treg cells #3

description: B6 EA35092

value: 10 weeks


title: C57BL/6 CD4+ CD25+ T effector cells #3

description: B6 #1 EA21753

source_name: mouse spleen anti-CD3 48 hr

treatment_protocol: Unfractionated spleen cells were cultured with anti-CD3 for 48 hr and then the activated CD4+ T cells were purified

value: 14 weeks

value: spleen stimulated with anti-CD3

value: 48 hr after stimulation, CD4+ T cell were enriched by MACS for CD4+ T cells then sorted for CD4+ CD25hi cells

tag: % CD4+ CD25+ post sort


title: C57BL/6-2Rbeta-WT/thymus transgenic CD4+ CD25+ T effector cells #2

description: C57BL/6-2Rbeta-WT/thymus transgenic  #1 EA21755

extract_protocol: RNA isolated with Trizol reagent and purified with RNAeassy minikit (Qiagen) and amplified 1X IVT as per Affymetrix technical manual


title: C57BL/6-2Rbeta-WT/thymus transgenic CD4+ CD25+ Treg cells #2

description: C57BL/6-2Rbeta-WT/thymus transgenic  EA33258

value: 13 weeks


title: C57BL/6-2Rbeta-WT/thymus transgenic CD4+ CD25+ T effector cells #1

description: C57BL/6-2Rbeta-WT/thymus transgenic  #1 EA21754

value: 15 weeks


title: C57BL/6-2Rbeta-WT/thymus transgenic CD4+ CD25+ T effector cells #3

description: C57BL/6-2Rbeta-WT/thymus transgenic  EA21756

value: 9 weeks


title: C57BL/6 CD4+ CD25+ T effector cells #2

description: B6 #2 EA21752

value: 48 hr after stimulation, CD4+ T cells were enriched by MACS for CD4+ cells then sorted for CD4+ CD25hi cells


title: Lesion Skin, LS-27

status: Public on Feb 20 2009

city: Gaithersburg

first: Brandon

middle: W

last: Higgs

state: MD

address: One MedImmune Way

department: Translational Science

institute: MedImmune, LLC

description: HGU133 Plus array data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using ArrayAssist Lite.

source_name: Skin biopsy, lesional

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

extract_protocol: Qiagen RNeasy Fibrous Tissue Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease

value: psoriasis

tag: skin

value: lesional


title: C57BL/6 CD4+ CD25+ T effector cells #1

description: B6 #1 EA21751

value: 48 hr after stimulation CD4+ T cells were enriched by MACS for CD4+ cells then sorted for CD4+ CD25hi cells


title: Uninvolved Skin, NS-30

description: HGU133 Plus array data

source_name: Skin biopsy, non-lesional

value: non-lesional


title: Lesion Skin, LS-32

description: HGU133 Plus array data


title: Uninvolved Skin, NS-29

description: HGU133 Plus array data


title: Lesion Skin, LS-31

description: HGU133 Plus array data


title: Uninvolved Skin, NS-25

description: HGU133 Plus array data


title: Lesion Skin, LS-28

description: HGU133 Plus array data


title: Lesion Skin, LS-25

description: HGU133 Plus array data


title: Lesion Skin, LS-33

description: HGU133 Plus array data


title: Lesion Skin, LS-26

description: HGU133 Plus array data


title: Lesion Skin, LS-30

description: HGU133 Plus array data


title: Uninvolved Skin, NS-24

description: HGU133 Plus array data


title: Uninvolved Skin, NS-27

description: HGU133 Plus array data


title: Lesion Skin, LS-20

description: HGU133 Plus array data


title: Lesion Skin, LS-21

description: HGU133 Plus array data


title: Lesion Skin, LS-19

description: HGU133 Plus array data


title: Uninvolved Skin, NS-22

description: HGU133 Plus array data


title: Uninvolved Skin, NS-26

description: HGU133 Plus array data


title: Lesion Skin, LS-29

description: HGU133 Plus array data


title: Lesion Skin, LS-23

description: HGU133 Plus array data


title: Lesion Skin, LS-18

description: HGU133 Plus array data


title: Uninvolved Skin, NS-28

description: HGU133 Plus array data


title: Uninvolved Skin, NS-23

description: HGU133 Plus array data


title: Lesion Skin, LS-24

description: HGU133 Plus array data


title: Uninvolved Skin, NS-21

description: HGU133 Plus array data


title: Uninvolved Skin, NS-19

description: HGU133 Plus array data


title: Uninvolved Skin, NS-20

description: HGU133 Plus array data


title: Lesion Skin, LS-22

description: HGU133 Plus array data


title: Uninvolved Skin, NS-18

description: HGU133 Plus array data


title: Lesion Skin, LS-17

description: HGU133 Plus array data


title: Uninvolved Skin, NS-14

description: HGU133 Plus array data


title: Uninvolved Skin, NS-17

description: HGU133 Plus array data


title: Uninvolved Skin, NS-16

description: HGU133 Plus array data


title: Lesion Skin, LS-12

description: HGU133 Plus array data


title: Lesion Skin, LS-11

description: HGU133 Plus array data


title: Lesion Skin, LS-10

description: HGU133 Plus array data


title: Uninvolved Skin, NS-12

description: HGU133 Plus array data


title: Lesion Skin, LS-14

description: HGU133 Plus array data


title: Lesion Skin, LS-16

description: HGU133 Plus array data


title: Uninvolved Skin, NS-13

description: HGU133 Plus array data


title: Lesion Skin, LS-15

description: HGU133 Plus array data


title: Lesion Skin, LS-9

description: HGU133 Plus array data


title: Lesion Skin, LS-13

description: HGU133 Plus array data


title: Lesion Skin, LS-7

description: HGU133 Plus array data


title: Lesion Skin, LS-8

description: HGU133 Plus array data


title: Uninvolved Skin, NS-9

description: HGU133 Plus array data


title: Lesion Skin, LS-6

description: HGU133 Plus array data


title: Uninvolved Skin, NS-7

description: HGU133 Plus array data


title: Uninvolved Skin, NS-4

description: HGU133 Plus array data


title: Lesion Skin, LS-2

description: HGU133 Plus array data


title: Lesion Skin, LS-4

description: HGU133 Plus array data


title: Uninvolved Skin, NS-5

description: HGU133 Plus array data


title: Uninvolved Skin, NS-11

description: HGU133 Plus array data


title: Lesion Skin, LS-5

description: HGU133 Plus array data


title: Uninvolved Skin, NS-6

description: HGU133 Plus array data


title: Lesion Skin, LS-3

description: HGU133 Plus array data


title: Uninvolved Skin, NS-8

description: HGU133 Plus array data


title: Uninvolved Skin, NS-2

description: HGU133 Plus array data


title: Lesion Skin, LS-1

description: HGU133 Plus array data


title: Normal Skin, Normal-21

description: HGU133 Plus array data

source_name: Skin biopsy, normal

value: normal


title: Uninvolved Skin, NS-1

description: HGU133 Plus array data


title: Normal Skin, Normal-16

description: HGU133 Plus array data


title: Uninvolved Skin, NS-3

description: HGU133 Plus array data


title: Normal Skin, Normal-14

description: HGU133 Plus array data


title: Normal Skin, Normal-19

description: HGU133 Plus array data


title: Normal Skin, Normal-17

description: HGU133 Plus array data


title: Normal Skin, Normal-13

description: HGU133 Plus array data


title: Normal Skin, Normal-18

description: HGU133 Plus array data


title: Normal Skin, Normal-10

description: HGU133 Plus array data


title: Normal Skin, Normal-15

description: HGU133 Plus array data


title: Normal Skin, Normal-12

description: HGU133 Plus array data


title: Normal Skin, Normal-20

description: HGU133 Plus array data


title: Normal Skin, Normal-7

description: HGU133 Plus array data


title: Normal Skin, Normal-11

description: HGU133 Plus array data


title: Normal Skin, Normal-6

description: HGU133 Plus array data


title: Normal Skin, Normal-4

description: HGU133 Plus array data


title: Normal Skin, Normal-9

description: HGU133 Plus array data


title: Normal Skin, Normal-5

description: HGU133 Plus array data


title: Normal Skin, Normal-8

description: HGU133 Plus array data


title: Normal Skin, Normal-3

description: HGU133 Plus array data


title: Normal Skin, Normal-1

description: HGU133 Plus array data


title: Progen_dKO_3

city: Epalinges

first: Elisa

last: Laurenti

address: Chemin Des Boveresses 155

department: ISREC

institute: EPFL

hyb_protocol: Affymetrix GeneChip® Hybridization Control Kit

scan_protocol: Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.

data_processing:
Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE = GSM315273
Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE = GSM315274
Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE = GSM315275
Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE = GSM315276
Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE = GSM315277
Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.

label_protocol: See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit

extract_protocol: RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.

treatment_protocol: 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice

tag: Mouse model

value: MxCre c-myc f2 N-myc f2 on a mixed background

value: 8 weeks old

value: Bone marrow progenitor cells (Lin- Sca1+ CD150+ CD48+)


title: Progen_dKO_1

data_processing: Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.


title: Normal Skin, Normal-2

description: HGU133 Plus array data


title: SLE10-TC

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

description: Additional details provided in accompanying manuscript, SLE10-TC

hyb_protocol: Standard Affymetrix FS450_0001

scan_protocol: Affymetrix GeneChip Scanner 7G Plus

source_name: T cells

label_protocol: Standard Affymetrix Two Cycle IVT Protocol

extract_protocol: RNeasy (Qiagen)

treatment_protocol: Unstimulated

tag: >95% CD3+ T cells negatively isolated with Dynal kit from SLE patient


title: SLE6-TC

description: Additional details provided in accompanying manuscript, SLE6-TC


title: SLE9-TC

description: Additional details provided in accompanying manuscript, SLE9-TC


title: Progen_Control_3

value: c-myc f2 N-myc f2 on a mixed background


title: SLE7-TC

description: Additional details provided in accompanying manuscript, SLE7-TC


title: Progen_Control_2


title: Progen_dKO_2


title: Progen_Control_1

value: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48+)


title: HSC_dKO_2

data_processing: Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org).  Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.

value: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)


title: HSC_dKO_3


title: SLE8-TC

description: Additional details provided in accompanying manuscript, SLE8-TC


title: HSC_Control_2

value: c-myc f2 M-Myc f2 on a mixed background


title: HSC_Control_1


title: HSC_dKO_1


title: BC8 TC

description: Additional details provided in accompanying manuscript, BC8 TC

tag: >95% CD3+ T cells negatively isolated with Dynal kit


title: SLE5-TC

description: Additional details provided in accompanying manuscript, SLE5-TC


title: SLE4-TC

description: Additional details provided in accompanying manuscript, SLE4-TC


title: SLE2-TC

description: Additional details provided in accompanying manuscript, SLE2-TC


title: BC5 TC

description: Additional details provided in accompanying manuscript, BC5 TC


title: SLE1-TC

description: Additional details provided in accompanying manuscript, SLE1-TC


title: BC7 TC

description: Additional details provided in accompanying manuscript, BC7 TC


title: BC9 TC

description: Additional details provided in accompanying manuscript, BC9 TC


title: BC4 TC_TCR

description: Additional details provided in accompanying manuscript, BC4 TC_TCR

treatment_protocol: Stimulated through CD3/CD28 for 24hr


title: BC4 TC_NOC

description: Additional details provided in accompanying manuscript, BC4 TC_NOC

treatment_protocol: Stimulated with Nitric Oxide (NOC-18) 600 uM 24hr


title: BC4 TC

description: Additional details provided in accompanying manuscript, BC4 TC


title: BC6 TC

description: Additional details provided in accompanying manuscript, BC6 TC


title: BC3 TC_TCR

description: Additional details provided in accompanying manuscript, BC3 TC_TCR


title: BC2 TC_TCR

description: Additional details provided in accompanying manuscript, BC2 TC_TCR


title: HSC_Control_3


title: BC3 TC

description: Additional details provided in accompanying manuscript, BC3 TC


title: BC2 TC_NOC

description: Additional details provided in accompanying manuscript, BC2 TC_NOC


title: BC2 TC

description: Additional details provided in accompanying manuscript, BC2 TC


title: doxycycline control

status: Public on Feb 19 2009

description:
>99.5% TOP2A expression can be silenced in HTETOP cells by the addition of tetracycline
pooled RNA from cell passage 15, 16, 17 was used for hybridization

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: control HTETOP cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

treatment_protocol: HTETOP cells were treated with 1 µg/ml doxycycline or vehicle for 24 hours.

tag: cell line

value: HTETOP


title: BC1 TC

description: Additional details provided in accompanying manuscript, BC1-TC


title: BC1 TC_NOC

description: Additional details provided in accompanying manuscript, BC1TC_NOC


title: SLE3-TC

description: Additional details provided in accompanying manuscript, SLE3-TC


title: BC3 TC_NOC

description: Additional details provided in accompanying manuscript, BC3 TC_NOC


title: BC1 TC_TCR

description: Additional details provided in accompanying manuscript, BC1 TC_TCR


title: doxycycline

source_name: doxycycline-treated HTETOP cells


title: mRNA quantitation of HighEF heart-PM12

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

description: LV myocytes of a HighEF patient was hybridized.

hyb_protocol: 2 ug of cDNA were hybridized for 18 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The mean value for the internal control probe sets (defined by Affymetrix) was set to be 500.

source_name: HighEF PM12

label_protocol: Biotinylated cDNA were prepared according to the Ovation Biotin RNA Amplification and Labeling System, NuGEN Technologies, Inc.

extract_protocol: Total RNA was extracted by RNeasy mini spin column (Qiagen, Inc).

tag: LV myocytes isolated from HighEF patient PM12


title: mRNA quantitation of DCM heart-20

description: LV myocytes of a CHF patient was hybridized.

source_name: CHF ID20

tag: LV myocytes isolated from CHF patient ID20


title: female_virgin_rep4

city: Uppsala

first: Paolo

last: Innocenti

address: Norbyvägen 18D

department: Dept. of Animal Ecology

country: Sweden

institute: Uppsala university

hyb_protocol: as from Affymetrix Technical Manual (Expression Analysis Technical Manual, 2001, Affymetrix).

data_processing: RMA standard, affy package, R 2.7, Bioconductor 2.2

organism: Drosophila melanogaster

source_name: Drosophila melanogaster female, virgin

label_protocol: Affymetrix One-Cycle Target Labeling (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All flies used were derived from a large outbred wild-type population of Drosophila melanogaster (LHM) that has been maintained under the same rearing protocol for over 400 non-overlapping generations. The population is maintained in a set of 56 vials at a large size (1792 adults) under competitive conditions and at moderate larval density. The timing, density and protocol used in the mating experiments matched as close as possible the conditions to which the base population has evolved.

extract_protocol: Trizol (Invitrogen) + Rneasy (Qiagen) purification (modified, available on request)

treatment_protocol: To start the experiment a set of 14 vials, each containing 150 eggs (Day 0), were obtained from the base population (LHM) following the base population culturing protocol (see Rice et al. 2005). On day 9, 200 virgin females were collected under light CO2 anesthesia within a period of 3 hours, ensuring that all females used in the experiment were of a nearly identical age. Females were housed individually and vials were checked for fertile eggs on day 12 (none found). Tester males, to which the focal females were mated, were obtained by crossing virgin females and males from two inbred lines derived from LHM following 8 rounds of sib-sib matings. These tester males will show identical heterozygosity across all loci. Tester males were also collected individually on day 9 but as non-virgins. Females were assigned to 3 experimental mating treatments (see Figure 3): virgin (V), single mated (S) and double mated (D). On day 12, all females were transferred to a new vial provisioned with 0.375 mg live yeast. This is equivalent to 1/16th of the 6 mg yeast that groups of 16 females get on Day 12 in the base population protocol. Females were kept in these vials for the remainder of the mating experiments. 80 tester males were then placed, without anesthesia, together with 80 females (treatment D), the remaining 120 virgin females (belonging to V and S treatments) were left without males. All females were then moved to a rearing chamber with controlled temperature, light and humidity and all matings observed. After 60 minutes all vials were removed from the chamber and tester males were removed under brief CO2 anesthesia and discarded. Females in the V and S treatments were also briefly anesthetized. Any females assigned to the D treatment that had either not mated or were still in copula after 60 minutes were discarded. All females were then returned to the rearing chamber until the following day. On day 13, the second round of matings was performed – 140 tester males were placed individually with S and D females without anesthesia. Again all matings were observed and after 60 minutes males from the S treatment were removed using brief anesthesia. Any females that failed to mate or were still in copula after 60 minutes were discarded. When at least 40 D females had remated males were removed under CO2 and any D females that had not remated were discarded. Females in the V treatment were also briefly anesthetized at this time.

tag: wild type, LHm pop., whole fly


title: female_double_rep3

scan_protocol: as from Affymetrix Technical Manual (Expression Analysis Technical Manual, 2001, Affymetrix).

source_name: Drosophila melanogaster female, double mated


title: Postnatal day 15 (P15) thyroid Slc26a4 (knockout) mice (sample4)

city: Manhattan

first: Philine

last: Wangemann

state: KS

address: 1600 Dension Avenue

department: Anatomy and Physiology

institute: Kansas State University

description: Thyroid was microdissected from the mouse, RNA was isolated and hybridized on Affymetrix mouse 430.2 chips

hyb_protocol: Affymetrix small sample

scan_protocol: Affymetrix

data_processing: GCOS software used to obtain data. No normalization performed

label: Streptavidin

source_name: Thyroid RNA

label_protocol: Ovation (NuGen protocol)

extract_protocol: Qiagen extraction kit

tag: Strain 129S6, Age 15 days, Tissue Thyroid


title: female_single_rep4

source_name: Drosophila melanogaster female, single mated


title: mRNA quantitation of DCM heart-14

source_name: CHF ID14

tag: LV myocytes isolated from CHF patient ID14


title: Postnatal day 15 (P15) thyroid Slc26a4 (heterozygous) mice (sample3)


title: female_single_rep2


title: mRNA quantitation of HighEF heart-PM13

source_name: HighEF PM13

tag: LV myocytes isolated from HighEF patient PM13


title: mRNA quantitation of HighEF heart-PM14

source_name: HighEF PM14

tag: LV myocytes isolated from HighEF patient PM14


title: Postnatal day 15 (P15) thyroid Slc26a4 (heterozygous) mice (sample1)


title: female_single_rep1


title: female_double_rep2


title: female_single_rep3


title: female_double_rep4


title: Postnatal day 15 (P15) thyroid Slc26a4 (heterozygous) mice (sample5)


title: Postnatal day 15 (P15) thyroid Slc26a4 (knockout) mice (sample6)


title: mRNA quantitation of HighEF heart-PM8

source_name: HighEF PM8

tag: LV myocytes isolated from HighEF patient PM


title: female_virgin_rep3


title: mRNA quantitation of DCM heart-13

source_name: CHF ID13

tag: LV myocytes isolated from CHF patient ID13


title: Postnatal day 15 (P15) thyroid Slc26a4 (knockout) mice (sample2)


title: mRNA quantitation of DCM heart-18

source_name: CHF ID18

tag: LV myocytes isolated from CHF patient ID18


title: Postnatal day 10 (P10) stria vascularis Slc26a4 (knockout) mice (sample6)

description: Stria vascularis was isolated from the mouse cochlea, RNA was isolated and hybridized on Affymetrix mouse 430.2 chips

source_name: Stria Vascularis RNA

tag: Strain 129S6, Age 10 days, Tissue Ear


title: female_virgin_rep2


title: Postnatal day 10 (P10) stria vascularis Slc26a4 (heterozygote) mice (sample5)


title: Postnatal day 10 (P10) stria vascularis Slc26a4 (knockout) mice (sample4)


title: Postnatal day 10 (P10) stria vascularis Slc26a4 (knockout) mice (sample2)


title: Postnatal day 10 (P10) stria vascularis Slc26a4 (heterozygote) mice (sample1)


title: Postnatal day 10 (P10) stria vascularis Slc26a4 (heterozygote) mice (sample3)


title: female_virgin_rep1


title: female_double_rep1


title: DC3 5d veh

status: Public on Feb 15 2009

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

country: Hungary

institute: UNIVERSITY OF DEBRECEN

description: monocyte derived dendritic cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: GC-RMA algorithm

source_name: 5d immature dendritic cell - treated with vehicle for 5 days

label_protocol: standard Affymetrix protocol

extract_protocol: total RNA was isolated by using Rneasy kit/QIAGEN

treatment_protocol: 10 nM 1,25-vitD or vehicle were added to the cells

tag: immature dendritic cell, donor #136


title: Mo3

description: monocyte derived dendritic cells

source_name: CD14+ human monocyte

tag: CD14+ human monocyte, donor #136


title: DC2 12h veh

description: monocyte derived dendritic cells

source_name: 26h differentiating human dendritic cell - treated with vehicle for 12h, vehicle added 14h after separation

tag: differentiating human dendritic cell, donor #130


title: DC2 12h 1,25-vitD

description: monocyte derived dendritic cells

source_name: 26h differentiating human dendritic cell - treated with 1,25-vitD for 12h, 10 nM 1,25-vitD added 14h after separation


title: DC2 5d 1,25-vitD

description: monocyte derived dendritic cells

source_name: 5d immature dendritic cell - treated with 10 nM 1,25-vitD for 5 days

tag: immature dendritic cell, donor #130


title: DC1 12h veh

description: monocyte derived dendritic cells

tag: differentiating human dendritic cell, donor #129


title: DC3 12h 1,25-vitD

description: monocyte derived dendritic cells

tag: differentiating human dendritic cell, donor #136


title: Mo2

description: monocyte derived dendritic cells

tag: CD14+ human monocyte, donor #130


title: DC3 12h veh

description: monocyte derived dendritic cells


title: DC1 12h 1,25-vitD

description: monocyte derived dendritic cells


title: DC3 5d 1,25-vitD

description: monocyte derived dendritic cells


title: DC1 5d 1,25-vitD

description: monocyte derived dendritic cells

tag: immature dendritic cell, donor #129


title: DC2 5d veh

description: monocyte derived dendritic cells


title: spleen, immunized, BALB/cJ, biological replicate 1

city: Chicago

first: Tibor

middle: T

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

hyb_protocol: Following fragmentation, 1.5 ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.

scan_protocol: Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’.  Each array was analyzed for the following quality metrics:  3’/5’ signal ratio of house-keeping genes, signal intensity of species-specific house-keeping genes, signal intensities of Poly-A controls, signal intensities of hybridization controls, relative logarithmic probe cell intensity- and relative logarithmic expression signal values.

data_processing: Data was analyzed in GeneSpring GX 10.0 (Agilent Technologies, Santa Clara, CA).  Robust Multi-array Average (RMA) (Irizarry, 2003) summarization algorithm (with Quantile Normalization and Median Polish probe summarization procedure) and baseline transformation (baseline to median of all 12 samples) was run on data using logarithmic scale. All 12 samples passed quality control based on hybridization controls, 3'/5' ratios for internal controls, Pearson correlation and Principal Component Analysis (PCA). Probe sets were filtered by expression values based on percentiles. For pairwise comparisons, Student-Newman-Keuls (SNK) Post Hoc test was done on oneway ANOVA result to identify statistically significant (p-value cutoff 0.05), differentially expressed transcripts. Statistical test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated with GeneSpring GX 10.0.

source_name: spleen

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).

growth_protocol: Six female BALB/c mice were immunized intraperitonelly once with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant, while 6 mice left untreated.

extract_protocol: Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.

treatment_protocol: Spleens were harvested from all mice 12 days after the ip. injection. 50 mg pieces were used for RNA preparation.

tag: strain

value: BALB/c

tag: gender

value: female

tag: Once-immunized

tag: BALB/cJ


title: spleen, immunized, BALB/cByJ, biological replicate 1

tag: BALB/cByJ


title: spleen, immunized, BALB/cJ, biological replicate 3


title: spleen, naïve, BALB/cByJ, biological replicate 2

tag: Naïve


title: spleen, naïve, BALB/cJ, biological replicate 3


title: spleen, naïve, BALB/cJ, biological replicate 1


title: Jejunal biopsy, treatment, rep3

status: Public on Feb 14 2009

city: Barcelona

first: Cristina

last: Martinez

address: Paseo Valle Hebron 119-129

department: Digestive diseases research unit

country: Spain

institute: Institut de Recerca HUVH

description:
Treatment.
Replicate 3 of 4.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 60ºC on GeneChip Human Genome U133 Plus 2.0. 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. Raw expression values obtained directly from .CEL files were preprocessed using the RMA method. These normalized values were the basis for all the analyses.

source_name: Jejunal biopsy, d-IBS, treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Jejunal biopsies were obtained using the Watson's capsule in all participants. The instrument was orally inserted under fluoroscopic control 5 to 10 cm distal to the Treitz’s angle. Then, a tissue sample was obtained by suction with a 50 ml syringe.

extract_protocol: Extraction of total RNA was performed using the Rneasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Biopsies were placed in RNA later solution and stored at -80ºC until processed.

tag: tissue

value: jejunal mucosa

tag: location

value: 10 cm from Treitz

tag: disease

value: diarrhea-IBS

tag: treatment

value: oral cromoglycate


title: DC1 5d veh

description: monocyte derived dendritic cells


title: spleen, naïve, BALB/cJ, biological replicate 2


title: Jejunal biopsy, control, rep5

description:
No treatment.
Replicate 5 of 5.

source_name: Jejunal biopsy, d-IBS, control


title: spleen, naïve, BALB/cByJ, biological replicate 3


title: spleen, naïve, BALB/cByJ, biological replicate 1


title: Jejunal biopsy, treatment, rep2

description:
Treatment.
Replicate 2 of 4.


title: Jejunal biopsy, treatment, rep4

description:
Treatment.
Replicate 4 of 4.


title: Jejunal biopsy, control, rep4

description:
No treatment.
Replicate 4 of 5.


title: Jejunal biopsy, treatment, rep1

description:
Treatment.
Replicate 1 of 4.


title: Mo1

description: monocyte derived dendritic cells

tag: CD14+ human monocyte, donor #129


title: Jejunal biopsy, healthy, rep2

description:
Healthy.
Replicate 2 of 4.

source_name: Jejunal biopsy, healthy

value: healthy


title: spleen, immunized, BALB/cJ, biological replicate 2


title: Jejunal biopsy, healthy, rep4

description:
Healthy.
Replicate 4 of 4.


title: Jejunal biopsy, control, rep1

description:
No treatment.
Replicate 1 of 5.


title: spleen, immunized, BALB/cByJ, biological replicate 2


title: Jejunal biopsy, healthy, rep1

description:
Healthy.
Replicate 1 of 4.


title: Jejunal biopsy, control, rep2

description:
No treatment.
Replicate 2 of 5.


title: Jejunal biopsy, healthy, rep3

description:
Healthy.
Replicate 3 of 4.


title: Jejunal biopsy, control, rep3

description:
No treatment.
Replicate 3 of 5.


title: Jejunal biopsy, baseline, rep3

description:
Baseline.
Replicate 3 of 5.

source_name: Jejunal biopsy, d-IBS, baseline


title: Jejunal biopsy, baseline, rep5

description:
Baseline.
Replicate 5 of 5.


title: Jejunal biopsy, baseline, rep4

description:
Baseline.
Replicate 4 of 5.


title: Jejunal biopsy, baseline, rep2

description:
Baseline.
Replicate 2 of 5.


title: Jejunal biopsy, baseline, rep1

description:
Baseline.
Replicate 1 of 5.


title: spleen, immunized, BALB/cByJ, biological replicate 3


title: RD MD-E, rep1

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

description: Gene expression data from RD cells infected with retroviral vector expressing MyoD~E heterodimers

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were normalized by RMA using the Affy package of Bioconductor

source_name: RD cells infected with retrovirus expressing MyoD~E heterodimers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RD cells were grown in DMEM media supplemented with 10% Bovine Calf Serum.

extract_protocol: Total RNAs were prepared using Qiagen RNeasy Mini Kit according to the manufacture's protocol

treatment_protocol: RD cells were retrovirally infected with either MyoD~E heterodimer or an empty control vector, selected for 48 hours in the presence of 1 ug/mL puromycin, and then placed in DMEM media supplemented with 1%Horse serum, Insulin and Transferrin for 24 hours.

tag: cell line

value: RD cells

tag: infection


title: RD MD-E, rep2

value: retrovirus expressing MyoD~E heterodimers


title: RD, rep3

description: Gene expression data from RD cells infected with control vector.

source_name: RD cells infected with control vector

value: control vector


title: RD, rep1


title: RD, rep2


title: RD MD-E, rep3


title: ctrl_wt_01

status: Public on Feb 13 2009

city: Zurich

first: Stefanie

last: Tiefenboeck

address: Schafmattstrasse 18

department: Biology

institute: ETH Zurich

hyb_protocol: Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Drosophila Genome 2.0 Arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the polyA spike in controls and the prokaryotic control.

source_name: Larval fat body

label_protocol: The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using an IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.

extract_protocol: 20 fat bodies of 5d old mutant larvae were dissected into RNAlater. The RNA was isolated using Macherey-Nagel NucleoSpin RNA II isolation Kit following the manufacturer’s protocol.

treatment_protocol: Larvae were heat-shocked for 30min. at 37°C 13h prior to dissection to induce expression of UAS-Inr by the hs-Flp; tub>CD2>UAS-Gal4, UAS-GFP system

tag: "ctrl"

value: no expression of UAS-Inr; "wt":wildtype background; tissue:larval fat body; 4d AED (days after egg deposition)


title: KG_02

source_name: Larval fat body, srl1/srl1

tag: Larval fat body, srl1/srl1


title: Inr_wt_01

tag: "inr"

value: expression of UAS-Inr; "wt":wildtype background; tissue:larval fat body; 4d AED (days after egg deposition)


title: Inr_KG_02

value: expression of UAS-Inr; "KG":srl1/srl1 mutant background; tissue:larval fat body; 5d AED (days after egg deposition)


title: Inr_wt_02


title: ctrl_KG_03

value: no expression of UAS-Inr; "KG":srl1/srl1 mutant background; tissue:larval fat body; 5d AED (days after egg deposition)


title: Inr_wt_03


title: ctrl_KG_01


title: ctrl_KG_02


title: KG_01

tag: Larval fat body, srl1/srl1, 5d AED (after egg deposition)


title: wt_02

source_name: Larval fat body, srlwt/srlwt

tag: Larval fat body, srlwt/srlwt, 4d AED


title: wt_03


title: Resting T cells_rep4

status: Public on Feb 11 2009

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

country: United Kingdom

institute: University of Oxford

description: we set up an in vitro system within which to analyse bystander T cell activation in human T cells, in the absence of the possibility for TCR cross-reactivity. In addition, we have investigated the genetic, phenotypic, and functional characteristics of bystander activated T cells.

hyb_protocol: Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). A 200µl of this hybridization cocktail was used on the chip and incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v5, Affymetrix) of double-staining and post-hybridisations washes.

scan_protocol: Fluorescent images were captured using gene Array Scanner 3000 and GCOS1.2 software (Affymetrix).

data_processing: We have used the genechip robust multi-array average expression measurements (RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 54,675 probe sets (transcripts) on each of these arrays.

source_name: Resting T cells

label_protocol: Two-cycle cDNA synthesis kit (Affymetrix # 900494) used to convert 50ng total RNA together with appropriate dilutions of GeneChip eukaryotic poly-A RNA spike controls (Affymetrix # 900433) to double-stranded cDNA with superscript II using T7-(dT)24 primer. This was used in an in vitro transcription to generate biotin-labelled cRNA probes.

growth_protocol: T cells expressing Vβ17 TCRs respond specifically to stimulation with the superantigen staphylococcal enterotoxin B (SEB) – this method was used to generate the “directly activated” sample of T cells. T cells expressing Vβ13.1 TCRs do not respond to direct SEB stimulation, however, when cultured with soluble factors produced by whole PBMC stimulated with SEB, a proportion of Vβ13.1 T cells will upregulate activation markers – these cells are used as the “bystander activated” T cell sample.The “Resting” T cell sample consists of those Vβ13.1 T cells which do not upregulate activation markers in response to the bystander stimulus.

extract_protocol: RNA was extracted using RNeasy kits (Qiagen).

treatment_protocol: Vβ13.1+ T cells were plated out in the top well of transwell inserts and co-cultured with whole autologous PBMC plated in the lower well. Vβ17+ T cells were plated out in 24 well plates mixed with whole autologous PBMC, present at an identical ratio of PBMC to purified T cells to that used in the transwell culture. All wells were treated with 2.5 μg/ml SEB. Cultures were incubated for five days at 37 ˚C in the presence of 5% CO2, then the top wells of transwell cultures and whole mixed wells were harvested and stained. Cells were sorted by FACS into bystander activated “B” (CD3+, Vβ13.1+, CD25+), resting “R” (CD3+, Vβ13.1+, CD25-) and directly activated “D” (CD3+, Vβ17+, CD25+) populations.

tag: Briefly, PBMCs were isolated from buffy coats by density gradient centrifugation. Vβ13.1 and Vβ17 expressing T cells were enriched using PE-conjugated antibodies with MACS anti-PE microbeads. Resting T cells - cells expressing a TCR which does not specifically recognize SEB (Vβ13.1 T cells) and did not upregulate the activation marker CD25 in response to transwell SEB-stimulated co-culture over a 5 day period.


title: Inr_KG_03


title: Inr_KG_01


title: ctrl_wt_03


title: Resting T cells_rep3


title: Resting T cells_rep2

tag: Briefly, PBMCs were isolated from buffy coats by density gradient centrifugation. Vβ13.1 and Vβ17 expressing T cells were enriched using PE-conjugated antibodies with MACS anti-PE microbeads.

tag: Resting T cells - cells expressing a TCR which does not specifically recognize SEB (Vβ13.1 T cells) and did not upregulate the activation marker CD25 in response to transwell SEB-stimulated co-culture over a 5 day period.


title: wt_01

tag: Larval fat body, srlwt/srlwt, 4d AED (days after egg deposition)


title: Resting T cells_rep1

source_name: Resting cells


title: T cell directly activated_rep4

source_name: T cell directly activated


title: T cell bystander activated_rep4

source_name: T cell bystander activated


title: T cell directly activated_rep3


title: T cell bystander activated_rep3


title: T cell bystander activated_rep1


title: T cell directly activated_rep1


title: GM5659_AA_rep3

status: Public on Feb 10 2009

city: Porto

first: Tiago

last: Duarte

address: Rua do Campo Alegre, 823

country: Portugal

institute: IBMC - Institute for Molecular and Cell Biology

hyb_protocol: Fragmented, labelled cRNA (15 µg) was added to 15 µl of 2× hybridisation buffer (final 1× concentration is 100 mM 2-Morpholinoethanesulfonic acid (MES), 1 M [Na+], 20 mM EDTA, 0.01% Tween 20), 3 µl of 10 mg/ml herring sperm DNA (Promega, Southampton, UK), 3 µl of 50 mg/ml acetylated bovine serum albumin (BSA) (Invitrogen, Paisley, UK) and 30 µl of DMSO. The hybridisation buffer was spiked with 5 µl of 3nM control oligonucleotide B2 and 15 µl of the 20× eukaryotic cRNA controls bioB, bioC, bioD and cre (final concentration is 1.5, 5, 25 and 100 pM, respectively), all controls were from the GeneChip Eukaryotic Hybridisation Control Kit (Affymetrix). The hybridisation mixture was heated to 99 °C for 5 minutes, cooled to 45 °C for 5 minutes and centrifuged at 14,000 × g for 5 minutes to remove any insoluble material from the hybridisation mixture. Each hybridisation mixture containing 10 µg of fragmented biotin-labelled cRNA (200 µl) was hybridised to a pre-wetted (with hybridisation buffer) GeneChip Human U133 Plus 2.0 array (Affymetrix) for 16 hours at 45 °C with permanent rotation at 60 rpm in a Affymetrix Hybridisation Oven 640. Probe array washing and staining were performed according to EukGE-WS2v5 Gene Chip protocol (Affymetrix) in the Affymetrix Fluidics Station 400. Briefly, arrays were washed in a non-stringent wash buffer containing 6× SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA) (Cambrex, Berkshire, UK) and 0.01% Tween-20 at 25 °C, then with a stringent buffer containing 100 mM MES, 0.1 M [Na+], 0.01% Tween-20 at 50 °C. Following this wash, the probe arrays were stained with a solution containing 10 µg/ml of streptavidin-phycoerythrin (SAPE) conjugate (Invitrogen, Paisley, UK) and 2 mg/ml acetylated BSA (Invitrogen) dissolved in a buffer containing 100 mM MES, 1 M [Na+], 0.05% Tween 20. Following staining, the probe arrays were exposed to 3 µg/ml goat biotinylated anti-streptavidin antibody (Vector laboratories, Peterborough, UK) in a buffer as above containing 0.1 mg/ml normal goat IgG (Sigma, Poole, UK) and 2 mg/ml acetylated BSA (Invitrogen). Finally, the probe arrays were re-stained with SAPE as described above.

scan_protocol: Probe arrays were scanned once at 570 nm using an Affymetrix GeneChip scanner and the fluorescence intensity of the scanned image registered in CEL intensity files.

data_processing: DNA-Chip Analyser (dChip) software (Li and Wong 2001 PNAS, 98:31) was used to automatically select probes, detect outliers/artefacts, normalise the fluorescence intensity over multiple arrays and calculate model-based expression values from CEL intensity files using the PM/MM values.

source_name: GM5659 human primary fibroblasts, AA-treated

label_protocol:
The One-cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, California, USA) was used to convert the mRNA in the T-RNA samples into ds-cDNA by reverse transcription with an oligo-dT primer. Initially, first strand cDNA was formed in a reaction containing 6 g of T-RNA, 2 µl of diluted poly-A RNA controls, 2 µl of 50 µM T7-oligo (dT) primer and RNase-free water to a final volume of 12 µl. This mixture was incubated at 70 °C for 10 minutes and chilled at 4 °C for 5 minutes, after which the following reagents were added: 4 µl of first strand reaction mix, 2 µl of 100 mM dithiothreitol (DTT) and 1 µl of 10 mM dNTP. Tubes were placed at 42 °C for 2 minutes to equilibrate the temperature prior to the addition of Superscript II reverse transcriptase (1µl) and further incubated for 1 hour at 42 °C. The second strand cDNA synthesis was performed by adding, to the solution containing the first strand cDNA, 3 µl of 10mM dNTP, 1 µl of E. coli DNA ligase, 4 µl of E. coli DNA polymerase I, 1 µl of E. coli RNase H, 30 µl of second strand reaction buffer and 91 µl of RNase-free water. The reaction was incubated for 2 hours at 16 °C. Following this incubation, 2 µl of T4 DNA polymerase were added and incubated for 5 minutes at 16 °C. The reaction was stopped by the addition of 10 µl of 0.5 M EDTA. The resulting ds-cDNA was cleaned up using the Affymetrix Sample Cleanup Module, according to the manufacturer’s instructions.
Synthesis of biotin labelled cRNA was performed by in vitro transcription using the Affymetrix IVT labelling kit. Briefly, the ds-cDNA synthesised above (12 µl) was used as template, and added to 4 µl of 10× IVT labelling buffer, 12 µl of Labeling NTP mix, 4 µl of IVT Labeling Enzyme mix and 8 µl of RNase-free water. The reaction was incubated at 37 °C for 16 hours. This step was followed by cRNA cleanup with the Affymetrix Sample Cleanup Module, according to the manufacturer’s specifications. Quantification of cRNA was performed in a spectrophotometer by measuring the absorbance at 260 nm and the adjusted cRNA yield calculated taking into account the carryover of unlabelled T-RNA by the following formula: adjusted cRNA yield = RNAm – (T-RNAi)(y), where RNAm is the amount of cRNA measured after the IVT reaction, T-RNAi is the starting amount of T-RNA and y is the fraction of cDNA used in the IVT reaction. Size distribution of the labelled transcripts was investigated in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA). The appropriate amount of cRNA (20 µg) was fragmented by adding 8 µl of the fragmentation buffer provided in the Sample Cleanup Module and RNase-free water to a final volume of 40 µl, and incubating at 94 °C for 35 minutes. Fragmentation efficiency was confirmed by analysing the size distribution of the fragmented, labelled transcripts in the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Nano assay.

growth_protocol: Cells were grown as a monolayer culture in Nunclon culture flasks (Invitrogen, Paisley, UK) at 37 °C in a humidified atmosphere containing 5 % CO2. Cells were grown in MEM with Earle’s salts containing non-essential amino acids supplemented with 2 mM Glutamax-I and 10 % (v/v) FBS. Cells were passaged when nearly confluent. For passaging, growth medium was removed and cells were washed in pre-warmed sterile phosphate buffered saline (PBS). Cells were incubated in PBS containing 0.05 % (w/v) porcine trypsin and 0.02 % (w/v) tetrasodium EDTA at 37 °C for 2 minutes or until cells started to separate. The flask was then gently tapped to help release the cells. Once cells were floating, growth medium was added to the flasks to inactivate the trypsin and cells were centrifuged at 300 × g for 4 minutes. With the supernatant removed, the tube was gently tapped to disaggregate the pellet and the cells were resuspended in an appropriate volume of growth medium and distributed into new flasks (split ratio 1:3).

extract_protocol: T-RNA was extracted using TRI Reagent (Sigma, Poole, UK), according to the manufacturer’s instructions. All additional reagents used were of molecular biology grade and purchased from Sigma (Poole, UK). Briefly, cells were lysed directly in the culture dish with 1 ml TRI Reagent and the resulting cell lysate passed several times through a pipette to achieve homogenisation. The homogenised samples were incubated in microcentrifuge tubes at room temperature for 5 minutes to permit the complete dissociation of nucleoprotein complexes. 200 µl of chloroform were added to each homogenised sample, tubes shaken vigorously by hand for 15 seconds and incubated at room temperature for 2 to 3 minutes. Samples were centrifuged at 12,000 × g for 15 minutes at 4 °C, after which the aqueous phase was transferred to a fresh tube. RNA was precipitated from the aqueous phase by mixing with 0.5 ml isopropyl alcohol. Samples were incubated at room temperature for 10 minutes and centrifuged at 12,000 × g for 10 minutes at 4 °C. Supernatant was removed and RNA pellet washed once with 1 ml of 75 % ethanol. Samples were mixed by vortexing and centrifuged at 7,500 × g for 5 minutes at 4 ºC. At the end of the procedure, the RNA pellet was briefly air-dried for 5 to 10 minutes, after which RNA was dissolved in an appropriate volume of RNase/DNase-free water, pre-warmed to 60 ºC, by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60 ºC. A second RNA cleanup was performed using the QIAGEN RNeasy Mini kit according to the manufacturer’s instructions. T-RNA concentration was determined by measuring the absorbance of a 1:100 diluted solution at 260 nm in a GeneQuant II RNA/DNA calculator spectrophotometer (Pharmacia Biotech, Cambridge, UK), assuming that if A260 = 1, the content equals 40 µg/ml of RNA. T-RNA integrity was investigated in the Agilent 2100 Bioanalyzer, by assessing size distribution of the T-RNA using the Eukaryote Total RNA Nano assay (Agilent Technologies, Palo Alto, California, USA), according to the manufacturer’s specifications.

treatment_protocol: Cells were grown to confluence prior to the experiments. Millimolar solutions of ascorbic acid (AA) were prepared using PBS (pH 7.4) immediately prior to the experiments. Solutions were sterilised by passing through a 0.22 µm membrane and protected from direct light. The solutions were then diluted in pre-warmed medium to obtain the desired concentrations and added to the cells. Post-confluent HDFs were supplemented with 100 µM AA added fresh every day for a period of 5 days.

tag: GM5659 human primary skin fibroblasts


title: T cell directly activated_rep2


title: GM5659_AA2P_rep2

source_name: GM5659 human primary fibroblasts, AA2P-treated

treatment_protocol: Cells were grown to confluence prior to the experiments. Millimolar solutions of ascorbic acid 2-phosphate (AA2P) were prepared using PBS (pH 7.4) immediately prior to the experiments. Solutions were sterilised by passing through a 0.22 µm membrane and protected from direct light. The solutions were then diluted in pre-warmed medium to obtain the desired concentrations and added to the cells. Post-confluent HDFs were supplemented with 100 µM AA2P added fresh every day for a period of 5 days.


title: GM5659_Control_rep1

source_name: GM5659 human primary fibroblasts, Control

treatment_protocol: Cells were grown to confluence prior to the experiments. Post-confluent HDFs were supplemented with growth medium added fresh every day for a period of 5 days.


title: T cell bystander activated_rep2


title: GM5659_AA_rep1


title: GM5659_AA_rep2


title: GM5659_Control_rep3


title: GM5659_Control_rep2


title: control mammary gland, biological replicate 3

city: Cambridge

first: Dmitriy

last: Sonkin

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

description: Gene expression data from control mammary gland.

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Model 3000 7G scanner with autoloader

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 500.

source_name: control mammary gland

label_protocol: Affymetrix protocol

extract_protocol: RNA was extracted by homogenizing tumors and tissues in 3 ml Trizol reagent (Invitrogen). After phase separation, an equal volume of 70% ethanol was added to the aqueous phase and purified through PureLink Micro-to-Midi Total RNA Purification System (Invitrogen), following manufacturer's instruction.

tag: control mammary gland


title: GM5659_AA2P_rep3


title: mammary tumor, biological replicate 2

description: Gene expression data from mammary tumor.

source_name: mammary tumor

tag: mammary tumor


title: GM5659_AA2P_rep1


title: control mammary gland, biological replicate 2


title: ctrl_wt_02


title: mammary tumor, biological replicate 3


title: control mammary gland, biological replicate 1


title: mammary tumor, biological replicate 1


title: OT-I_T_cell_Naïve_rep2

city: New Haven

first: Ian

last: Parish

state: CT

address: The Anlyan Center, 300 Cedar St.

department: Immunobiology

institute: Yale School of Medicine

description: Gene expression data from sorted, CFSE labelled, Ly5.1+ OT-I cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Expression set 430 Version 2.0 microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Expression data was background-corrected and normalized using the gcRMA algorithm, yielding log2-expression summaries for each probeset

source_name: OT-I cells, undivided and naïve, sorted from B6 mice

label_protocol: Biotinylated cRNA was prepared from 100ng total RNA using the Affymetrix GeneChip® Two-Cycle Target Labeling and Control Reagents kit according to the Affymetrix protocol (Expression Analysis Technical Manual, 2005, Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed from 100-150 000 cells according to the manufacturer's instructions.

treatment_protocol: CD8+ (OT-I) cells were purified from spleen and lymph nodes of Ly5.1 OT-I transgenic mice by negative depletion with magnetic beads, and the CD44lo cells were then isolated by AUTOMACS, CFSE-labelled and i.v. injected into the respective mouse.  Prior to sorting, CD8+ T cells were enriched from the respective tissue and stained for CD8 and Ly5.1.  The CD8+Ly5.1+ cells with the appropriate CFSE level were sorted on a MoFlo sorter.

tag: Strain

value: C57BL/6, Tissue:Spleen, Mouse number:pooled cells from 10 mice


title: OT-I_T_cell_OCS/LPS_rep1

source_name: OT-I cells, divided and undergoing priming, sorted from OVA coated splenocyte/LPS treated mice


title: yw rep1B

city: St. Louis

first: Nicole

middle: Christina

last: Riddle

state: MO

address: 1 Brookings Dr.; CB1137

institute: Washington University

description: gene expression data from adult fly heads with the yw control genotype

hyb_protocol: Hybridization was carried out according to the protocols recommended by Affymetrix (see 3' IVT manual available at www.affymetrix.com) on a SS450 fluidics station.

scan_protocol: Scanning was carried out according to the protocols recommended by Affymetrix (see 3' IVT manual available at www.affymetrix.com) with a 7G3000 scanner.

data_processing: RMA data for this sample was not included in the final analysis.

source_name: D.m. adult heads yw

label_protocol: Preparation of the samples for hybridization was carried out following the protocols recommended by Affymetrix (see 3' IVT manual available at www.affymetrix.com).

growth_protocol: Flies were raised at 25C with 70% humidity on standard corn meal food.

extract_protocol: RNA was isolated using Trizol (Invitrogen) according to the manufacturer's recommendations.

tag: developmental stage

value: adult

tag: tissue

value: heads

tag: genotype

value: yw control genotype


title: OT-I_T_cell_RIP-OVAhi_rep2

source_name: OT-I cells, divided and undergoing deletional tolerance, sorted from RIP-OVAhi mice

value: C57BL/6, Tissue:Sacral and pancreatic lymph node, Mouse number:pooled cells from 20 mice


title: OT-I_T_cell_Naïve_rep1


title: OT-I_T_cell_Rag_rep1

source_name: OT-I cells, divided and undergoing lymphopenia induced proliferation, sorted from Rag-/- mice


title: OT-I_T_cell_OCS/LPS_rep2


title: OT-I_T_cell_RIP-OVAhi_rep1