title: CD11b-high DC, Expt1

status: Public on Mar 15 2010

city: Charlottesville

first: Sun-sang

middle: J.

last: Sung

state: VA

address: Box 800133, U. of Virginia Health Sciences Center

institute: University of Virginia

description: CD11b-high lung DC gene expression

hyb_protocol: cRNA were fragmented, hybridized to gene chips at 45° C for 16 h, and washed using the Affymetrix Gene Chip System.

scan_protocol: Arrays were scanned by the Affymetrix GeneChip Scanner 3000 controled by the Affymetrix GCOS software.

data_processing: Data were extracted by MAS5 using Affymetrix default settings.

source_name: Lung DC

label_protocol: Biotinylated cRNA were synthesized by standard Affymetrix protocols using Superscript RT II and 1-8 μg total DC RNA.  Following second strand cDNA synthesis, incubation with T4 DNA polymerase and cleanup with the Affymetrix Cleanup Module, biotinylated cR

growth_protocol: 6-8 week old naïve BALB/cByJ mice

extract_protocol: Sorted DC were lysed and RNA was extracted with an RNeasy kit.

treatment_protocol: Perfused lungs were digested for 60-90 min in collagenase, Dnase I and hyaluronidase.  Single cell suspensions were treated with hypotonic saline for red blood cell lysis, and filtered through cotton plug.  CD11c+ cells were isolated by anti-CD11c+ magnet

value: lung

value: 6-8 week old

value: BALB/cByJ


title: CD11b-high DC, Expt3

type: RNA

department: Medicine

country: USA

description: CD11b-high lung DC gene expression

label: Biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age

tag: strain


title: CD11b-high DC, Expt2

description: CD11b-high lung DC gene expression


title: CD103+ DC, Expt.1

description: CD103+ lung DC gene expression


title: 78_129_WT

status: Public on Mar 09 2010

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description: Gene expression data from temporal lobe of wfs1 deficient mice

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with GCRMA and further analyzed using Bioconductir software based on R language

label: biotin

source_name: temporal lobe

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.2 ug total RNA (One-Cycle Target Labeling kit).

growth_protocol: Frozen in liquid nitrogen

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

treatment_protocol: Temporal lobes were dissected under dissection microscope

value: temporal lobe

tag: genotype

value: WT


title: CD103+ DC, Expt.2

description: CD103+ lung DC gene expression


title: 70_129_WT


title: 53_129_KO

value: WFS1 KO


title: 57_129_KO


title: 55_129_KO


title: 59_129_KO


title: 58_129_KO


title: 52_129_KO


title: 72_129_WT


title: 56_129_KO


title: 71_129_WT


title: 54_129_KO


title: 51_129_KO


title: 79_129_WT


title: 76_129_WT


title: 74_129_WT


title: CD103+ DC, Expt.3

description: CD103+ lung DC gene expression


title: 73_129_WT


title: 77_129_WT


title: 26_C57_WT


title: 42_C57_WT


title: 40_C57_WT


title: 09_C57_KO


title: 25_C57_WT


title: 29_C57_WT


title: 34_C57_WT


title: 37_C57_WT


title: 33_C57_WT


title: 50_129_KO


title: 10_C57_KO


title: 17_C57_KO


title: 03_C57_KO


title: 08_C57_KO


title: 02_C57_KO


title: 07_C57_KO


title: 01_C57_KO


title: 05_C57_KO


title: Stable-P9 (B737)

status: Public on Mar 08 2010

city: Stanford

first: Shai

last: Shen-Orr

state: CA

address: 251 Campus Dr. Rm.X-251

institute: Stanford University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: gcRMA

organism: Homo sapiens

source_name: Whole blood

label_protocol: Affymetrix protocol

extract_protocol: Whole blood was collected in PAXgene Blood RNA Tubes (PreAnalytiX, Qiagen), and total RNA was extracted using the PAXgene Blood RNA Kit (PreAnalytiX, Qiagen). Total RNA concentration was measured by NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE), and the integrity of the extracted total RNA was assessed with the Agilent 2100 Bioanalyzer using RNA Nano Chips (Agilent Technologies, Santa Clara, CA). Total RNA was stored at –80°C until sample preparation for the microarray experiments.

tag: transplant state

value: Stable


title: AR-P15 (B740)

value: Acute Rejection


title: Stable-P3


title: AR-P11


title: Stable-P8


title: AR-P5


title: Stable-P5


title: AR-P7


title: AR-P14


title: AR-P8


title: AR-P12


title: AR-P3


title: AR-P2


title: AR-P10


title: AR-P9


title: Stable-P2


title: Stable-P6


title: AR-P6


title: AR-P4


title: Stable-P1 (B022)


title: AR-P1 (B145)


title: Stable-P4


title: AR-P13


title: Stable-P7


title: Caco-2, coculture_48h

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

description: No additional information

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

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

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

source_name: 14 day old Caco-2 cells

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolatedusing ISOGEN (Nippon Gene Co., Ltd., Toyama, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

tag: cell line

tag: time point


title: Caco-2, coculture_6h

description: No additional information


title: Caco-2, coculture_1h

description: No additional information


title: caPI3K MI 1123

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

institute: The Westmead Institute for Medical Research

description: Constitutively active PI3K transgenic mice treated with myocardial infarction operation. Array - 1123

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

scan_protocol: Affymetrix arrays were scanned with the Affymetrix GeneArray scanner. Please refer to Expression Analysis Technical Manual available from Affymetrix website (GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)

data_processing: The images were analyzed using Microarray Suite 5.0 software (MAS5.0; Affymetrix Inc., Santa Clara, CA). Expression ratios were computed by comparative analysis of MAS5 values. The data were filtered using MAS5's signal detection and change calls generated at recommended default settings. The ratios included were those that had present calls for signal detection or an increase or decrease call associated with the ratio

source_name: Constitutively active (ca) PI3K mutant mice - Myocardial infarction (MI) group heart tissue

label_protocol:
cRNA targets for the Affymetrix arrays were synthesized, labeled, and purified according to vendor's (Affymetrix) instructions.
Please refer to Expression Analysis Technical Manual available from Affymetrix website
(GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)

growth_protocol: The mice were on a standard chow diet, and were kept in temperature controlled cages (21 - 23 degree celcius) and maintained a 12 hour light/dark cycle.

extract_protocol:
Heart was homogenized individually using motar and pestile in liquid nitrogen. Total RNA from the samples was collected by the addition of of TRIzol® Reagent (Invitrogen). Cells suspended in TRIzol® reagent were disrupted by repeated pipetting and then transferred into microfuge tubes. This protocol was modified from manufacturer’s instructions and is described here. The lysate was further homogenized using syringe and needle for 30 s and incubated at room temperature (~21ºC) for 5 min, and 200 l of chloroform was added. The tubes were shaken vigorously for 15 s to mix the phases and incubated for 3 min at room temperature. The phases were separated by centrifugation at 12,000 x g for 15 min at 4ºC. The upper aqueous phase was transferred into a fresh microfuge tube and 500 µl of ice cold isopropanol added to precipitate the
RNA. The contents were mixed by gentle inversion and then incubated for 10 min at room temperature. The RNA was recovered by centrifugation at 12,000 x g for 10 min at 4ºC. A gelatinous pellet was left on the side of the tube after removal of the supernatant. The RNA pellet was washed with 1 ml of 75% ethanol and the tube was vortexed briefly to resuspend the pellet. The RNA was recovered by centrifugation at 7,500 x g for 5 min at 4ºC. This washing step was repeated twice. After removal of the supernatant, the RNA pellet was airdried briefly and then resuspended in 20 µl Nuclease-free H2O (Ambion Inc., Austin, TX, USA) and stored in -80ºC for further processing.

treatment_protocol: The myocardial infarction (MI) operation was performed on mice at 4 months of age. After 8 weeks, cardiac function of the mice were measured by echo cardiograph and heart was removed. Total RNA was extracted following the removal.

tag: Organism

value: Mus musculus

tag: Strain

value: FVB/N

tag: Source organ

value: heart

value: Constitutively active (ca) phosphoinositide 3 kinase (PI3K) mutant, transgene expressed in mouse heart. Myocardial infarction operation performed. Over-expression of PI3K is considered good for the heart. Normal function and histology at baseline. Molecular signature reflecting a heart that is protective against a pathological insult. Some gene changes reflecting stress of surgical procedure.


title: Caco-2, coculture_0h

description: No additional information


title: caPI3K sham 1417

description: Constitutively active PI3K transgenic mice treated with sham operation to serve as controls. Array - 1417.

source_name: Constitutively active (ca) PI3K mutant mice - sham (control) group heart tissue

treatment_protocol: The sham (control) operation was performed on mice at 4 months of age. After 8 weeks, cardiac function of the mice were measured by echo cardiograph and heart was removed. Total RNA was extracted following the removal.

value: Constitutively active (ca) phosphoinositide 3 kinase (PI3K) mutant, transgene expressed in mouse heart. Control group. Over-expression of PI3K is considered good for the heart. Normal function and histology at baseline. Molecular signature reflecting a heart that is protective against a pathological insult. Some gene changes reflecting stress of surgical procedure.


title: Caco-2, coculture_24h

description: No additional information


title: caPI3K sham 1416

description: Constitutively active PI3K transgenic mice treated with sham operation to serve as controls.

source_name: Constitutively active (ca) PI3K mutant mice - sham (control) group heart tissue - array 1416


title: dnPI3K sham 418

description: Dominant negative PI3K transgenic mice treated with sham operation to serve as controls.

source_name: Dominant negative (dn) PI3K mutant mice - sham (control group) heart tissue - array 418

value: dominant negative (dn) PI3K mutant, transgene expressed in mouse heart. Normal function and histology at baseline. Molecular signature reflecting a heart that is susceptible to a pathological insult. Some gene changes reflecting stress of surgical procedure.


title: dnPI3K MI 228

description: Dominant negative PI3K transgenic mice treated with myocardial infarction operation.

source_name: Dominant negative (dn) PI3K mutant mice - Myocardial infarction (MI group) heart tissue - array 228

value: dominant negative (dn) PI3K mutant, transgene expressed in mouse heart. Myocardial infarction (MI) operation performed. Very poor function, more fibrosis than MI alone. Signature reflecting accelerated heart failure compared to MI alone.


title: caPI3K MI 257

description: Constitutively active PI3K transgenic mice treated with myocardial infarction operation. Array - 257


title: Caco-2, coculture_3h

description: No additional information


title: caPI3K MI 987

description: Constitutively active PI3K transgenic mice treated with myocardial infarction operation. Array - 987


title: dnPI3K MI 87

source_name: Dominant negative (dn) PI3K mutant mice - Myocardial infarction (MI group) heart tissue - array 87


title: Eol1 cells treated with Glivec

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: Gene expression data from cells treated with 100 nM Glivec for 4 hours.

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

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

source_name: Eol1 cells cultured in presence of Glivec

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 5 µg total mRNA.

growth_protocol: Eol1 cells were grown in RPMI medium additioned with 10% FBS, penicillin and streptomycin.

extract_protocol: Total mRNA was extracted using Rneasy mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Cells were left untreated or incubated for 4 hours with 100 nM Glivec. Both samples were washed once with PBS before RNA extraction.

tag: treatment

value: Glivec


title: 28_C57_WT


title: caPI3K MI 261

description: Constitutively active PI3K transgenic mice treated with myocardial infarction operation. Array - 261


title: dnPI3K sham 1191

source_name: Dominant negative (dn) PI3K mutant mice - sham (control group) heart tissue - array 1191


title: caPI3K sham 1413

description: Constitutively active PI3K transgenic mice treated with sham operation to serve as controls. Array - 1413.


title: dnPI3K MI 1117

source_name: Dominant negative (dn) PI3K mutant mice - Myocardial infarction (MI group) heart tissue - array 1117


title: dnPI3K sham 1181

source_name: Dominant negative (dn) PI3K mutant mice - sham (control group) heart tissue - array 1181


title: dnPI3K MI 927

source_name: Dominant negative (dn) PI3K mutant mice - Myocardial infarction (MI group) heart tissue - array 927


title: caPI3K sham 1410

description: Constitutively active PI3K transgenic mice treated with sham operation to serve as controls. Array - 1410.


title: ZBTB20-KO P2 hippocampus rep1

city: Shanghai

first: Weiping

middle: J

last: Zhang

address: 800 Xiangyin Road

department: Pathophysiology

country: China

institute: Second Military Medical University

description: Gene expression data from P2 hippocampus.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using  the Affymetrix GeneArray TM Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: P2 knockout hippocampus

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

treatment_protocol: After anesthesia on ice, hippocampi were manually dissected under the dissecting scope and snap-frozen in liquid nitrogen before storage at -80C.

value: Hippocampus

value: ZBTB20 knockout


title: Eol1 cells untreated

description: Gene expression data from untreated cells.

source_name: Eol1 cells cultured in absence of Glivec

value: untreated


title: wildtype P2 hippocampus rep1

source_name: P2 control hippocampus

value: wildtype


title: ZBTB20-KO P2 hippocampus rep2


title: Ntg MI 1127

description: Non-transgenic mice treated with myocardial infarction operation

source_name: Non-transgenic (Ntg) mice - MI (myocardial infarction group) heart tissue - array 1127

label_protocol:
cRNA targets for the Affymetrix arrays were synthesized, labeled, and purified according to vendor's (Affymetrix)
instructions.
Please refer to Expression Analysis Technical Manual available from Affymetrix website
(GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)

extract_protocol:
Heart was homogenized individually using motar and pestile in liquid nitrogen. Total RNA from the samples was collected by the addition of of TRIzol® Reagent (Invitrogen). Cells suspended in TRIzol® reagent were disrupted by repeated pipetting and then transferred into microfuge tubes. This protocol was modified from manufacturer’s instructions and is described here. The lysate was further homogenized using syringe and needle for 30 s and incubated at room temperature (~21ºC) for 5 min, and 200 l of chloroform was added. The tubes were shaken vigorously µ for 15 s to mix the phases and incubated for 3 min at room temperature. The phases were separated by centrifugation at 12,000 x g for 15 min at 4ºC. The upper aqueous phase was transferred into a fresh microfuge tube and 500 µl of ice cold isopropanol added to precipitate the
RNA. The contents were mixed by gentle inversion and then incubated for 10 min at room temperature. The RNA was recovered by centrifugation at 12,000 x g for 10 min at 4ºC. A
gelatinous pellet was left on the side of the tube after removal of the supernatant. The RNA pellet was washed with 1 ml of 75% ethanol and the tube was vortexed briefly to resuspend the pellet. The RNA was recovered by centrifugation at 7,500 x g for 5 min at 4ºC. This washing step was repeated twice. After removal of the supernatant, the RNA pellet was airdried briefly and then resuspended in 20 µl Nuclease-free H2O (Ambion Inc., Austin, TX, USA) and stored in -80ºC for further processing.

tag: Ntg-MI

value: Poor function, fibrosis, heart failure signature.


title: dnPI3K sham 417

source_name: Dominant negative (dn) PI3K mutant mice - sham (control group) heart tissue - array 417


title: wildtype P2 hippocampus rep2


title: Ntg MI 1174

source_name: Non-transgenic (Ntg) mice - MI (myocardial infarction group) heart tissue - array 1174


title: Ntg sham 416

description: Non-transgenic mice treated with sham operation to serve as controls

source_name: Non-transgenic (Ntg) mice - sham (control group) heart tissue - array 416

extract_protocol:
Heart was homogenized individually using motar and pestile in liquid nitrogen.
Total RNA from the samples was collected by the addition of of TRIzol® Reagent (Invitrogen).
Cells suspended in TRIzol® reagent were disrupted by repeated pipetting and then transferred into microfuge tubes.
This protocol was modified
from manufacturer’s instructions and is described here. The lysate was further homogenized
using syringe and needle for 30 s and incubated at room temperature (~21ºC) for 5 min, and
200 l of chloroform was added. The tubes were shaken vigorously µ for 15 s to mix the
phases and incubated for 3 min at room temperature. The phases were separated by
centrifugation at 12,000 x g for 15 min at 4ºC. The upper aqueous phase was transferred
into a fresh microfuge tube and 500 µl of ice cold isopropanol added to precipitate the
RNA. The contents were mixed by gentle inversion and then incubated for 10 min at room
temperature. The RNA was recovered by centrifugation at 12,000 x g for 10 min at 4ºC. A
gelatinous pellet was left on the side of the tube after removal of the supernatant. The RNA
pellet was washed with 1 ml of 75% ethanol and the tube was vortexed briefly to resuspend
the pellet. The RNA was recovered by centrifugation at 7,500 x g for 5 min at 4ºC. This
washing step was repeated twice. After removal of the supernatant, the RNA pellet was airdried
briefly and then resuspended in 20 µl Nuclease-free H2O (Ambion Inc., Austin, TX,
USA) and stored in -80ºC for further processing.

tag: Ntg-sham

value: Normal function, histology and molecular signature. Some gene changes reflecting stress of surgical

tag: procedure.


title: Ntg sham 1184

source_name: Non-transgenic (Ntg) mice - sham (control group) heart tissue - array 1184


title: Ntg sham 415

source_name: Non-transgenic (Ntg) mice - sham (control group) heart tissue - array 415

value: Normal function, histology and molecular signature. Some gene changes reflecting stress of surgical procedure.


title: Ntg sham 1185

source_name: Non-transgenic (Ntg) mice - sham (control group) heart tissue - array 1185


title: Ntg MI 1190

source_name: Non-transgenic (Ntg) mice - MI (myocardial infarction group) heart tissue - array 1190


title: Ntg MI 140

source_name: Non-transgenic (Ntg) mice - MI (myocardial infarction group) heart tissue - array 140


title: OPC-37 ℃ -rep4

status: Public on Mar 06 2010

city: Shinjuku

first: Masahiro

last: Yamamoto

state: Tokyo

address: 35 Shinano-machi

department: Department of Kampo Medicine

institute: Keio University School of Medicine

hyb_protocol: The labeled cRNA was fragmented, hybridized to Mouse430 2.0 array (Affymetrix, Santa Clara, CA) using an Affymetrix fluidics station according to the Affymetrix protocols.

scan_protocol: GeneChips were scanned with an Affymetrix scanner, according to the Affymetrix protocols.

source_name: OPC cultured at 37 ℃

label_protocol: The labeled cRNA was prepared from by in vitro transcription (Enzo Biochem, New York, NY)

growth_protocol: Oligodendrocyte precursor cells were prepared from primary mixed cell cultures of embryonic mouse cerebral hemispheres. The cerebral hemispheres from 15-day-old mouse embryos were enzymatically dissociated, seeded and cultured for 5 days in D-MEM containing 10% FBS.

extract_protocol: Total RNA was extracted from mice (n = 3 per each group) using TRIzol (Life Technologies, Rockville, TX) and re-purified by RNeasy spin columns (Quiagen, Valencia, CA), according to the manufacturer’s instructions.

treatment_protocol: The cells were passaged to serum-free basal medium  and cultured for further 48 hr at 37 ℃ and 31.5 ℃.

value: ICR

tag: cell type

value: oligodendrocyte precursor cells

tag: temperature


title: OPC-31.5 ℃ -rep2

source_name: OPC cultured at 31.5 ℃


title: OPC-37 ℃ -rep3


title: OPC-37 ℃ -rep2


title: OPC-37 ℃ -rep1


title: OPC-31.5 ℃ -rep4


title: OPC-31.5 ℃ -rep1


title: Zygotic_Diploid_Blastocysts

city: Tampa

first: Sean

last: Yoder

state: FL

address: 12902 Magnolia Dr.

department: Molecular Genomics Core Facility

institute: Moffitt Cancer Center & Research Institute

description: Comparison of mouse development in normal fertilized embryos and parthenogenetic embryos. This experiment looked at day 4 blastocysts which are indistinguishable morphologically but differ in their gene expression profiles.  The normal diploid blastocysts were derived from development of zygotes for 96 hours

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip scanner 3000, 1.5 micrometer resolution

data_processing: Signal values calculated in MAS 5.0 and scaled to generate a trimmed mean intensity of 500. The data provided here has not been processed further.

label_protocol: Affymetrix two-cycle amplification protocol

extract_protocol: Ambion RNAqueous MICRO kit

tag: mouse embryos 96 hours in culture, fertilized


title: kidney of 8 month old, diabetic 3

city: Louisville

first: lu

last: yang

state: KY

address: 570 S Preston Str

institute: University of Louisville

description: Gene expression data from 8 month old kidney of diabetic mouse.

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

scan_protocol: Arrays were scanned using a GCS 3000 7G scanner and GCOS software (Affymetrix, Santa Clara, CA)

data_processing: Median-centered normalization and repeated permutation of the data using SAM 3.0, Stanford, CA)

source_name: 8 month old diabetic mouse kidney

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

tag: tissue

value: whole kidney

value: FVB/NJ

value: 8 month


title: kidney of 8 month old, diabetic 5

tag: age


title: kidney of 8 month old, control 2

description: Gene expression data from 8 month old kidney of control mouse.

source_name: 8 month old control mouse kidney

tag: strain


title: kidney of 8 month old, control 6


title: Zygotic_Tetraploid_Blastocysts

description: Comparison of mouse development in normal fertilized embryos and parthenogenetic embryos. This experiment looked at day 4 blastocysts which are indistinguishable morphologically but differ in their gene expression profiles.  This is the fertilized embryos fused to generate tetraploid embryos.

tag: mouse embryos 96 hours in culture, fertilized, fused at the two cell stage to generate tetraploid embryos


title: Parthogenetic_Tetraploid_Blastocysts

description: Comparison of mouse development in normal fertilized embryos and parthenogenetic embryos. This experiment looked at day 4 blastocysts which are indistinguishable morphologically but differ in their gene expression profiles.  This is the parthenogenetic embryos fused to generate tetraploid embryos.

tag: mouse embryos 96 hours in culture, maternal genome only, fused at two cell stage to generate tetraploid embryos


title: kidney of 4 month old, control 2

description: Gene expression data from 4 month old kidney of control mouse.

source_name: 4 month old control mouse kidney

value: 4 month


title: OPC-31.5 ℃ -rep3


title: kidney of 8 month old, diabetic 1


title: kidney of 8 month old, control 3


title: kidney of 8 month old, control 1


title: kidney of 8 month old, control 4


title: kidney of 8 month old, diabetic 6


title: kidney of 4 month old, diabetic 6

description: Gene expression data from 4 month old kidney of diabetic mouse.

source_name: 4 month old diabetic mouse kidney


title: kidney of 4 month old, diabetic 7


title: kidney of 8 month old, control 5


title: kidney of 8 month old, diabetic 4


title: kidney of 4 month old, control 1


title: kidney of 8 month old, diabetic 2


title: kidney of 4 month old, control 4


title: kidney of 4 month old, control 3


title: Mouse_Parthenogenetic_Diploid_Blastocysts

description: Comparison of mouse development in normal fertilized embryos and parthenogenetic embryos.  This experiment looked at day 4 blastocysts which are indistinguishable morphologically but differ in their gene expression profiles.

data_processing: Signal values calculated in MAS 5.0 and scaled to generate a trimmed mean intensity of 500.  The data provided here has not been processed further.

tag: mouse embryos 96 hours in culture, maternal genome only


title: kidney of 4 month old, diabetic 2


title: kidney of 4 month old, diabetic 5


title: kidney of 4 month old, diabetic 3


title: kidney of 2 month old, control 4

description: Gene expression data from 2 month old kidney of control mouse.

source_name: 2 month old control mouse kidney

value: 2 month


title: kidney of 4 month old, diabetic 4


title: kidney of 2 month old, diabetic 5

description: Gene expression data from 2 month old kidney of diabetic mouse.

source_name: 2 month old diabetic mouse kidney


title: kidney of 2 month old, control 5


title: kidney of 2 month old, diabetic 4


title: kidney of 2 month old, control 6


title: kidney of 2 month old, control 3


title: kidney of 2 month old, diabetic 2


title: kidney of 2 month old, control 2


title: kidney of 2 month old, diabetic 1


title: kidney of 2 month old, control 1


title: kidney of 2 month old, diabetic 6


title: kidney of 2 month old, diabetic 3


title: kidney of 4 month old, diabetic 1


title: THP-1 +SS2, biological rep1

city: Wuhan

first: Liu

middle: Man

last: li

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

description: Gene expression data from THP-1 cells after incubated with Streptcoccus suis 2 strain SC19 for 3 hours

hyb_protocol: GeneChips were hybridiza using hybridization oven 640, and washed and stained with a GeneChip Fluidics Station 450 using the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the GeneArrayTM scanner 3000.

data_processing:
The data were analyzed with GCOS1.4 (Affymetrix), and GeneSpring 7.31 (Agilent) for normalization (MAS5). P-value was analyzed by Welch T-test and cutoff for differential expression genes was set at 0.05.
Fold change≥2 and the p<0.05 belonged to the up-regulated, and fold change≤-2 belonged to the down-regulated and the p<0.05.

source_name: THP-1 cells infected Streptcoccus suis 2 strain SC19,3 hours

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

growth_protocol: 48 h cultures of THP-1 cells were washed twice with phosphate-buffered saline (PBS) and resuspended in 1640 maintenance media in appropriate dilution.

extract_protocol: Trizol was used for total RNA extraction according to the manufacturer's instructions.

treatment_protocol: Streptococcus suis 2 strain SC19 added to THP-1 cells at a MOI of 1:1 (bacteria/cells). Uninfected control cells were added a same volume PBS instead.

value: monocyte

tag: cell line

tag: growth properties

value: suspension

tag: infected with bacterial strain

value: Streptcoccus suis 2 strain SC19


title: THP-1 +SS2, biological rep2


title: NK cell stimulated by high dose IL2, Replicate 1

city: Memphis

first: Noriko

last: Shimasaki

state: TN

address: 262 Danny Thomas Place

department: Oncology

institute: St. Jude Children's Research Hospital

description: Biological replicate 1 of 3. Primary human NK cell.

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

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

source_name: Total RNA from primary human NK cells, stimulated by high dose IL2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA (Expression Analysis Technical Manual, 200Biotinylated cRNA were pre1, Affymetrix).

extract_protocol: TriZol procedure

value: human NK cells

tag: passage

value: primary

tag: source

value: healthy donor


title: NK cell stimulated by low dose IL2, Replicate 3

description: Biological replicate 3 of 3. Primary human NK cell.

source_name: Total RNA from primary human NK cells, stimulated by low dose IL2


title: THP-1 control, biological rep1

description: Gene expression data from THP-1 cells after incubated with PBS for 3 hours

source_name: THP-1 cells with PBS,3 hours


title: Primary human NK cell, Replicate 5

description: Biological replicate 5 of 5. Primary human NK cell.

source_name: Total RNA from primary human NK cells


title: Primary human NK cell, Replicate 4

description: Biological replicate 4 of 5. Primary human NK cell.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 200Biotinylated cRNA were pre1, Affymetrix).


title: NKAES-derived NK cell, Replicate 3

description: Biological replicate 3 of 5. NKAES-derived NK cell.

source_name: Total RNA from NKAES-derived NK cells after 7 days of culture

value: expanded


title: Primary human NK cell, Replicate 3

description: Biological replicate 3 of 5. Primary human NK cell.


title: Primary human NK cell, Replicate 2

description: Biological replicate 2 of 5. Primary human NK cell.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 200Biotinylated cRNA were pre1, Affymetrix).


title: THP-1 control, biological rep2


title: NK cell stimulated by low dose IL2, Replicate 2

description: Biological replicate 2 of 3. Primary human NK cell.


title: NKAES-derived NK cell, Replicate 1

description: Biological replicate 1 of 5. NKAES-derived NK cell.


title: NK cell stimulated by high dose IL2, Replicate 2


title: NK cell stimulated by low dose IL2, Replicate 1


title: NKAES-derived NK cell, Replicate 2

description: Biological replicate 2 of 5. NKAES-derived NK cell.


title: Primary human NK cell, Replicate 1

description: Biological replicate 1 of 5. Primary human NK cell.


title: NKAES-derived NK cell, Replicate 4

description: Biological replicate 4 of 5. NKAES-derived NK cell.


title: NKAES-derived NK cell, Replicate 5

description: Biological replicate 5 of 5. NKAES-derived NK cell.


title: liver_co_14M_rep2

status: Public on Mar 05 2010

city: Kiel

first: Frank

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

country: Germany

institute: Christian-Albrechts-University Kiel

description: 4-week old mice at study begin

hyb_protocol: 15 µg of fragmented cRNA was hybridized to a Mouse Genome 430 2.0 Array for 16 hr at 45 °C at 60 rpm. Arrays were washed on GeneChip®  Fluidics station 450 (Affymetrix) and stained with streptavidin-phycoerythrin

scan_protocol: Microarrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Expression data was normalized with Affymetrix GeneChip Operating Software (GCOS) 1.4 using mean value (global normalization).

source_name: liver, control, 14 months

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (IVT Labeling Kit, Affymetrix).

growth_protocol: SAMP1 mice were reared in the Division of Laboratory Animal Research, Research Center for Human and Environmental Sciences, Shinshu University, under specific pathogen-free (SPF) conditions at 24 + 2 °C and a 12-h light-dark cycle. Water and food intake were available ad libitum. At the beginning of the long-term controlled study, 4-week-old female SAMP1 mice were purchased from Japan SLC (Hamamatsu, Japan) and housed 3 to 6 per cage (20 cm wide, 30 cm long, 10 cm deep). Grouping of the animals remained unchanged throughout the study. Body weights, food intake and degree of senescence were calculated monthly while mice were inspected daily.

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

treatment_protocol: Mice were supplemented with the oxidized (Q10) or reduced form (QH2) of CoQ10, or a respective control diet for 6 or 14 months. Based on mean food intake and mean body weight, mice consumed 500 mg/ kg BW/ d QH2 or Q10. After supplementation period (6 or 14 months), mice were sacrificed, corresponding to an age of  7 or 15 months in total.

tag: gender

value: female

value: Senescence accelerated mice prone 1

value: liver

value: 14 months


title: liver_Q10_14M_rep2

description: 4-week old mice at study begin

source_name: liver, Q10, 14 months


title: liver_QH2_14M_rep3

description: 4-week old mice at study begin

source_name: liver, QH2, 14 months


title: liver_QH2_14M_rep2

description: 4-week old mice at study begin


title: liver_co_14M_rep1

description: 4-week old mice at study begin


title: liver_Q10_14M_rep3

description: 4-week old mice at study begin


title: liver_QH2_6M_rep3

description: 4-week old mice at study begin

source_name: liver, QH2, 6 months

value: 6 months


title: liver_Q10_14M_rep1

description: 4-week old mice at study begin


title: liver_QH2_14M_rep1

description: 4-week old mice at study begin


title: NK cell stimulated by high dose IL2, Replicate 3


title: liver_co_14M_rep3

description: 4-week old mice at study begin


title: liver_QH2_6M_rep1

description: 4-week old mice at study begin


title: liver_QH2_6M_rep2

description: 4-week old mice at study begin


title: kidney_QH2_14M_rep1

description: 4-week old mice at study begin

source_name: kidney, QH2, 14 months

value: kidney


title: liver_Q10_6M_rep1

description: 4-week old mice at study begin

source_name: liver, Q10, 6 months


title: liver_co_6M_rep3

description: 4-week old mice at study begin

source_name: liver, control, 6 months


title: kidney_Q10_14M_rep2

description: 4-week old mice at study begin

source_name: kidney, Q10, 14 months


title: kidney_QH2_14M_rep3

description: 4-week old mice at study begin


title: kidney_QH2_14M_rep2

description: 4-week old mice at study begin


title: liver_Q10_6M_rep2

description: 4-week old mice at study begin


title: liver_co_6M_rep1

description: 4-week old mice at study begin


title: liver_Q10_6M_rep3

description: 4-week old mice at study begin


title: kidney_Q10_14M_rep1

description: 4-week old mice at study begin


title: liver_co_6M_rep2

description: 4-week old mice at study begin


title: kidney_QH2_6M_rep2

description: 4-week old mice at study begin

source_name: kidney, QH2, 6 months


title: kidney_co_14M_rep1

description: 4-week old mice at study begin

source_name: kidney, control, 14 months


title: kidney_QH2_6M_rep3

description: 4-week old mice at study begin


title: kidney_Q10_14M_rep3

description: 4-week old mice at study begin


title: kidney_Q10_6M_rep3

description: 4-week old mice at study begin

source_name: kidney, Q10, 6 months


title: kidney_co_14M_rep2

description: 4-week old mice at study begin


title: kidney_co_6M_rep2

description: 4-week old mice at study begin

source_name: kidney, control, 6 months


title: kidney_co_14M_rep3

description: 4-week old mice at study begin


title: kidney_QH2_6M_rep1

description: 4-week old mice at study begin


title: kidney_co_6M_rep3

description: 4-week old mice at study begin


title: heart_QH2_14M_rep1

description: 4-week old mice at study begin

source_name: heart, QH2, 14 months

value: heart


title: heart_QH2_14M_rep2

description: 4-week old mice at study begin


title: kidney_Q10_6M_rep2

description: 4-week old mice at study begin


title: heart_Q10_14M_rep1

description: 4-week old mice at study begin

source_name: heart, Q10, 14 months


title: kidney_Q10_6M_rep1

description: 4-week old mice at study begin


title: heart_Q10_14M_rep3

description: 4-week old mice at study begin


title: heart_QH2_14M_rep3

description: 4-week old mice at study begin


title: heart_Q10_14M_rep2

description: 4-week old mice at study begin


title: heart_co_14M_rep2

description: 4-week old mice at study begin

source_name: heart, control, 14 months


title: kidney_co_6M_rep1

description: 4-week old mice at study begin


title: heart_QH2_6M_rep3

description: 4-week old mice at study begin

source_name: heart, QH2, 6 months


title: heart_co_14M_rep3

description: 4-week old mice at study begin


title: heart_QH2_6M_rep1

description: 4-week old mice at study begin


title: heart_Q10_6M_rep3

description: 4-week old mice at study begin

source_name: heart, Q10, 6 months


title: heart_Q10_6M_rep1

description: 4-week old mice at study begin


title: heart_QH2_6M_rep2

description: 4-week old mice at study begin


title: heart_Q10_6M_rep2

description: 4-week old mice at study begin


title: heart_co_6M_rep3

description: 4-week old mice at study begin

source_name: heart, control, 6 months


title: Lcl-balanced-4

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: Comparison of the transcriptomes of cell lines from control and t(11;22)(q23;q11) individuals.

hyb_protocol: Affymetrix HG-U133 Plus 2.0 arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

label_protocol: 200ng of total RNA were amplified and labeled using the Message Amp II-biotin Enhanced reagents (Ambion; catalog #AM1791)

growth_protocol: Cells were cultured in RPMI-1640 Medium with GlutaMAX (Gibco, Invitrogen), supplemented with 10% (v/v) Fetal calf serum, and 1% (v/v) penicillin and streptomycin at 37oC in 5% CO2

extract_protocol: TRIzol reagent (Invitrogen, Carlsbad, NM, USA), cleaned on RNeasy columns (Qiagen) according to the manufacturers' instructions

tag: Cell type

value: Lymphoblastoid cell lines

tag: Gender

value: Female

tag: Age


title: Lcl-balanced-3


title: Lcl-balanced-5


title: heart_co_6M_rep2

description: 4-week old mice at study begin


title: brain_QH2_14M_rep3

description: 4-week old mice at study begin

source_name: brain, QH2, 14 months

value: brain


title: Lcl-balanced-7


title: heart_co_6M_rep1

description: 4-week old mice at study begin


title: Lcl-control-12

source_name: Control (46,XX)


title: Lcl-balanced-8


title: Lcl-balanced-9

value: Male


title: Lcl-balanced-6


title: Lcl-control-13


title: Lcl-control-10

source_name: Control (46,XY)


title: Lcl-unbalanced-4


title: brain_Q10_14M_rep2

description: 4-week old mice at study begin

source_name: brain, Q10, 14 months


title: brain_QH2_14M_rep2

description: 4-week old mice at study begin


title: brain_QH2_14M_rep1

description: 4-week old mice at study begin


title: brain_co_14M_rep3

description: 4-week old mice at study begin

source_name: brain, control, 14 months


title: Lcl-control-8


title: Lcl-control-11


title: Lcl-control-7


title: Lcl-balanced-2


title: brain_Q10_14M_rep3

description: 4-week old mice at study begin


title: brain_Q10_14M_rep1

description: 4-week old mice at study begin


title: heart_co_14M_rep1

description: 4-week old mice at study begin


title: Lcl-unbalanced-3

value: 9 months


title: Lcl-control-9


title: brain_co_14M_rep2

description: 4-week old mice at study begin


title: Lcl-balanced-1


title: Lcl-unbalanced-2

value: 4 days


title: brain_QH2_6M_rep2

description: 4-week old mice at study begin

source_name: brain, QH2, 6 months


title: brain_QH2_6M_rep3

description: 4-week old mice at study begin


title: brain_co_14M_rep1

description: 4-week old mice at study begin


title: Lcl-control-6


title: Lcl-control-5


title: Lcl-control-1


title: brain_QH2_6M_rep1

description: 4-week old mice at study begin


title: brain_Q10_6M_rep1

description: 4-week old mice at study begin

source_name: brain, Q10, 6 months


title: Lcl-unbalanced-1


title: brain_co_6M_rep1

description: 4-week old mice at study begin

source_name: brain, control, 6 months


title: Lcl-control-4


title: CLL-19

status: Public on Mar 04 2010

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

country: Spain

institute: IDIBAPS

description: no additional information

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

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

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: Peripheral blood cd19+ tumor cells

tag: disease state

value: CLL (Chronic Lymphocytic Leukemia)


title: Lcl-control-2


title: brain_co_6M_rep3

description: 4-week old mice at study begin


title: LF-3

description: no additional information

value: LF (follicular lymphoma)


title: brain_co_6M_rep2

description: 4-week old mice at study begin


title: LF-6

description: no additional information


title: CLL-18

description: no additional information


title: LF-4

description: no additional information


title: LF-1

description: no additional information


title: brain_Q10_6M_rep2

description: 4-week old mice at study begin


title: CLL-17

description: no additional information


title: LF-5

description: no additional information


title: Lcl-control-3


title: LF-7

description: no additional information


title: LF-2

description: no additional information


title: CLL-15

description: no additional information


title: CLL-16

description: no additional information


title: CLL-12

description: no additional information


title: CLL-6

description: no additional information


title: brain_Q10_6M_rep3

description: 4-week old mice at study begin


title: CLL-11

description: no additional information


title: CLL-10

description: no additional information


title: CLL-7

description: no additional information


title: CLL-4

description: no additional information


title: CLL-2

description: no additional information


title: CLL-3

description: no additional information


title: lung_CLP_PPTA knockout_rep1

city: Singapore

first: Akhil

last: Hegde

address: Centre for life Sciences,#03-06, 28 Medical Drive

department: Pharmacology

country: Singapore

institute: National University of Singapore

description:
Gene expression data from PPTA knockout mice 8 h after cecal ligation and puncture surgery.
M-1

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing:
GeneChip Operating Software (GCOS) with Affymetrix Microarray Suite 5.0 (MAS5) algorithm was used to define the probe cells and compute intensity for each cell. The Expression ConsoleTM software was used to enable probe set summarization and to verify if the hybridization results and initial data were of sufficient quality for secondary analysis.

The Sample data table represents the GCOS data. The GCOS and Expression Console (EC) CHP files are attached to the Sample record as supplementary files.

source_name: mouse PPTA knockout lung 8 h after cecal ligation and puncture surgery

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

value: lung

tag: genotype

value: PPTA knockout

tag: treatment

value: cecal ligation and puncture surgery

value: 8-10 weeks


title: CLL-5

description: no additional information


title: SMLZ-6

description: no additional information

value: SMLZ (Splenic Marginal Zone Lymphoma)


title: SMLZ-10

description: no additional information


title: lung_CLP_PPTA knockout_rep2

description:
Gene expression data from PPTA knockout mice 8 h after cecal ligation and puncture surgery.
M-2

tag: tissue

tag: age


title: lung_CLP_PPTA knockout_rep3

description:
Gene expression data from PPTA knockout mice 8 h after cecal ligation and puncture surgery.
M-3


title: lung_sham_PPTA knockout_rep2

description:
Gene expression data from PPTA knockout mice 8 h after sham surgery.
MS-2

source_name: mouse PPTA knockout lung 8 h after sham surgery

value: sham surgery


title: lung_CLP_wildtype_rep2

description:
Gene expression data from wild-type mice 8 h after cecal ligation and puncture surgery.
B-2

source_name: mouse wild-type lung 8 h after cecal ligation and puncture surgery

tag: strain

value: Balb/c

value: wild-type


title: lung_CLP_wildtype_rep1

description:
Gene expression data from wild-type mice 8 h after cecal ligation and puncture surgery.
B-1


title: CLL-8

description: no additional information


title: SMLZ-5

description: no additional information


title: lung_CLP_wildtype_rep3

description:
Gene expression data from wild-type mice 8 h after cecal ligation and puncture surgery.
B-3


title: lung_sham_PPTA knockout_rep1

description:
Gene expression data from PPTA knockout mice 8 h after sham surgery.
MS-1


title: lung_sham_wildtype_rep3

description:
Gene expression data from wild-type mice 8 h after sham surgery.
BS-3

source_name: mouse wild-type lung 8 h after sham surgery


title: HCL4

description: no additional information

value: HCL (Hairy Cell Leukemia)


title: HCL3

description: no additional information


title: HCL-variant-5

description: no additional information

value: HCL (Hairy Cell Leukemia)-variant


title: MCL-conventional-15

description: no additional information

value: cMCL (conventional)


title: HCL-variant-1

description: no additional information


title: MCL-conventional-11

description: no additional information

value: cMCL (conventional mantle cell lymphoma)


title: SMLZ-2

description: no additional information


title: MCL-conventional-13

description: no additional information


title: lung_sham_wildtype_rep2

description:
Gene expression data from wild-type mice 8 h after sham surgery.
BS-2


title: HCL2

description: no additional information


title: MCL-conventional-14

description: no additional information


title: MCL-conventional-12

description: no additional information


title: lung_sham_PPTA knockout_rep3

description:
Gene expression data from PPTA knockout mice 8 h after sham surgery.
MS-3


title: MCL-conventional-6

description: no additional information


title: MCL-conventional-8

description: no additional information


title: MCL-conventional-7

description: no additional information


title: MCL-conventional-4

description: no additional information


title: MCL-conventional-3

description: no additional information


title: MCL-conventional-5

description: no additional information


title: MCL-conventional-9

description: no additional information


title: MCL-indolente-4

description: no additional information

value: iMCL (indolent mantle cell lymphoma)


title: CLL-1

description: no additional information


title: MCL-indolente-6

description: no additional information


title: MCL-indolente-5

description: no additional information


title: MCL-indolente-3

description: no additional information


title: MCL-conventional-1

description: no additional information


title: MCL-conventional-2

description: no additional information


title: MCL-indolente-7

description: no additional information


title: MCL-indolente-1

description: no additional information


title: MCL-indolente-2

description: no additional information


title: MCL-conventional-10

description: no additional information


title: 06-06-A279A_Tumor_41

status: Public on Mar 03 2010

city: Philadelphia

first: Jay

last: Johnson

state: PA

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

hyb_protocol: Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0 Wash A1 Temperature (C)=30 Number of Wash A1 Cycles=10 Mixes per Wash A1 Cycle=2 Wash B Recovery Mixes=0 Wash B Temperature (C)=50 Number of Wash B Cycles=6 Mixes per Wash B Cycle=15 Stain Temperature (C)=35 First Stain Time (seconds)=300 Wash A2 Recovery Mixes=0 Wash A2 Temperature (C)=30 Number of Wash A2 Cycles=10 Mixes per Wash A2 Cycle=4 Second Stain Time (seconds)=300 Third Stain Time (seconds)=300 Wash A3 Recovery Mixes=0 Wash A3 Temperature (C)=35 Number of Wash A3 Cycles=15 Mixes per Wash A3 Cycle=4< Holding Temperature (C)=25

scan_protocol: The probe array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: standard Affymetrix protocol

source_name: Liposarcoma

label_protocol: The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix.  The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).

extract_protocol: Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.

tag: tumor

value: Liposarcoma

tag: subtype

value: well-differentiated


title: 5228r2

description: Replicate #2

value: pleomorphic


title: LS2r2

description: Replicate #2

source_name: Liposarcoma 5228, Tumor 27

growth_protocol: LS2 is maintained in RPMI 1640 + Glutamax (Invitrogen) supplemented with 20% FBS (Invitrogen), MEM Vitamin Mixture (BioWhittaker), ITES (Lonza), Penicillin (4U/ml) Streptomycin (4 ug/ml) L-Glutamine (0.29 mg/m) mixture (Invitrogen), 1mM sodium pyruvate (CellGro) and MEM Eagle Non-essential amino acid solution (Lonza) with 5% CO2.

tag: cell line

value: LS2 derived from sample 5228, Tumor 27


title: LS2r1

description: Replicate #1


title: CLL-9

description: no additional information

value: CLL (Chronic Lymphocytic Leukemia)


title: D27666_Tumor_44


title: 96-10-P004_Tumor_43


title: D27674_Tumor_46


title: 06-05-152A_Tumor_39

value: myxoid round cell


title: Control_HepG2_Rep1

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

description: Gene expression profile of normal HepG2 cells (control)

hyb_protocol: The labelled cRNA obtained was fragmented and 15 microg of cRNA were hybridized to the Affymetrix HG-U133 plus 2.0 chip according to the protocols described by the manufacturer.

scan_protocol: The genechips were washed thoroughly after hybridisation and scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data was normalised with MAS 5.0 using the GCOS Software from Affymetrix using default settings. The normalization target was set to 500.

source_name: Human Hepatocarcinoma cells (HepG2)

label_protocol: Biotinylated cRNA were prepared from 6 microg total RNA using the GeneChip Expression IVT Labelling kit from Affymetrix (USA) according to the manufacturers instructions.

extract_protocol: HepG2 cells were grown to confluency and total RNA was isolated using Trizol (Invitrogen, CA, USA) according to the manufacturers instructions. The RNA so obtained was purified using the RNeasy Mini-kit (Qiagen, Germany)

tag: HepG2 (ATCC Number

value: HB-8065) is an adherent hepatocellular carcinoma cell line.

tag: Organism

value: Homo sapiens

tag: Source


title: 3000p8573_Tumor_37

value: dedifferentiated


title: D27667_Tumor_45


title: Control_HepG2_rep3

source_name: Human Hepatocellular Carcinoma (HepG2)


title: Control_HepG2_rep2


title: 03-08-1037A_Tumor_40


title: Treated_HepG2_rep1

description: Gene expression profile of HepG2 cells treated with TNF alpha (0.5nM, 12h)


title: D27667_Tumor_47


title: 5228_Tumor_27

description: This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)


title: D27669_Tumor_33


title: 1071403A2_Tumor_42


title: D27671_Tumor_35


title: D27670_Tumor_34


title: lung_sham_wildtype_rep1

description:
Gene expression data from wild-type mice 8 h after sham surgery.
BS-1

value: lung

value: sham surgery

value: 8-10 weeks


title: Treated_HepG2_rep2


title: Treated_HepG2_rep3


title: D27673_Tumor_36


title: 02-390_Tumor_16


title: 03-098_Tumor_2


title: 97-212_Tumor_21


title: 03-159_Tumor_10


title: 97-096_Tumor_19


title: 97-166_Tumor_32R2

value: well-differentiated spindle cell

tag: tumor type

value: Recurrence of 96-249, Tumor 32R1


title: 96-249_Tumor_32R1


title: 93-185_Tumor_23

value: myxoid


title: 99_217_Tumor_7

value: not specified


title: 95-124_Tumor_31R2

value: Recurrence of Tumor 94-215 (Tumor 31R1)


title: 94-215_Tumor_31R1

value: Liposarcoma

value: Well-differentiated spindle cell


title: 03-199_Tumor_15


title: 6272_Tumor_29


title: 96-389_Tumor_6

value: well-differentiated


title: 98-310_Tumor_17


title: vCRC4

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Gene expression data from laser microdissected colonic epithelial cells

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

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: The data were preprocessed by the function mas5 from the Bioconductor affy package

source_name: laser microdissected human colonic epithelial cell sample

label_protocol: Biotinylated cRNA was prepared according to the two-round Affymetrix protocol from total RNA

extract_protocol: RNeasy Micro extraction of total RNA was performed according to the manufacturer instructions

tag: isolation method

value: laser microdissected

tag: cell type

value: colonic epithelial cells

value: colorectal cancer


title: vn4

value: normal


title: vn6


title: vn2


title: vn5


title: vCRC6


title: vn1


title: vCRC1


title: vCRC2


title: vad5

value: adenoma


title: vad6


title: vad4


title: vn3


title: vCRC5


title: vCRC3


title: vad3


title: vad2


title: volunteer10_forearm epdermis_025-0h-e_080307 (matrix 2)

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

description: volunteer1_forearm epdermis

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: dCHIP

source_name: forearm epdermis

label_protocol: For the microarray experiment, RNA from 16 buttocks full thickness skin samples and 13 epidermal samples was amplified with the MessageAmp II Enhanced kit (Applied biosystems/Ambion), following the manufacturer’s instructions for single-round amplification using 500 ng total RNA.

extract_protocol: Samples were thawed for 30 min and carefully transferred to new 2.0 mL microtubes containing one stainless steel bead (Qiagen) and 350 mL of buffer RLT (supplied with the RNeasy Micro Kit) according to the manufacturer’s instructions.   Next, the new microtubes were placed in a TissueLyser® (Qiagen) bead beater to homogenize the tissue for 2 x 2 min (epidermis) or 2 x 3 min (dermis) at 30 Hz. RNA was extracted using the RNeasy Micro Kit (Qiagen) following the manufacturer’s instructions. For dermal samples a protein digestion step (proteinase K, Qiagen) was added as recommended in the fibrous tissue protocol.

treatment_protocol: Punch biopsies from normal forearm skin were incubated in ammonium thiocyanate for 30 min and separated. Epidermal fractions were stored in RNAlater for 48h and then at -80 Celcius until further processing.

tag: tissue type

value: forearm epdermis

tag: subject

value: volunteer


title: volunteer13_forearm epdermis_034-0h-e_080215 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer12_forearm epdermis_029-0h-e_080215 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer7_forearm epdermis_017-0h-e_080227 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer8_forearm epdermis_020-0h-e_080227 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer11_forearm epdermis_026-0h-e_080227 (matrix 2)

description: volunteer1_forearm epdermis


title: vcontrol 1

description: Gene expression data from HT29 colon adenocarcinoma cell line

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

source_name: HT29 human colon adenocarcinoma cell line sample

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA

extract_protocol: RNeasy Mini extraction of total RNA was performed according to the manufacturer instructions

value: control


title: volunteer2_forearm epdermis_007-0h_e_080307 (matrix 2)

description: volunteer1_forearm epdermis


title: vcontrol 3


title: vNS398-treated 3


title: volunteer4_forearm epdermis_014-0h-e_080213 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer1_forearm epdermis_004-0h-e_080212 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer6_forearm epdermis_016-0h-e_080215 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer3_forearm epdermis_009-0h-e_080212 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer9_forearm epdermis_023-0h-e_080214 (matrix 2)

description: volunteer1_forearm epdermis


title: volunteer5_forearm epdermis_015-0h-e_080213 (matrix 2)

description: volunteer1_forearm epdermis


title: vad1

tag: disease state


title: vNS398-treated 1


title: vcontrol 2


title: Susa_rep2

city: LONDON

first: YONG-JIE

last: LU

address: Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: BLSMD, Queen Mary University of London

description:
Gene expression profiling from human TGCT cell line, Susa
Replicate 2 of 2

hyb_protocol: Affymetrix U133 plus 2.0 gene expression assay protocol

scan_protocol: Scanned using Affymetrix GeneChip® 3000-7G scanner

data_processing: Data analysis workflow for GeneChip® Human Genome U133 plus 2.0 Arrays using the Microarray Suite version 5.0 (MAS 5.0) and the Affymetrix default analysis settings and global scaling as normalization method.

source_name: Susa cell line

extract_protocol: Trizol extraction

tag: Human TGCT cell line, Susa


title: GCT27_cisplatin_resistant_rep2

description:
Gene expression profiling from human cisplatin-resistant TGCT cell line, GCT27R
Replicate 2 of 2

source_name: GCT27 cell line, cisplatin-resistant

label_protocol: Affymetrix U133 plus 2.0 gene expression assay protocol

tag: Human TGCT cell line, cisplatin-resistant derivative, GCT27R


title: GCT27_cisplatin_resistant_rep1

description:
Gene expression profiling from human cisplatin-resistant TGCT cell line, GCT27R
Replicate 1 of 2


title: GCT27_rep1

description:
Gene expression profiling from human TGCT cell line, GCT27
Replicate 1 of 2

source_name: GCT27 cell line

tag: Human TGCT cell line, GCT27


title: Susa_rep1

description:
Gene expression profiling from human TGCT cell line, Susa
Replicate 1 of 2


title: GCT27_rep2

description:
Gene expression profiling from human TGCT cell line, GCT27
Replicate 2 of 2


title: Susa_cisplatin_resistant_rep1

description:
Gene expression profiling from human cisplatin-resistant TGCT cell line, SusaR
Replicate 1 of 2

source_name: Susa cell line, cisplatin-resistant

tag: Human TGCT cell line, cisplatin-resistant derivative, SusaR


title: 833K_cisplatin_resistant_rep2

description:
Gene expression profiling from human cisplatin-resistant TGCT cell line, 833KR
Replicate 2 of 2

source_name: 833K cell line, cisplatin-resistant

tag: Human TGCT cell line, cisplatin-resistant derivative, 833KR


title: 833K_rep1

description:
Gene expression profiling from human TGCT cell line, 833K
Replicate 1 of 2

source_name: 833K cell line

tag: Human TGCT cell line, 833K


title: DEC-PeptCD25neg2

status: Public on Mar 02 2010

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to the array in a cocktail containing control oligos at 45°C for 16 hours, rotated at 60rpm, in the Affymetrix GeneChip Hybridization Oven 640. After hybridization, the arrays were automatically cycled through buffer washes and stained with streptavidin R-phycoerythrin conjugate (Invitrogen) in the Affymetrix GeneChip Fluidics Station 400 (EukGE-WS2v4 protocol).

scan_protocol: After staining and washing, the arrays were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GCOS (GeneChip Operating Software) to automatically generate .CEL files.

data_processing: Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

source_name: CD4+ CD25- converted T cells from DEC-Pept treated mice

label_protocol: According to Affymetrix protocol

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: genotype/variation

value: HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a single injection of DEC-HAPeptide (50ng/mouse)

tag: age

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25- T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts

tag: number of mice per chip

tag: gender

value: male


title: 93-010_Tumor_20

tag: tumor

value: liposarcoma

tag: subtype


title: 833K_cisplatin_resistant_rep1

description:
Gene expression profiling from human cisplatin-resistant TGCT cell line, 833KR
Replicate 1 of 2


title: DEC-PeptCD25neg1


title: 833K_rep2

description:
Gene expression profiling from human TGCT cell line, 833K
Replicate 2 of 2


title: HomeoFoxp3neg1

source_name: CD4+ Foxp3-GFP- converted T cells from RAG-/- mice

value: BDC2.5/NOD/Foxp3-GFP- CD4+ T cells were transferred into NOD RAG-/- mice

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP- T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts


title: DEC-PeptConvertno1

source_name: CD4+ CD25+ converted T cells from DEC-Pept treated mice

value: HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a singel injection of DEC-HAPeptide (50ng/mouse)

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25+ T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts.


title: TregCD103+Klrg1+no1

source_name: CD4+ Foxp3-GFP+ CD103+ Klrg1+ Treg cells sorted from peripheral lymph nodes

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103+Klrg1+ T cells were sorted from the peripheral lymph nodes.


title: Susa_cisplatin_resistant_rep2

description:
Gene expression profiling from human cisplatin-resistant TGCT cell line, SusaR
Replicate 2 of 2


title: TregCD103-Klrg1-no2

source_name: CD4+ Foxp3-GFP+ CD103- Klrg1- Treg cells sorted from peripheral lymph nodes

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103-Klrg1- T cells were sorted from the peripheral lymph nodes.


title: DEC-PeptCD25neg3


title: TregCD103+Klrg1-no1

source_name: CD4+ Foxp3-GFP+ CD103+ Klrg1- Treg cells sorted from peripheral lymph nodes

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103+Klrg1- T cells were sorted from the peripheral lymph nodes.


title: DEC-PeptConvertno3


title: TregCD103-Klrg1-no1


title: HomeoFoxp3neg2


title: DEC-PeptCD25neg4


title: TregCD103+Klrg1+no2


title: TregCD103+Klrg1-no2


title: HomeoFoxp3neg3


title: vNS398-treated 2

tag: cell line

tag: treatment


title: DEC-PeptConvertno2

tag: cell type


title: HomeoConvertno3

source_name: CD4+ Foxp3-GFP+ converted T cells from RAG-/- mice

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+ T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts.


title: HomeoConvertno2


title: TconvLPno2

source_name: CD4+ Foxp3-GFP- T cells sorted from the small intestinal lamina propria

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP- T cells were sorted from the small intestinal lamina propria (cell isolation from Sun et al J. Exp. Med. 2007).


title: TregLPno2

source_name: CD4+ Foxp3-GFP+ T cells sorted from the small intestinal lamina propria

value: CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+ T cells were sorted from the small intestinal lamina propria (cell isolation from Sun et al J. Exp. Med. 2007).


title: TconvLPno1


title: TregLPno1


title: HIV-HRN sample 9

first: Paul

last: McLaren

address: 77 Avenue Louis Pasteur, NRB150

description: Gene expression data from unstimulated CD4+ T cells of an HIV resistant commercial sex-worker from Nairobi, Kenya

hyb_protocol: Hybridization was carried out following the manufacturers instructions for the Affymetrix U133 Plus 2.0 GeneChips

scan_protocol: Scannig was performed on an Affymetrix GeneChip Scanner 3000

data_processing: Data were analysed using ArrayAssist software (Stratagene). Data were normalized unsing the PLIER algorithm

label_protocol: 50ng of total RNA was amplified and labeled using GeneChip Two-Cycle Target Labeling Kits (Affymetrix) and MEGA script T7 kits (Ambion) following manufacturers instructions.

growth_protocol: PBMC isolated from whole blood were cultured for 24 hours in RPMI+10%FCS, 2% pen/strep at 37C and 5% CO2

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini kit plus kits following manufacturers instructions

treatment_protocol: PBMC were unstimulated and negatively selected for being CD4+ by magentic bead purification

tag: HIV high-risk negative


title: HIV-HRN sample 7


title: HIV-HRN sample 3


title: HIV-HRN sample 6


title: HIV-HRN sample 8


title: HIV-R sample 9

tag: HIV resistant


title: HIV-HRN sample 1


title: HIV-R sample 7


title: MCF10A cells; biological rep 3

city: Nashville

first: Linda

last: Sealy

address: 2202 Pierce Ave

department: Cancer Biology

institute: Vanderbilt University Medical Center

description: gene expression

hyb_protocol: The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Genome Plus 2.0 Array  containing 54,000 sets of 11 to 25-mer oligomers, representing 47,000 mouse transcripts (38,500 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.

data_processing: Three independent  replicates were performed to allow for statistical analysis.  CEL files were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis)  (Bolstad et al., 2003).  All probesets showing at least a 2 fold change in one of the C/EBPbeta-2 overexpressing MCF10A cells compared to parental MCF10A were tested with a Welch’s t-test and a p-value cutoff of 0.05. This restriction tested 3,721 genes.  As a result 443 genes were found to be differentially expressed upon C/EBPbeta-2 overexpression in MCF10A cells.  Of these differentially expressed genes, 86 were found to be upregulated 2 fold or more while 121 were found to be downregulated 2 fold or more.

source_name: MCF10A cells

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA).  Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides

growth_protocol: Cells were grown  in a 1:1 mixture of Dulbecco’s modified Eagle medium (DMEM) and Ham’s F12 containing 2.5 mM L-glutamine and supplemented with 5% horse serum (Sigma, St. Louis MO), 10 micrograms/ml recombinant human insulin (Invitrogen Corp., Grand Island NY), 0.5 micrograms/ml hydrocortisone, 10 ng/ml epidermal growth factor (EGF), 100 ng/ml cholera toxin, 50 U/ml penicillin, and 50 micrograms/ml streptomycin.

extract_protocol: RNeasy Mini kit and RNase-Free DNase kit (Qiagen)

value: MCF10A cells


title: HIV-R sample 5

department: Medicine


title: MCF10A cells with C/EBPbeta-2; biological rep 2

description: gene expression

source_name: MCF10A cells with C/EBPbeta-2


title: HIV-R sample 8


title: HIV-R sample 6


title: HIV-R sample 4


title: HIV-HRN sample 2


title: MCF10A cells with C/EBPbeta-2; biological rep 3

description: gene expression


title: MCF10A cells; biological rep 2

description: gene expression


title: HIV-R sample 2


title: MCF10A cells with C/EBPbeta-2; biological rep 1

description: gene expression


title: HIV-R sample 3


title: MCF10A cells; biological rep 1

description: gene expression


title: HIV-HRN sample 4


title: HIV-R sample 1


title: HomeoConvertno1


title: 1390 (HIV+)

status: Public on Mar 01 2010

city: Omaha

first: Karen

last: Deffenbacher

state: NE

address: 987660 Nebraska Medical Center

department: Pathology and Microbiology

institute: University of Nebraska Medical Center

description: Gene expression data from frozen ARL tumor specimen

hyb_protocol: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed by the Affymetrix 3000 Scanner.

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

source_name: Frozen Tumor Biopsy_LN

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

extract_protocol: Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

tag: specimen

value: frozen ARL tumor biopsy

tag: tumor biopsy origin

value: LN

tag: age at diagnosis

value: Male

tag: pathology diagnosis

value: DLBCL (PC)

tag: molecular diagnosis

value: ABC DLBCL

tag: ebv status

value: positive


title: HIV-HRN sample 5


title: S03 (HIV+)

source_name: Frozen Tumor Biopsy_Spinal/Epidural

value: Spinal/Epidural


title: 1376 (HIV+)

source_name: Frozen Tumor Biopsy_Sm Bowel

value: Sm Bowel

value: High Grade, UC

value: negative


title: 1392 (HIV+)

source_name: Frozen Tumor Biopsy_Neck

value: Neck

value: GCB DLBCL


title: 1379 (HIV+)

source_name: Frozen Tumor Biopsy_Hilar/Lung

value: Hilar/Lung

value: DLBCL


title: 1383 (HIV+)

source_name: Frozen Tumor Biopsy_Colon

value: Colon


title: 1388 (HIV+)

source_name: Frozen Tumor Biopsy_Pleural Fluid

value: Pleural Fluid


title: 1378 (HIV+)

source_name: Frozen Tumor Biopsy_Jejunum

value: Jejunum


title: 1375 (HIV+)

value: frozen ARL tumor biopsy


title: 1373 (HIV+)

value: LN

value: BL


title: S02 (HIV+)

value: Male

value: DLBCL (PC)


title: 1380 (HIV+)

value: positive


title: 1387 (HIV+)

source_name: Frozen Tumor Biopsy_Hilar

value: Hilar


title: 1391 (HIV+)

source_name: Frozen Tumor Biopsy_Mediastinal/Atrial

value: Mediastinal/Atrial


title: 1377 (HIV+)


title: 1397 (HIV+)

value: ABC DLBCL


title: 1374 (HIV+)

source_name: Frozen Tumor Biopsy_Lung

value: Lung

value: negative


title: Ihhd/d, Replicate 1

city: Houston

first: Heather

middle: L

last: Franco

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Ihhd/d, Replicate 1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed using dCHIP using invariant set normalization.  A two sample comparison according to the following criteria: lower bound of 90% confidence interval of fold-change greater than 1.2 and an absolute value of difference between group means greater than 50 was performed.

source_name: mouse uterus, mutant SmoM2

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

growth_protocol: Mice were maintained in the designated animal care facility at Baylor College of Medicine according to the institutional guidelines for the care and use of laboratory animals.  Ihhf/f mice were obtained from Dr. Beate Lanske and were crossed to the PRcre mouse model to conditionally ablate Indian hedeghog in the uterus.

extract_protocol: Total RNA was extracted from uterine tissues using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.

tag: genotype/variation

value: Ihhd/d


title: Ihhd/d, Replicate 3

description: Ihhd/d, Replicate 3


title: Ihhd/d, Replicate 2

description: Ihhd/d, Replicate 2


title: Ihhf/f, Replicate 2

description: Ihhf/f, Replicate 2

source_name: mouse uterus, wild-type SmoM2

value: Ihhf/f (Control)


title: Ihhf/f, Replicate 3

description: Ihhf/f, Replicate 3


title: BMP4

city: Beijing

first: Bing

last: Zhou

address: Datun Road

department: Center for Molecular Systems Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description:
3 samples:
Untreated control, R1 ES cells
BMP4 (20ng/ml) 4h, R1 ES cells
Noggin (100ng/ml) 4h, R1 ES cells

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using confocal laser scanner.

data_processing: Signal intensity were normalized with RMA algorithm

source_name: murine R1 ES cells, treated with BMP4

label_protocol: Standard Affymetrix procedures

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's guidelines Label protocol Standard Affymetrix procedures.

treatment_protocol: Undifferentiated R1 ES cells were treated for 4 h with 20ng/ml BMP4.

value: embryonic stem cells

tag: differentiation state

value: undifferentiated

tag: treatment time

value: 4 hours


title: Control

source_name: murine R1 ES cells, untreated

treatment_protocol: Undifferentiated R1 ES cells were untreated.

value: untreated


title: Noggin

source_name: murine R1 ES cells, treated with noggin

treatment_protocol: Undifferentiated R1 ES cells were treated for 4 h with 100ng/ml noggin.

value: noggin


title: Ihhf/f, Replicate 1

description: Ihhf/f, Replicate 1


title: Myc Lo R2

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description: WT Lineage negative, c-Kit and Sca1 (LSK) positive c-Myc eGFP Lo expressing bone marrow progenitors

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.

source_name: Total RNA, LSK, c-Myc-eGFP Lo

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

extract_protocol: Qiagen RNEasy Plus Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: total bone marrow was flushed from freshly dissected femurs and sorted for Lineage negative, c-Kit and Sca1 (LSK) progenitor cells based on c-Myc-eGFP protein expression (Hi and Lo)

tag: strain


title: Myc Hi R2

description: WT Lineage negative, c-Kit and Sca1 (LSK) positive c-Myc eGFP Hi expressing bone marrow progenitors

source_name: Total RNA, LSK, c-Myc-eGFP Hi


title: Myc Lo R1


title: Myc Hi R1


title: cochlea at P13, ko, biological rep 1

first: Douglas

last: Vetter

address: 136 Harrison Ave.

department: Dept. Neuroscience

institute: Tufts Univ. Sch. Med.

description:
Gene expression data from cochleas of  nicotinic cholinergic receptor alpha9 subunit knockout mice at P13.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P13_a9knockout_rep1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hrs at 45C on Affymetrix Mouse430.2 Mouse Genome GeneChip. Subsequently, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed using Bioconductor (R-project)  packages. Specifically, gene expression data were normalized using RMA background correction, quantile normalization and Tukey biweight summary method. Data were filtered on variance and differentially expressed genes were identified using LIMMA library.

source_name: Cochleae from a9 null mice at P13

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol for One-Cycle Target Labeling Assay from 5 ug of total RNA.

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

value: 129S6 x CBA/CaJ

tag: tissue

value: cochlea

tag: genotype

value: a9 knockout

tag: age


title: cochlea at P3, ko, biological rep 1

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P3.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P3_a9knockout_rep1

source_name: Cochleae from a9 null mice at P3


title: cochlea at P3, ko, biological rep 2

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P3.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P3_a9knockout_rep2


title: cochlea at P7, wt, biological rep 2

description:
Gene expression data from cochleas of wild type mice at P7.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P7_wildtype_rep2

source_name: Cochleae from wild type mice at P7

value: wild type


title: cochlea at P7, ko, biological rep 2

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P7.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P7_a9knockout_rep2

source_name: Cochleae from a9 null mice at P7


title: cochlea at P13, ko, biological rep 2

description:
Gene expression data from cochleas of  nicotinic cholinergic receptor alpha9 subunit knockout mice at P13.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P13_a9knockout_rep2


title: cochlea at P7, wt, biological rep 3

description:
Gene expression data from cochleas of wild type mice at P7.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P7_wildtype_rep3


title: cochlea at P60, ko, biological rep 3

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P60.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P60_a9knockout_rep3

source_name: Cochleae from a9 null mice at P60


title: cochlea at P7, ko, biological rep 3

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P7.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P7_a9knockout_rep3


title: cochlea at P60, wt, biological rep 3

description:
Gene expression data from cochleas of wild type mice at P60.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P60_wildtype_rep3

source_name: Cochleae from wild type mice at P60


title: cochlea at P7, wt, biological rep 1

description:
Gene expression data from cochleas of wild type mice at P7.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P7_wildtype_rep1


title: cochlea at P60, wt, biological rep 2

description:
Gene expression data from cochleas of wild type mice at P60.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P60_wildtype_rep2


title: cochlea at P7, ko, biological rep 1

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P7.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P7_a9knockout_rep1


title: cochlea at P60, ko, biological rep 1

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P60.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P60_a9knockout_rep1


title: cochlea at P13, wt, biological rep 3

description:
Gene expression data from cochleas of wild type mice at P13.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P13_wildtype_rep3

source_name: Cochleae from wild type mice at P13


title: cochlea at P13, ko, biological rep 3

description:
Gene expression data from cochleas of  nicotinic cholinergic receptor alpha9 subunit knockout mice at P13.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P13_a9knockout_rep3


title: cochlea at P13, wt, biological rep 1

description:
Gene expression data from cochleas of wild type mice at P13.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P13_wildtype_rep1


title: cochlea at P60, wt, biological rep 1

description:
Gene expression data from cochleas of wild type mice at P60.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P60_wildtype_rep1


title: cochlea at P3, wt, biological rep 2

description:
Gene expression data from cochleas of wild type mice at P3.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P3_wildtype_rep2

source_name: Cochleae from wild type mice at P3


title: cochlea at P60, ko, biological rep 2

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P60.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P60_a9knockout_rep2


title: cochlea at P3, wt, biological rep 3

description:
Gene expression data from cochleas of wild type mice at P3.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P3_wildtype_rep3


title: TGFb-HT_10cGy-4wk_repeat_2

hyb_protocol: 12.5 micrograms of fragmented cRNA was hybridized for 16 hr to the Affymetrix MG 430 2.0 arrays using GeneChip Hybridization Oven 640 and Genechip® fluidics station FS 450, following standard Affymetrix protocols.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by Affymetrix GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent GeneSpring GX10 program. No further adjustments were made to the data in the table.

label: biotinylated UTP

source_name: 4th mammary gland, TGFb-HT, 4wks post 10cGy

label_protocol: 80 ng of total RNA were used to prepare cRNA following the Affymetrix 3’IVT Express Kit labeling protocol

growth_protocol: 10-week-old Balb/c Tgfb1 wild type and  heterozygote littermates were used.

extract_protocol: Total RNA was extracted using Trizol Reaget (Invitrogen), according to manufacturer's instructions.

treatment_protocol: Two days prior to irradiation with 10cGy ionizing radiation, estrus cycles were normalized in all mice by injection with estrogen and progesterone mixture.  Mice were irradiated or sham-irradiated, and then housed for either 1 week or 4 weeks before whole 4th (inguinal) mammary glands were removed.  Lymph nodes were removed before RNA extraction from posterior third of inguinal mammary gland.

value: Balb/c TGFb1-HT

value: 10 week old

value: posterior 3rd of inguinal gland, no lymph node


title: TGFb-HT_10cGy-1wk_repeat_2

source_name: 4th mammary gland, TGFb-HT, 1wk post 10cGy


title: TGFb-HT_10cGy-4wk_repeat_1


title: TGFb-HT_10cGy-4wk_repeat_3


title: TGFb-HT_sham-1wk_repeat_3

source_name: 4th mammary gland, TGFb-HT, 1wk post sham


title: cochlea at P3, wt, biological rep 1

description:
Gene expression data from cochleas of wild type mice at P3.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P3_wildtype_rep1


title: TGFb-HT_10cGy-1wk_repeat_1


title: cochlea at P13, wt, biological rep 2

description:
Gene expression data from cochleas of wild type mice at P13.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P13_wildtype_rep2


title: wild-type_sham-1wk_repeat_3

source_name: 4th mammary gland, wild-type, 1wk post sham

value: Balb/c wild-type


title: wild-type_10cGy-1wk_repeat_3

source_name: 4th mammary gland, wild-type, 1wk post 10cGy


title: wild-type_sham-1wk_repeat_1


title: wild-type_10cGy-4wk_repeat_2

source_name: 4th mammary gland, wild-type, 4wks post 10cGy


title: wild-type_10cGy-1wk_repeat_1


title: wild-type_10cGy-4wk_repeat_3


title: TGFb-HT_sham-1wk_repeat_1


title: TGFb-HT_sham-1wk_repeat_2


title: wild-type_10cGy-4wk_repeat_1


title: cochlea at P3, ko, biological rep 3

description:
Gene expression data from cochleas of nicotinic cholinergic receptor alpha9 subunit knockout mice at P3.
The mice are a hybrid strain. They are 129S6 (old nomenclature: 129Sv/Ev) x CBA/CaJ. They have been backcrossed to the CBA/CaJ line at least 7 generations.
P3_a9knockout_rep3


title: mKras-MEFs-6

city: Stanford

last: Sweet-Cordero

address: CCSR-1215B, 269 Campus Dr

department: Pediatrics

institute: Stanford University

description: Affymetrix protocol

hyb_protocol: Standard Affymetrix protocols were used.

data_processing: Microarray data was normalized with Expression Console software (Affymetrix, Santa Clara) using RMA algorithms for normalization.

source_name: K-rasLSL-G12D MEFs were infected with adenoviral Cre to activate K-ras

extract_protocol: RNA was isolated using Trizol 7 days after infection. RNA was further prepared by passage over an RNeasy column. cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430_2 was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).

value: Mouse embryonic fibroblasts (MEFs)

tag: genome/variation

value: K-ras mut


title: mKras-Wt1 null-MEFs-5

description: Affymetrix protocol

scan_protocol: Standard Affymetrix protocols were used.

source_name: MEFs were infected with adenoviral Cre to activate K-ras and delete Wt1

tag: cell type

value: K-ras mut/Wt1-null


title: wild-type_10cGy-1wk_repeat_2


title: mKras-Wt1 null-MEFs-4

description: Affymetrix protocol

label_protocol: Standard Affymetrix protocols were used.


title: mKras-MEFs-5

description: Affymetrix protocol


title: mKras-Wt1 null-MEFs-2

description: Affymetrix protocol


title: wild-type_sham-1wk_repeat_2


title: mKras-Wt1 null-MEFs-6

description: Affymetrix protocol


title: mKras-MEFs-4

description: Affymetrix protocol


title: mKras-Wt1 null-MEFs-7

description: Affymetrix protocol


title: mKras-Wt1 null-MEFs-1

description: Affymetrix protocol


title: MEFs-4

description: Affymetrix protocol

source_name: MEFs were treated with an nonspecific adenoGFP virus.


title: mKras-MEFs-3

description: Affymetrix protocol


title: MEFs-5

description: Affymetrix protocol


title: mKras-Wt1 null-MEFs-3

description: Affymetrix protocol


title: MEFs-3

description: Affymetrix protocol


title: MEFs-2

description: Affymetrix protocol


title: Wt1-null MEFs-3

description: Affymetrix protocol

source_name: WT1-null mouse embryonic fibroblasts

treatment_protocol: Wt1f/f MEFs were infected with adenoviral Cre to knockout Wt1.


title: Wt1-null MEFs-4

description: Affymetrix protocol

extract_protocol: RNA was isolated using Trizol 7 days after infection. RNA was further prepared by passage over an RNeasy column. cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430_2containing was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).


title: N2A KDM7 KD2

city: Fukuoka

first: Yuichi

last: Tsukada

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu university

description: neuroblastoma cell line Neuro2A transfected with vector 2 for KDM7 knock down

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Srandard culture condition for Neuro2A

extract_protocol: Total RNA was extracted from cells and purified with the use of Qiashredder spin-columns (Qiagen) and an RNeasy Plus Mini Kit (Qiagen).

tag: cell line

value: Neuro2A (N2A)

value: neuroblastoma


title: Upper-SP_rep2

first: Grant

middle: Anthony

last: Challen

department: Center For Cell And Gene Therapy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MOE 430 2.0 chips. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450

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

data_processing: The raw image and intensity files were generated using GCOS 1.0 software. Normalization and model-based expression measurements were performed with GC-RMA.

source_name: Mouse bone marrow upper-SP hematopoietic stem cells

label_protocol: Biotinylated cRNA was prepared with the MessageAMP aRNA kit (Ambion) with 2 ronds of in vitro transcription according to the manufacturers protocols

growth_protocol: Mice were house in a specific-pathogen free facility and experiments performed in accordance with Baylor College of Medicine institutional guidelines

extract_protocol: Total RNA was extracted with the RNAqueous kit (Ambion) according to the manufacturers protocols

treatment_protocol: HSCs were purified on a MoFlo cell sorter by phenotype of lower- or upper-SP / Lineage- / Sca-1+ / c-Kit+.  Samples were reflowed to assess purity and in all cases it was >98%

value: 10-weeks old

tag: gender

value: male

value: bone marrow

value: Upper-SP HSC


title: N2A empty vector

description: neuroblastoma cell line Neuro2A transfected with empty vector

source_name: Neuro2A transfected with empty vector


title: N2A KDM7 KD1

description: neuroblastoma cell line Neuro2A transfected with vector 1 for KDM7 knock down


title: MEFs-1

description: Affymetrix protocol


title: Wt1-null MEFs-5

description: Affymetrix protocol


title: Upper-SP_rep1


title: N2A EGFP KD

description: neuroblastoma cell line Neuro2A transfected with vector for EGFP knock down


title: Upper-SP_rep3


title: Lower-SP_rep1

source_name: Mouse bone marrow lower-SP hematopoietic stem cells

value: Lower-SP HSC


title: N2A

description: neuroblastoma cell line Neuro2A


title: Lower-SP_rep2


title: Lower-SP_rep3