title: HVDRR EBV-transformed B-cells, biological replicate 2

description:
Gene expression data from a B-cell line derived from a patient with hereditary vitamin D resistant rickets
JK_minusVitD_2


title: SEZ_GFPprom, biological replicate 4

status: Public on Nov 19 2010

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

hyb_protocol: According to the Affymetrix expression protocol

data_processing: RMA probeset summary and normalisation employing the loess smoother

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: neural stem

label_protocol: MessageAmp (1. round) and MessageAmp II-Biotin Enhanced (2.round) 2-cycle protocoll (Ambion)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: FACS sorting was performed as described (Pinto et al. Mol Cell Neurosci. 2008)

tag: cell type

value: neural stem

tag: tissue

value: the subependymal zone of eight weeks old hGFAP eGFP mice (Nolte C. et al. Glia. 2001)

tag: selection protocol

value: Selected by FACS for positive staining for GFP and prominin (Prom1)


title: E2_ICI_182_780_23

status: Public on May 09 2012

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

hyb_protocol: Gene Chip hG-133 plus 2.0 (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing:
GC-RMA (JMP Genomics 4.1), adjustment for batch effects (Distance-weighted discrimination)
Log2 GC-RMA, quantile normalization, summary by median polish, adjusted for batch effects.

label: Biotin

organism: Homo sapiens

source_name: MCF-7 cells

label_protocol: Ambion MessageAmp Premier Labeling

growth_protocol: MCF7 cells were plated in 6 well culture dishes at a density of 4x105 cells per well.

extract_protocol: RNA isolation (BioRad, Aurum total RNA mini kit) was performed per kit manufacturer’s instructions.

treatment_protocol: 48 hours after plating, cells were treated with ER ligands using 1 nM final concentration vehicle (ethanol) or E2 in the presence or absence of vehicle (DMSO) or SERM (100 nM).  After 24 hours treatment, cells were washed once in PBS prior to lysis.

tag: cell line

tag: agonist

tag: antagonist

tag: co-treatment


title: HVDRR EBV-transformed B-cells treated with vitamin D, biological replicate 1

description:
Gene expression data from a B-cell line derived from a patient with hereditary vitamin D resistant rickets
JK_plusVitD_3

hyb_protocol: According to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: According to the Affymetrix expression protocol

data_processing: RMA probeset summary and quantile normalisation (Expression console)

source_name: HVDRR EBV-transformed B-cells

label_protocol: MessageAmp II-Biotin Enhanced 1-cycle protocoll (Ambion)

growth_protocol: Cells were maintained in RPMI 1640 medium, 37°C in 5% CO2

treatment_protocol: Vitamin D treatment (1,25(OH)2D3 (Biomol, USA))

tag: individual

value: Patient with hereditary vitamin D resistant rickets

tag: gender

value: female

value: B-cell

tag: agent

value: vitamin D


title: SEZ_Prom, biological replicate 1

value: Selected by FACS for positive staining for prominin (Prom1)


title: SEZ_GFPprom, biological replicate 3


title: SEZ_Prom, biological replicate 2


title: Wild type EBV-transformed B-cells, biological replicate 2

description:
Gene expression data from a B-cell line derived from a healthy donor
wt_minusVitD_2

source_name: Wild type EBV-transformed B-cells

value: Healthy donor


title: Adrenal gland medullary hyperplasia, biological replicate 02

description: Gene expression data from adrenal gland medullary hyperplasia

data_processing: RMA probeset summary and quantile normalisation

organism: Rattus norvegicus

source_name: Adrenal gland medullary hyperplasia from p27Kip1 mutant rats

extract_protocol: Trizol extraction and RNeasy Mini Kit (Qiagen) including DNase treatment

tag: strain

value: Sprague–Dawley white eye/Wistar–Kyoto

tag: age

value: 2 months

tag: genotype

value: p27Kip1 (Cdknb1) mutant


title: Adrenal gland medullary hyperplasia, biological replicate 03


title: Adrenal gland medullary hyperplasia, biological replicate 07

value: male


title: Adrenal gland medulla pool 02

description: Gene expression data from adrenal gland medulla

source_name: Adrenal gland medulla from wildtype rats, pool of 3 animals

value: wildtype


title: SEZ_GFPprom, biological replicate 1


title: Adrenal gland medullary hyperplasia, biological replicate 05


title: Adrenal gland medulla pool 01

source_name: Adrenal gland medulla from wildtype rats, pool of 2 animals


title: Adrenal gland medullary hyperplasia, biological replicate 08


title: SEZ_CD24, biological replicate 1

source_name: ependymal

value: ependymal

value: Selected by FACS for positive staining for CD24 (CD24a antigen)


title: Adrenal gland medullary hyperplasia, biological replicate 01


title: Adrenal gland medullary hyperplasia, biological replicate 04


title: SEZ_GFPprom, biological replicate 2


title: SEZ_CD24, biological replicate 2


title: Adrenal gland medulla pool, biological replicate 1

value: 10 months


title: Adrenal gland medulla pool, biological replicate 2

value: 12+17 months


title: Adrenal gland medullary hyperplasia, biological replicate 06


title: SEZ_GFP, biological replicate 2

value: neural stem

value: the subependymal zone of eight weeks old hGFAP eGFP mice (Nolte C. et al. Glia. 2001)

value: Selected by FACS for positive staining for GFP


title: SEZ_GFP, biological replicate 1


title: DIEC_GFP, biological replicate 3

source_name: astrocytes

value: astrocytes

value: diencephalon of eight weeks old hGFAP eGFP mice (Nolte C. et al. Glia. 2001)


title: DIEC_GFP, biological replicate 2


title: DIEC_GFP, biological replicate 4


title: Adrenal gland pheochromocytoma, biological replicate 04

description: Gene expression data from adrenal gland pheochromocytoma

source_name: Adrenal gland pheochromocytoma from p27Kip1 mutant rats

value: 9 months


title: Adrenal gland pheochromocytoma, biological replicate 01

value: 8 months

value: female


title: Adrenal gland pheochromocytoma, biological replicate 03

value: Sprague–Dawley white eye/Wistar–Kyoto


title: Adrenal gland pheochromocytoma, biological replicate 02


title: DIEC_GFP, biological replicate 1


title: scpk/WT/83

status: Public on May 06 2005

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

description: unfractionated thymocytes from a 3-week old WT mouse (C57Bl6 background)

source_name: WT thymocytes


title: Thymic tumor from mouse RJ21

status: Public on Sep 03 2010

description: gene expression data from a thymic tumor from an Ikaros deficient thymic lymphoma with a Notch promoter/exon1 deletion

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 7G System

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. Target intensity was set at 100.

source_name: transformed T cells from a mouse thymic lymphoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNAs were extracted with the RNAeasy kit, following the manufacturer's instructions (including DNAse I treatment)

treatment_protocol: Thymic lymphomas were dissected from euthanized sick mice and tumor cells collected after tissue disruption between frosted ends of microscope slides

value: 8-10 weeks

tag: disease state

value: lymphoma

value: thymus

value: transformed T cells

tag: genotype/variation

value: IkL/L Notch1f/f CD4-Cre+


title: scpk/ikLL/57

description: unfractionated thymocytes from a 3-week old IkL/L mouse (C57Bl6 background)

source_name: IkL/L thymocytes


title: scpk/ikLLtumor/163

description: advanced thymic tumor from a homozygote mouse with a hypomorphic Ikaros mutation

source_name: thymic tumor IKL/L mouse


title: scpk/ikLL/192


title: Thymic tumor from mouse RJ11

description: gene expression data from a thymic tumor from an Ikaros deficient thymic lymphoma

value: 18-20 weeks

value: IkL/L Notch1+/+ CD4-Cre+


title: scpk/WT/17

source_name: WT thymocyte


title: Thymic tumor from mouse RJ10


title: scpk/ikLLtumor/21

source_name: thymic tumor IkL/L mouse


title: Thymic tumor from mouse RJ12


title: scpk/ikLLtumor/77


title: Thymic tumor from mouse RJ27


title: scpk/ikLLtumor/90


title: scpk/ikLLtumor/126


title: Thymic tumor from mouse RJ28


title: scpk/ikLLtumor/146

source_name: IkL/L mouse thymic tumor


title: YP1

status: Public on Aug 21 2002

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: RNA was obtained from vastus lateralis muscle biopsies taken from 8 healthy men, 21-24 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software.

source_name: human muscle


title: B4

description:
Vastus lateralis muscle biopsy from 73 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 software.
Keywords = muscle, aging


title: YP2

description: RNA was obtained from vastus lateralis muscle biopsies from 4 healthy men, 22-31 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software.


title: OP2

description:
RNA obtained from vastus lateralis muscle biopsies from 8 healthy men, 62-72 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software.
Keywords = muscle, aging


title: B2

description:
Vastus lateralis muscle biopsy from 69 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 sotware.
Keywords = muscle, aging


title: A4

description: Vastus lateralis muscle biopsy from 26 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 software.


title: B1

description: Vastus lateralis muscle biopsy from 69 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 software.


title: B3

description:
Vastus lateralis muscle biopsy from 68 year old healthy male. Analysis done with Affymetrix Microarray Suite 5.0 software.
Keywords = muscle, aging


title: A3

description: Vastus lateralis biopsy from healthy 24 year old male. Analysis done with Affymetrix Microarray Suite 5.0 software


title: Y132

description:
Vastus lateralis muscle biopsy taken from 29 year old healthy male volunteer. Analysis done with Affymetric Microarray Suite 5.0 software.
Keywords = muscle, aging


title: A1

description: Vastus lateralis muscle biopsy from healthy 25 year old male volunteer. Analysis done with Affymetrix Microarray Suite 5.0 software


title: OP1

description:
RNA obtained from vastus lateralis biopsies from 7 healthy men, 66-77 years old. RNA was pooled before cDNA synthesis. Analysis done with Affymetrix Microarray Suite 5.0 software.
Keywords = muscle, aging