title: pDC flu 4h, biological rep1

city: Philadelphia

first: Amaya

middle: I

last: Wolf

state: PA

address: 3601 Spruce street

institute: Wistar Institute

description: Gene expression data from  activated plasmacytoid dendritic cells cultured with influenza A/PR/8 virus for 4h

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99oC for 5 min and hybridized for 16 h at 45oC to GeneChip microarrays.  The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.  Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: The GeneChip 3000 scanner was used to collect fluorescence signal after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Data were processed using Affymetrix GCOS v1.4 software and probe intensity files (.cel files) were further analyzed using the GeneSpring v7.0 software (Silicon Genetics). GCRMA algorithm was used to summerize and normalize data.

source_name: pDC cultured in medium with PR8 (flu) for 4h

label_protocol: 5ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporates the T7 promoter.  Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP using the Enzo High-Yield amplification kit.

growth_protocol: DPEGFPxRag1-/- were injected 12-14 days prior to sort with 2x10^6 B16F10-Flt-3L cells, which leads to expansion of immature pDCs in spleens of mice

extract_protocol: isolation of total RNA was performed using the Rneasy Micro Kit according to manufacturer's instructions (Qiagen)

treatment_protocol: pDC were sorted from spleens of Flt-3L-treated DPExRag1-/- mice  and cultured  at 1x106/ml for 1h with 300 HAU/ml purified and UV-inactivated influenza A/PR/8 virus in complete media (RPMI supplemented with 10% heat-inactivated FBS (Valley Biomedical, Inc.), Penicillin/Streptomycin (Invitrogen), 10mM HEPES (Invitrogen), 2mM L-Glutamine (Invitrogen), 10mM pyruvate (Invitrogen), 50µM 2-mercaptoethanol (Sigma).

tag: pDC isolated from spleen of Flt-3L-treated DPEGFPxRag1-/- mice


title: HepG2/C3A cells cysteine depletion for 42 h (long -Cys) #1

status: Public on Dec 13 2007

type: RNA

city: Ithaca

first: Wei

last: Wang

state: NY

address: T2-003 Vet Res Tower

country: USA

institute: Cornell University

description: Affymetrix standard

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Affymetrix 1 cycle

extract_protocol: Qiagen RNeasy

tag: C3A cells derived from HepG2 cells; human hepatoma cell line; study of cysteine deprivation


title: HepG2/C3A cells cysteine depletion for 42 h (long -Cys) #2

description: Affymetrix standard

source_name: C3A cells derived from HepG2 cells; human hepatoma cell line


title: pDC CpG 4h, biological rep3

description: Gene expression data from  activated plasmacytoid dendritic cells cultured with CPG for 4h

organism: Mus musculus

source_name: pDC cultured in medium with CpG for 4h

treatment_protocol: pDC were sorted from spleens of Flt-3L-treated DPExRag1-/- mice  and cultured  at 1x106/ml for 4h with 5 µg/ml CpG 1826 (MWG) in complete media (RPMI supplemented with 10% heat-inactivated FBS (Valley Biomedical, Inc.), Penicillin/Streptomycin (Invitrogen), 10mM HEPES (Invitrogen), 2mM L-Glutamine (Invitrogen), 10mM pyruvate (Invitrogen), 50µM 2-mercaptoethanol (Sigma).


title: pDC CpG 4h, biological rep2


title: HepG2/C3A cells cysteine depletion for 42 h (long -Cys)  #3

description: Affymetrix standard


title: HepG2/C3A cells control medium for 42 h  (Long +Cys) #7

description: Affymetrix standard

source_name: human cell line


title: pDC CpG 4h, biological rep1


title: pDC flu 4h, biological rep2


title: pDC medium 4h, biological rep2

description: Gene expression data from  plasmacytoid dendritic cells cultured in medium for 4h

source_name: pDC cultured in medium for 4h

treatment_protocol: pDC were sorted from spleens of Flt-3L-treated DPExRag1-/- mice  and cultured  at 1x106/ml for 4h in complete media (RPMI supplemented with 10% heat-inactivated FBS (Valley Biomedical, Inc.), Penicillin/Streptomycin (Invitrogen), 10mM HEPES (Invitrogen), 2mM L-Glutamine (Invitrogen), 10mM pyruvate (Invitrogen), 50µM 2-mercaptoethanol (Sigma).


title: pDC CpG 1h, biological rep1

description: Gene expression data from activated plasmacytoid dendritic cells with CPG for 1h

source_name: pDC cultured in medium with CpG for 1h

treatment_protocol: pDC were sorted from spleens of Flt-3L-treated DPExRag1-/- mice  and cultured  at 1x106/ml for 1h with 5 µg/ml CpG 1826 (MWG) in complete media (RPMI supplemented with 10% heat-inactivated FBS (Valley Biomedical, Inc.), Penicillin/Streptomycin (Invitrogen), 10mM HEPES (Invitrogen), 2mM L-Glutamine (Invitrogen), 10mM pyruvate (Invitrogen), 50µM 2-mercaptoethanol (Sigma).


title: pDC flu 1h, biological rep1

description: Gene expression data from activated plasmacytoid dendritic cells with influenza A/PR8 virus  (flu) for 1h

source_name: pDC cultured in medium with PR8 (flu) for 1h


title: pDC CpG 1h, biological rep2


title: pDC medium 4h, biological rep1


title: pDC medium 4h, biological rep3


title: pDC flu 1h, biological rep2


title: LA-2

city: Cork

first: Eileen

middle: Frances

last: Murphy

address: Biosciences Institute

department: Department of Food & Nutritional Sciences

country: Ireland

institute: University College Cork

description: Caco-2 cells were treated with Linoleic acid for 12 d

hyb_protocol: see manufacturer's website

scan_protocol: see manufacturer's website

data_processing: GCRMA-calculated Signal intensity

source_name: Caco-2 cells - Linoleic acid treated

label_protocol: see manufacturer's website

extract_protocol: Trizol

tag: Human colon carcinoma cell line


title: cis-9, trans-11 CLA treated

description: Caco-2 cells were treated with cis-9, trans-11 for 12 d

source_name: Caco-2 cells - cis-9 treated


title: 9.11-3


title: LA-3


title: LA-1


title: 10.12-3

description: Caco-2 cells were treated with trans-10, cis-12 CLA for 12 d

source_name: Caco-2 cells - cis-12 CLA treated


title: 9.11-2


title: trans-10, cis-12 CLA treated

hyb_protocol: see manufactures website

scan_protocol: see manufacture's website

label_protocol: see manufactures website


title: SOCS3 Cre plus C

status: Public on Dec 12 2007

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

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

data_processing: Bioconductor GCRMA normalization log2

source_name: liver

label_protocol: Total RNA (2 ug) was labeled and hybridized to the Mouse Genome 430 2.0 arrays and hybridized according to manufacurer’s instructions.

extract_protocol: Total RNA was isolated from whole liver tissue harvested 18h after PH, as described in Supplemental materials and methods.

treatment_protocol: Hepatocyte-specific excision of the Socs3 gene was achieved by breeding Socs3 fl/fl mice with mice expressing the Cre recombinase transgene under control of the albumin promoter (Alb-Cre+), yielding Socs3 h-KO mice (SOCS3 Cre plus). Socs3 fl/fl, Alb-Cre- littermates were used as controls for all experiments, and are referred to as SOCS3 Cre minus. All mice (C57BL/6) were free of Helicobacter species, housed in a specific pathogen free facility with 12-h light/dark cycles with free access to standard food and water. 2/3 partial hepatectomies (PH) were performed as previously described.


title: 10.12-2


title: TRT_compound B_4h_rep2

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 4h
replicate 2

hyb_protocol: cRNA fragmented samples were hybridized on Affymetrix HGU133plus2 chips for 16h in Genechip Hybridization Oven 640 (Affymetrix), wash and staining were performed on Genechip Fluidics Station 450 (Affymetrix) following standard procedure

scan_protocol: Hybridized chips were scanned using Affymetrix Genechip Scanner 3000

data_processing: Data were analyzed with RMA, day to day variation has been considered in the analysis using a liner model based approach

label_protocol: RNA samples were labelled using GeneChip Expression 3’Amplification One cycle target labeling and control reagents kit (Affymetrix, part no = 900493), following standard protocol

growth_protocol: A2780 cells were grown in RPMI 1640 medium (Gibco Invitrogen) + 10% Fetal Bovine Serum (Euroclone) and split before confluence seeding approx. 1X10E5 cells/ml.

extract_protocol: RNA was extracted using RNeasy Mini kit  (Qiagen, catalog no. 74106) according to manufacturer recommendation

treatment_protocol: 1X10E6 cells were plated in 100mm plates and after 24h were exposed to the different compounds

tag: compound

value: B

tag: time

tag: day

value: C


title: TRT_compound A_4h_rep1

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 4h
replicate 1

value: A

value: D


title: SOCS3 Cre plus B

description: All mice (C57BL/6) were free of Helicobacter species, housed in a specific pathogen free facility with 12-h light/dark cycles with free access to standard food and water.


title: SOCS3 Cre plus A

tag: All mice (C57BL/6) were free of Helicobacter species, housed in a specific pathogen free facility with 12-h light/dark cycles with free access to standard food and water.


title: TRT_compound B_5h_rep1

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 5h
replicate 1


title: TRT_compound B_4h_rep1

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 4h
replicate 1


title: CTRL_4h_rep2

description:
A2780 human ovarian cancer cell line left untreated, collected after 4h
replicate 2


title: CTRL_4h_rep1

description:
A2780 human ovarian cancer cell line left untreated, collected after 4h
replicate 1


title: TRT_compound A_4h_rep2

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 4h
replicate 2


title: CTRL_5h_rep2

description:
A2780 human ovarian cancer cell line left untreated, collected after 5h
replicate 2


title: pDC medium 1h, biological rep1

description: Gene expression data from plasmacytoid dendritic cells at baseline (medium 1h)

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99oC for 5 min and hybridized for 16 h at 45oC to GeneChip microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin.  Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: pDC cultured in medium for 1h

treatment_protocol: pDC were sorted from spleens of Flt-3L-treated DPExRag1-/- mice  and cultured  at 1x106/ml for 1h in complete media (RPMI supplemented with 10% heat-inactivated FBS (Valley Biomedical, Inc.), Penicillin/Streptomycin (Invitrogen), 10mM HEPES (Invitrogen), 2mM L-Glutamine (Invitrogen), 10mM pyruvate (Invitrogen), 50µM 2-mercaptoethanol (Sigma).


title: SOCS3 Cre minus A


title: CTRL_5h_rep1

description:
A2780 human ovarian cancer cell line left untreated, collected after 5h
replicate 1


title: SOCS3 Cre minus C


title: TRT_compound A_5h_rep2

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 5h
replicate 2


title: TRT_compound B_5h_rep2

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 5h
replicate 2


title: pDC medium 1h, biological rep2


title: TRT_compound B_2h_rep2

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 2h
replicate 2


title: TRT_compound A_5h_rep1

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 5h
replicate 1


title: Mouse Aorta, P465L_PPARG_KI_B

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

description: Gene expression data from blood vessel.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix 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.

source_name: Aorta from P465L PPAR gamma

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

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

treatment_protocol: Mouse chow, standard.

tag: Mouse

value: Gene-targeted, knock-in of dominant-negative P465L PPAR gamma into endogenous locus


title: TRT_compound B_2h_rep1

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 2h
replicate 1


title: Mouse Aorta, P465L_PPARG_KI_A

description: Gene expression data from blood vessel.


title: Mouse Aorta, Wildtype_for_P465L_PPARG_KI_C

description: Gene expression data from blood vessel.

source_name: Aorta from wildtype mice

value: Wildtype littermate


title: Mouse Aorta, Wildtype_for_P465L_PPARG_KI_B

description: Gene expression data from blood vessel.


title: Mouse Aorta, P465L_PPARG_KI_C

description: Gene expression data from blood vessel.


title: CTRL_2h_rep2

description:
A2780 human ovarian cancer cell line left untreated, collected after 2h
replicate 2


title: Mouse Aorta, Wildtype_for_P465L_PPARG_KI_A

description: Gene expression data from blood vessel.


title: Mouse Aorta, Rosiglitazone_dose10_time14_B

description: Gene expression data from blood vessel.

source_name: Aorta from mice at a dose of 10 mg/kg/day for 14 days

treatment_protocol: Mouse chow, contains rosiglitazone, 10 mg/kg/day, for 14 days

value: strain C57


title: TRT_compound B_1h_rep3

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 1h
replicate 3


title: CTRL_2h_rep1

description:
A2780 human ovarian cancer cell line left untreated, collected after 2h
replicate 1


title: Mouse Aorta, Rosiglitazone_dose10_time14_A

description: Gene expression data from blood vessel.


title: TRT_compound B_1h_rep1

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 1h
replicate 1


title: Mouse Aorta, Rosiglitazone_dose10_time2_C

description: Gene expression data from blood vessel.

source_name: Aorta from mice at a dose of 10 mg/kg/day for 2 days

treatment_protocol: Mouse chow, contains rosiglitazone, 10 mg/kg/day, for 2 days


title: TRT_compound A_2h_rep1

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 2h
replicate 1


title: TRT_compound B_1h_rep2

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 1h
replicate 2


title: Mouse Aorta, Rosiglitazone_dose10_time2_B

description: Gene expression data from blood vessel.


title: Mouse Aorta, Rosiglitazone_dose10_time2_A

description: Gene expression data from blood vessel.


title: TRT_compound A_2h_rep2

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 2h
replicate 2


title: CTRL_1h_rep2

description:
A2780 human ovarian cancer cell line left untreated, collected after 1h
replicate 2


title: Mouse Aorta, Rosiglitazone_dose3_time2_B

description: Gene expression data from blood vessel.

source_name: Aorta from mice at a dose of 3 mg/kg/day for 2 days

treatment_protocol: Mouse chow, contains rosiglitazone, 3 mg/kg/day, for 2 days


title: CTRL_1h_rep1

description:
A2780 human ovarian cancer cell line left untreated, collected after 1h
replicate 1


title: CTRL_1h_rep3

description:
A2780 human ovarian cancer cell line left untreated, collected after 1h
replicate 3


title: Mouse Aorta, Rosiglitazone_dose3_time14_C

description: Gene expression data from blood vessel.

source_name: Aorta from mice at a dose of 3 mg/kg/day for 14 days

treatment_protocol: Mouse chow, contains rosiglitazone, 3 mg/kg/day, for 14 days


title: Mouse Aorta, Rosiglitazone_dose3_time14_B

description: Gene expression data from blood vessel.


title: Mouse Aorta, Rosiglitazone_dose3_time14_A

description: Gene expression data from blood vessel.


title: Mouse Aorta, Rosiglitazone_dose3_time2_C

description: Gene expression data from blood vessel.


title: TRT_compound A_1h_rep3

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 1h
replicate 3


title: TRT_compound A_1h_rep2

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 1h
replicate 2


title: Mouse Aorta, Control_for_Rosiglitazone_C

description: Gene expression data from blood vessel.

source_name: Aorta from control mice

treatment_protocol: Mouse chow, vehicle for rosiglitazone.


title: Mouse Aorta, Rosiglitazone_dose3_time2_A

description: Gene expression data from blood vessel.


title: Mouse Aorta, Control_for_Rosiglitazone_B

description: Gene expression data from blood vessel.


title: TRT_compound B_3h_rep3

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 3h
replicate 3


title: TRT_compound B_3h_rep1

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 3h
replicate 1


title: Mouse Aorta, Control_for_Rosiglitazone_A

description: Gene expression data from blood vessel.


title: TRT_compound A_1h_rep1

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 1h
replicate 1


title: CTRL_3h_rep3

description:
A2780 human ovarian cancer cell line left untreated, collected after 3h
replicate 3


title: CTRL_3h_rep2

description:
A2780 human ovarian cancer cell line left untreated, collected after 3h
replicate 2


title: TRT_compound B_3h_rep2

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 3h
replicate 2


title: TRT_compound A_3h_rep1

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 3h
replicate 1


title: TRT_compound A_3h_rep3

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 3h
replicate 3


title: CTRL_3h_rep1

description:
A2780 human ovarian cancer cell line left untreated, collected after 3h
replicate 1


title: TRT_compound B_6h_rep2

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 6h
replicate 2


title: CTRL_6h_rep3

description:
A2780 human ovarian cancer cell line left untreated, collected after 6h
replicate 3


title: CTRL_6h_rep1

description:
A2780 human ovarian cancer cell line left untreated, collected after 6h
replicate 1


title: TRT_compound A_3h_rep2

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 3h
replicate 2


title: TRT_compound B_6h_rep1

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 6h
replicate 1


title: TRT_compound B_6h_rep3

description:
A2780 human ovarian cancer cell line treated with compound B, collected after 6h
replicate 3


title: TRT_compound A_6h_rep3

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 6h
replicate 3


title: TRT_compound A_6h_rep1

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 6h
replicate 1


title: BJ1-iPS1 iPS cells

status: Public on Dec 10 2007

city: Boston

first: In-Hyun

last: Park

state: MA

address: 300 Longwood

department: Hem/Onc

institute: Children's Hospital Boston

description: gene expresion of iPS production

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

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

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

source_name: BJ1-iPS1 iPS cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: hES cell, and iPS cells were cultured in hES medium containing bFGF. Somatic cells were cultured in alpha-MEM with 10% IFS.

treatment_protocol: Cells were washed with PBS and Rneasy kit was used to isolate total RNA

tag: iPS cells


title: MRC5-iPS2 iPS cells_2

description: gene expresion of iPS production

source_name: MRC5-iPS2 iPS cells

extract_protocol: Rneasy kit was used to isolate total RNA


title: CTRL_6h_rep2

description:
A2780 human ovarian cancer cell line left untreated, collected after 6h
replicate 2


title: dH1cf32-iPS2 iPS cells_20

description: gene expresion of iPS production

source_name: dH1cf32-iPS2 iPS cells


title: MRC5-iPS2 iPS cells_22

description: gene expresion of iPS production


title: dH1cf32-iPS2 iPS cells_10

description: gene expresion of iPS production


title: BJ1 fibroblast_47

description: gene expresion of iPS production

source_name: BJ1 fibroblast

tag: fibroblast


title: BJ1 fibroblast_48

description: gene expresion of iPS production


title: MRC5 fibroblast_40

description: gene expresion of iPS production

source_name: MRC5 fibroblast


title: dH1cf16-iPS5 iPS cells_32

description: gene expresion of iPS production

source_name: dH1cf16-iPS5 iPS cells


title: dH1cf16 fibroblast

description: gene expresion of iPS production

source_name: dH1cf16 fibroblast


title: MRC5 fibroblast_59

description: gene expresion of iPS production


title: RNAtotC_23, ZT6

status: Public on Dec 07 2007

city: Lausanne

first: Mehdi

last: Tafti

address: Genopode

department: CIG

country: Switzerland

institute: University of Lausanne

hyb_protocol: Affymetrix HG-U133 plus 2.0 microarrays (Affymetrix) were hybridized to 5 ug of labeled, amplified material and then, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression analysis manual. The fluidics protocol used was GE_WS2v4_450 as recommended by NuGen and not the GE_WS2v5_450 used for the Affymetrix amplification.

scan_protocol: The GeneChip Scanner 3000  (Affymetrix) was used to collect signals after excitation at 570 nm.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using the expresso function from Bioconductor affy package. This normalization follows the same procedure as for RMA, but replaces a quantiles normalization by a scaling normalization (Gautier et al.).

source_name: Whole brain, control

label_protocol: The quality of the mRNAs was investigated on Agilent 2100 bioanalyzer chips. 10ng of immunoprecipitated mRNA was amplified with the WT-Ovation™ Pico RNA Amplification System (catalog #3300-12; Manuel version 1,0).Using the FL-Ovation cDNA Biotin Module V2 (catalog #4200-12) 5μg of cDNA was used to generate labeled targets for hybridization to Affymetrix GeneChip® arrays.

growth_protocol: Experiments were performed on 12 weeks-old (+/- 1 week) male mice. Animals were sleep deprived at light onset or left undisturbed for 6 hrs and randomly sacrificed by cervical dislocation.

extract_protocol: Mice were sacrificed by cervical dislocation. Total RNA:  Whole brain total RNA was extracted and treated with DNase using the RNeasy Lipid Tissue Kit (Qiagen). PolyA RNA: the mRNA-tagging immunoprecipitation was modified from formerly published protocols. (P. J. Roy et al., 2002) (L. O. F. Penalva et al., 2004). Mice were anesthetized with pentobarbital (75mg/kg), and subsequently perfused with 20ml PBS-heparin (2U/ml), 20 ml PBS-formaldehyde 1%, 15ml gylcine 150mM, 20ml Tris-HCl 20mM, and 15ml NaCl 150mM. Brains were removed and homogenized at maximum speed on ice in 3ml lysis buffer (Hepes KOH pH7.3 50mM, EDTA 1mM, KCl 140mM, glycerol 10%, NP40 0.5%, dithiothreitol 1mM, vanadyl ribonucleoside complex 2mM, heparin 1000U/ml, 1 complete mini protease inhibitor cocktail tablet/50ml). Large debris were removed by centrifugation at 18’000g for 20 minutes at 4°C. The supernatants were incubated with 400μl of anti-FLAG M2 affinity gel beads (Sigma) and 80U Rnasine overnight at 4°C. After centrifugation, the pull-down supernatants were recovered for total RNA extraction. The beads were then washed three times with 7ml of lysis buffer, twice with 7ml of wash buffer (50mM Hepes-KOH  pH7.3, 1mM EDTA, 1M KCl, 10% glycerol, 0.5%NP-40, 1mM DTT) and once with 7ml of TE (10mM Tris-HCl pH 7.5, 0.5mM EDTA). The RNA-protein crosslink was reversed by incubating the beads with 3ml of elution buffer for 6 hours at 65°C (50mM Tris-HCl pH7.5, 10mM EDTA, 1% SDS, 2mM ribonucleoside vanadyl complex). Proteins were then digested with proteinase K for 45 minutes at 50°C. Finally mRNAs were isolated from proteins and DNA by a double phenol-chloroform extraction followed by isopropanol precipitation. The mRNA pellets were rinsed twice with 0.5ml 70% ethanol and dissolved in 20μl RNase free water.

treatment_protocol: At light onset, animals were either sleep deprived by gentle handling or left undisturbed for 6 hrs.

tag: total RNA, control


title: RNAtotC_22, ZT6


title: RNAtotC_24, ZT6


title: dH1f fibroblast_58

description: gene expresion of iPS production

source_name: dH1f fibroblast


title: dH1f fibroblast_44

description: gene expresion of iPS production


title: RNAtotC_25, ZT6


title: dH1cf16-iPS5 iPS cells_30

description: gene expresion of iPS production


title: dH1f-iPS3-3 iPS cells

description: gene expresion of iPS production

source_name: dH1f-iPS3-3 iPS cells


title: RNAtotSD_20, ZT6

source_name: Whole brain, 6 hrs sleep deprivation

tag: total RNA, sleep deprivation


title: TRT_compound A_6h_rep2

description:
A2780 human ovarian cancer cell line treated with compound A, collected after 6h
replicate 2


title: RNAtotSD_18, ZT6


title: RNAtotSD_19, ZT6


title: RNAtotSD_21, ZT6


title: surnC_16, ZT6

source_name: Homer1a negative cells,control

tag: total RNA pull-down supernatant, control


title: surnSD_14, ZT6

source_name: Homer1a negative cells, 6 hrs sleep deprivation

tag: total RNA pull-down supernatant, sleep deprivation


title: pull-downC_13, ZT6

molecule: polyA RNA

source_name: Homer1a expressing cells, control

tag: mRNAs pull-down, control


title: surnSD_15, ZT6


title: pull-downC_11, ZT6


title: pull-downC_3, ZT6


title: pull-downSD_12, ZT6

source_name: Homer1a expressing cells, 6hrs sleep deprivation

tag: mRNAs pull-down,sleep deprivation


title: pull-downSD_6, ZT6


title: surnSD_13, ZT6


title: pull-downSD_7, ZT6


title: pull-downC_8, ZT6


title: D2_SleepDep_ZT 12_3

hyb_protocol: Twelve micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor “affy” and “affyPLM” packages (Gautier et al., 2004).

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

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 12, replicat 3

label_protocol: Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used to perform the chiparray experiment according to the Affymetrix Gene Expression procedure.

extract_protocol: Mice were sacrificed by cervical dislocation. RNA from whole brain was isolated and purified with Rneasy Lipid tissue Midi kit (Qiagen) and Dnase treated. Equal amount of total RNA was pooled from 3 mice within each of the 24 experimental groups (3 strains, 2 conditions, 4 ZT = 24 ; in triplicate : 24 * 3 = 72 chips).

tag: Strain

value: DBA/2J, Gender:male, Age:12-13 weeks of age, Tissue:whole brain


title: D2_SleepDep_ZT 18_2

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 18, replicat 2


title: D2_SleepDep_ZT 18_1

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 18, replicat 1


title: pull-downSD_3, ZT6


title: pull-downSD_10, ZT6


title: pull-downSD_1, ZT6


title: pull-downC_4, ZT6


title: D2_SleepDep_ZT 6_2

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 2


title: pull-downC_9, ZT6


title: D2_SleepDep_ZT 6_3

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 3


title: D2_SleepDep_ZT 0_2

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 0, replicat 2


title: D2_SleepDep_ZT 12_1

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 12, replicat 1


title: D2_SleepDep_ZT 12_2

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 12, replicat 2


title: D2_Control_ZT 18_3

source_name: DBA/2J, control, time of sacrifice ZT 18, replicat 3


title: D2_SleepDep_ZT 0_3

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 0, replicat 3


title: D2_SleepDep_ZT 0_1

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 0, replicat 1


title: D2_SleepDep_ZT 6_1

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 1


title: D2_SleepDep_ZT 18_3

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 18, replicat 3


title: D2_Control_ZT 18_2

source_name: DBA/2J, control, time of sacrifice ZT 18, replicat 2


title: D2_Control_ZT 12_3

source_name: DBA/2J, control, time of sacrifice ZT 12, replicat 3


title: D2_Control_ZT 12_1

source_name: DBA/2J, control, time of sacrifice ZT 12, replicat 1


title: D2_Control_ZT 6_3

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 3


title: D2_Control_ZT 12_2

source_name: DBA/2J, control, time of sacrifice ZT 12, replicat 2


title: D2_Control_ZT 6_1

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 1


title: D2_Control_ZT 0_1

source_name: DBA/2J, control, time of sacrifice ZT 0, replicat 1


title: B6_SleepDep_ZT 18_1

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 18, replicat 1

value: C57BL/6J, Gender:male, Age:12-13 weeks of age, Tissue:whole brain


title: D2_Control_ZT 18_1

source_name: DBA/2J, control, time of sacrifice ZT 18, replicat 1


title: B6_SleepDep_ZT 18_3

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 18, replicat 3


title: D2_Control_ZT 6_2

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 2


title: D2_Control_ZT 0_3

source_name: DBA/2J, control, time of sacrifice ZT 0, replicat 3


title: D2_Control_ZT 0_2

source_name: DBA/2J, control, time of sacrifice ZT 0, replicat 2


title: B6_SleepDep_ZT 12_3

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 12, replicat 3


title: B6_SleepDep_ZT 6_1

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 1


title: B6_SleepDep_ZT 0_3

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 0, replicat 3


title: B6_SleepDep_ZT 6_2

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 2


title: B6_SleepDep_ZT 12_1

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 12, replicat 1


title: B6_SleepDep_ZT 12_2

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 12, replicat 2


title: B6_Control_ZT 18_1

source_name: C57BL/6J, control, time of sacrifice ZT 18, replicat 1


title: B6_Control_ZT 12_3

source_name: C57BL/6J, control, time of sacrifice ZT 12, replicat 3


title: B6_SleepDep_ZT 6_3

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 3


title: B6_Control_ZT 18_2

source_name: C57BL/6J, control, time of sacrifice ZT 18, replicat 2


title: AK_SleepDep_ZT 12_3

source_name: AKR/J, sleep deprived, time of sacrifice ZT 12, replicat 3

value: AKR/J, Gender:male, Age:12-13 weeks of age, Tissue:whole brain


title: B6_Control_ZT 12_1

source_name: C57BL/6J, control, time of sacrifice ZT 12, replicat 1


title: B6_SleepDep_ZT 0_1

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 0, replicat 1


title: B6_Control_ZT 0_1

source_name: C57BL/6J, control, time of sacrifice ZT 0, replicat 1


title: B6_Control_ZT 6_2

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 2


title: B6_Control_ZT 6_3

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 3


title: AK_SleepDep_ZT 6_1

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 1


title: B6_Control_ZT 12_2

source_name: C57BL/6J, control, time of sacrifice ZT 12, replicat 2


title: B6_SleepDep_ZT 18_2

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 18, replicat 2


title: B6_Control_ZT 18_3

source_name: C57BL/6J, control, time of sacrifice ZT 18, replicat 3


title: AK_SleepDep_ZT 18_1

source_name: AKR/J, sleep deprived, time of sacrifice ZT 18, replicat 1


title: B6_Control_ZT 0_3

source_name: C57BL/6J, control, time of sacrifice ZT 0, replicat 3


title: AK_SleepDep_ZT 18_2

source_name: AKR/J, sleep deprived, time of sacrifice ZT 18, replicat 2


title: B6_Control_ZT 6_1

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 1


title: B6_SleepDep_ZT 0_2

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 0, replicat 2


title: AK_SleepDep_ZT 12_1

source_name: AKR/J, sleep deprived, time of sacrifice ZT 12, replicat 1


title: AK_SleepDep_ZT 6_2

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 2


title: AK_SleepDep_ZT 6_3

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 3


title: AK_SleepDep_ZT 12_2

source_name: AKR/J, sleep deprived, time of sacrifice ZT 12, replicat 2


title: B6_Control_ZT 0_2

source_name: C57BL/6J, control, time of sacrifice ZT 0, replicat 2


title: AK_SleepDep_ZT 0_1

source_name: AKR/J, sleep deprived, time of sacrifice ZT 0, replicat 1


title: AK_SleepDep_ZT 0_2

source_name: AKR/J, sleep deprived, time of sacrifice ZT 0, replicat 2


title: AK_Control_ZT 18_2

source_name: AKR/J, control, time of sacrifice ZT 18, replicat 2


title: AK_Control_ZT 18_3

source_name: AKR/J, control, time of sacrifice ZT 18, replicat 3


title: AK_Control_ZT 12_3

source_name: AKR/J, control, time of sacrifice ZT 12, replicat 3


title: AK_Control_ZT 6_3

source_name: AKR/J, control, time of sacrifice ZT 6, replicat 3


title: AK_Control_ZT 0_2

source_name: AKR/J, control, time of sacrifice ZT 0, replicat 2


title: AK_SleepDep_ZT 0_3

source_name: AKR/J, sleep deprived, time of sacrifice ZT 0, replicat 3


title: AK_Control_ZT 0_1

source_name: AKR/J, control, time of sacrifice ZT 0, replicat 1


title: AK_Control_ZT 0_3

source_name: AKR/J, control, time of sacrifice ZT 0, replicat 3


title: AK_Control_ZT 6_2

source_name: AKR/J, control, time of sacrifice ZT 6, replicat 2


title: AK_Control_ZT 12_2

source_name: AKR/J, control, time of sacrifice ZT 12, replicat 2


title: L_D2_Control_ZT 6_2

hyb_protocol: Fifteen micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.

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

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 2, Liver

label_protocol: Target preparation were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the Genomics Platform of the NCCR Frontiers in Genetics at the University of Geneva (Switzerland) . Equal quantities of total RNA from three individual mice of each strain were pooled. We generated a hybridization mixture containing 15 ug of biotinylated cRNA according to the protocols provided by Affymetrix.

extract_protocol: RNA was isolated from whole brain and liver by a commercial RNA extraction kit (RNAXEL, Eurobio), treated with Dnase and cleaned using RNeasy columns (Qiagen). Equal amount of total RNA was pooled from 3 mice within each of the 6 experimental groups (3 strains, 2 conditions = 6 ; in triplicate : 6 * 3 = 18 chips) for both brain and liver ( 36 chips in total).

value: DBA/2J, Gender:male, Age:12-13 weeks of age, Tissue:Liver


title: AK_Control_ZT 6_1

source_name: AKR/J, control, time of sacrifice ZT 6, replicat 1


title: L_B6_SleepDep_ZT 6_2

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 2, Liver

value: C57BL/6J, Gender:male, Age:12-13 weeks of age, Tissue:Liver


title: L_D2_SleepDep_ZT 6_2

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 2, Liver


title: L_B6_SleepDep_ZT 6_1

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 1, Liver


title: L_D2_SleepDep_ZT 6_1

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 1, Liver


title: L_B6_SleepDep_ZT 6_3

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 3, Liver


title: L_D2_Control_ZT 6_1

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 1, Liver


title: AK_Control_ZT 18_1

source_name: AKR/J, control, time of sacrifice ZT 18, replicat 1


title: L_D2_Control_ZT 6_3

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 3, Liver


title: L_D2_SleepDep_ZT 6_3

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 3, Liver


title: AK_Control_ZT 12_1

source_name: AKR/J, control, time of sacrifice ZT 12, replicat 1


title: L_B6_Control_ZT 6_3

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 3, Liver


title: large flower buds of J03B, tech_rep1

city: Wuhan

first: hua

middle: cai

last: dong

state: Hubei

address: Xudong Second Road No2

department: Genomics and Molecular Biology

country: China

institute: Institute of Oil Crops Research of CAAS

description: Gene expression data from floura after anther abortion

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabindopsis ATH-1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using User Defined analysis settings and global scaling as normalization method. Normalization value was set to 1 and the target signal was set to 500.

organism: Brassica napus

source_name: large flower buds, fertile plants, J03

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Plants were prepared by growing the seeds in the rapeseed research field of Institute of Oil Crops Research, Chinese Academy of Agricultural Sciences.

extract_protocol: Total RNA was isolated from flower buds using Trizol reagent following instructions from the manufacturer (Invitrogen Corporation, Carlsbad, CA, USA), and was then purified on RNeasy columns (Qiagen, Valencia, CA, USA). Total RNA with an absorbance A260/A280 ratio >1.8 was used for further analysis.

treatment_protocol: Flower buds were isolated from B. napus and were dissected on intact plants under the same growth conditions from the same field. The flower buds that are <1, 1, 2, 3 and >3 mm were harvested. All harvested samples including stamens and pistils were removed and immediately (<2 sec) frozen in liquid nitrogen to minimize post-harvest changes in gene expression. Flower buds were collected from at least two different biological repetitions within each line, from between two and four inflorescences on each plant, and from between two and four different plants from each line. Different flower bud samples were collected at approximately the same time of the day to avoid diurnal effects on gene expression.

tag: Heterozygous two-type line J03B, Genotype

value: msmsrfrf

tag: flower buds bigger than 3mm, referred to anthers at trinucleate stage


title: L_B6_Control_ZT 6_2

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 2, Liver


title: large flower buds of J03B, tech_rep2


title: L_AK_SleepDep_ZT 6_3

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 3, Liver

value: AKR/J, Gender:male, Age:12-13 weeks of age, Tissue:Liver


title: middle flower buds of J03B, biol_rep1

description: Gene expression data from floura during anther abortion

source_name: middle flower buds, fertile plants, J03

tag: flower buds from 1mm to 3mm that contain tetrad stage and uninucleate stage


title: middle flower buds of J03B, biol_rep2


title: small flower buds of J03B, tech_rep1

description: Gene expression data from floura before anther abortion

source_name: small flower buds, fertile plants, J03

tag: flower buds less than 1mm, referred to anther development before meiosis


title: large flower buds of J03B, biol_rep1


title: small flower buds of J03B, tech_rep2


title: L_AK_SleepDep_ZT 6_2

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 2, Liver


title: L_B6_Control_ZT 6_1

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 1, Liver


title: middle flower buds of J03B, tech_rep2


title: large flower buds of J03B, biol_rep2


title: small flower buds of J03B, biol_rep2


title: small flower buds of J03B, biol_rep1


title: middle flower buds of J03A, tech_rep2

source_name: middle flower buds, sterile plants, J03

tag: Heterozygous two-type line J03A, Genotype

value: Msmsrfrf


title: middle flower buds of J03B, tech_rep1


title: H1-OGN hES cells

description: gene expresion of iPS production

source_name: H1-OGN hES cells

tag: hES cells


title: L_AK_SleepDep_ZT 6_1

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 1, Liver


title: large flower buds of J03A, tech_rep2

source_name: large flower buds, sterile plants, J03


title: middle flower buds of J03A, biol_rep2


title: large flower buds of J03A, biol_rep2


title: B_D2_SleepDep_ZT 6_3

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 3, Brain


title: large flower buds of J03A, tech_rep1


title: L_AK_Control_ZT 6_3

source_name: AKR/J, control, time of sacrifice ZT 0, replicat 3, Liver


title: B_D2_SleepDep_ZT 6_2

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 2, Brain


title: L_AK_Control_ZT 6_2

source_name: AKR/J, control, time of sacrifice ZT 0, replicat 2, Liver


title: L_AK_Control_ZT 6_1

source_name: AKR/J, control, time of sacrifice ZT 6, replicat 1, Liver


title: middle flower buds of J03A, biol_rep1


title: B_D2_SleepDep_ZT 6_1

source_name: DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 1, Brain


title: small flower buds of J03A, tech_rep2

source_name: small flower buds, sterile plants, J03


title: large flower buds of J03A, biol_rep1


title: small flower buds of J03A, biol_rep1


title: middle flower buds of J03A, tech_rep1


title: small flower buds of J03A, tech_rep1


title: small flower buds of J03A, biol_rep2


title: B_D2_Control_ZT 6_3

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 3, Brain


title: large flower buds of J10B, biol_rep1

source_name: large flower buds, fertile plants, J10

tag: Homozygous DGMS two-type line J10B, Genotype

value: MsMsRfrf


title: B_B6_SleepDep_ZT 6_3

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 3, Brain


title: large flower buds of J10B, tech_rep1


title: large flower buds of J10B, biol_rep2


title: B_D2_Control_ZT 6_1

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 1, Brain


title: B_B6_Control_ZT 6_3

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 3, Brain


title: middle flower buds of J10B, tech_rep1

source_name: middle flower buds, fertile plants, J10


title: B_D2_Control_ZT 6_2

source_name: DBA/2J, control, time of sacrifice ZT 6, replicat 2, Brain


title: small flower buds of J10B, biol_rep1

source_name: small flower buds, fertile plants, J10


title: B_B6_SleepDep_ZT 6_1

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 1, Brain


title: small flower buds of J10B, tech_rep2


title: middle flower buds of J10B, tech_rep2


title: middle flower buds of J10B, biol_rep1


title: small flower buds of J10B, biol_rep2


title: large flower buds of J10B, tech_rep2


title: B_B6_Control_ZT 6_2

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 2, Brain


title: small flower buds of J10B, tech_rep1


title: B_B6_SleepDep_ZT 6_2

source_name: C57BL/6J, sleep deprived, time of sacrifice ZT 6, replicat 2, Brain


title: large flower buds of J10A, tech_rep1

source_name: large flower buds, sterile plants, J10

tag: Homozygous DGMS two-type line J10A, Genotype

value: MsMsrfrf


title: B_B6_Control_ZT 6_1

source_name: C57BL/6J, control, time of sacrifice ZT 6, replicat 1, Brain


title: middle flower buds of J10A, tech_rep1

source_name: middle flower buds, sterile plants, J10


title: large flower buds of J10A, biol_rep1


title: large flower buds of J10A, tech_rep2


title: large flower buds of J10A, biol_rep2


title: small flower buds of J10A, tech_rep2

source_name: small flower buds, sterile plants, J10


title: middle flower buds of J10A, biol_rep2


title: B_AK_Control_ZT 6_3

source_name: AKR/J, control, time of sacrifice ZT 0, replicat 3, Brain


title: B_AK_SleepDep_ZT 6_2

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 2, Brain


title: middle flower buds of J10A, biol_rep1


title: B_AK_Control_ZT 6_2

source_name: AKR/J, control, time of sacrifice ZT 0, replicat 2, Brain


title: middle flower buds of J10A, tech_rep2


title: B_AK_SleepDep_ZT 6_3

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 3, Brain


title: small flower buds of J10A, biol_rep2


title: small flower buds of J10A, biol_rep1


title: small flower buds of J10A, tech_rep1


title: B_AK_SleepDep_ZT 6_1

source_name: AKR/J, sleep deprived, time of sacrifice ZT 6, replicat 1, Brain


title: B_AK_Control_ZT 6_1

source_name: AKR/J, control, time of sacrifice ZT 6, replicat 1, Brain


title: A27 treated with TGFb

status: Public on Dec 06 2007

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

institute: University of Modena and Reggio Emilia

hyb_protocol: standard Affymetrix Hybridization Protocol

scan_protocol: standard Affymetrix Scanner procedure

data_processing: data in the value column were generated and calculated with GCOS 1.4 (scaled to 120)

source_name: human bone marrow from iliac crest of normal donor

label_protocol: standard Affymetrix One-Cycle Target Labeling protocol

growth_protocol: A27 bone marrow aspirate was collected with informed consent. after red blood cells lysis, nucleated cells were counted and 4.7x10(5) cells per square centimeter were plated. cells were cultured in T75 flask (Becton Dickinson) containing 30mL of a growth medium consisting of a-MEM, 2mM L-glutamine, 100U/mL penicillin, 20% fetal bovine serum (FBS, Invitrogen). medium was replaced on day 1 and then twice a week. first passage was performed on days 12-16 when colonies began to merge and cells were replated in T75 flasks at 0.1x10(5) cells/cm(2). (Kuznetsov S.A. et al. JBMR volume 12, number 9, 1997 - "Single-Colony Derived Strains of Human Marrow Stromal Fibroblasts Form Bone After Transplantation In Vivo")

extract_protocol: Total RNA was extracted using TRIZOL (Invitrogen) following the manufacturer's instructions and then purified using RNeasy MicroKit (Qiagen) following manufacturer's recommendations

treatment_protocol: TGFbeta1 (Sigma Aldrich) was added to cultures at passage 3 for 1 week (10ng/ml) and the medium was changed every 2 days

tag: female, 34 years old


title: A27 treated with bFGF

treatment_protocol: bFGF (Sigma Aldrich) was added to cultures at passage 3 for 1 week (10ng/ml) and the medium was changed every 2 days


title: A23

growth_protocol: A23 bone marrow aspirate was collected with informed consent. after red blood cells lysis, nucleated cells were counted and 4.7x10(5) cells per square centimeter were plated. cells were cultured in T75 flask (Becton Dickinson) containing 30mL of a growth medium consisting of a-MEM, 2mM L-glutamine, 100U/mL penicillin, 20% fetal bovine serum (FBS, Invitrogen). medium was replaced on day 1 and then twice a week. first passage was performed on days 12-16 when colonies began to merge and cells were replated in T75 flasks at 0.1x10(5) cells/cm(2). (Kuznetsov S.A. et al. JBMR volume 12, number 9, 1997 - "Single-Colony Derived Strains of Human Marrow Stromal Fibroblasts Form Bone After Transplantation In Vivo")

tag: unknown


title: 6 month old adult male littermate control +/Y, biol rep1

city: Lexington

first: Marilyn

middle: L.

last: Getchell

state: KY

address: 800 South Limestone St.

department: Anatomy and Neurobiology

institute: University of Kentucky

description: Gene expression data from olfactory epithelium of littermate control mice (+/Y)

hyb_protocol: Following fragmentation, 13.33 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.

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

data_processing: The data were analyzed with Affymetrix MicroArray Suite 5.0 using Affymetrix default analysis settings.  A threshold value of 1,500 was used to normalize the data across all the microarrays.

source_name: microdissected olfactory epithelium

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: The mice were purchased from Jackson Laboratories (Bar Harbor, ME) at 13 weeks of age and were maintained in an animal facility at the University of Kentucky Department of Laboratory Animal Research (DLAR) until they reached six months of age.  At the DLAR, they were kept on a 12 hr light:dark cycle in Bioclean units with sterile-filtered air and provided food and water ad libitum.

extract_protocol: Snap-frozen microdissected olfactory epithelium was pulverized in TRI Reagent (Sigma-Aldrich, St. Louis, MO) and processed through a QIAshredder column (Qiagen, Valencia, CA).  The total RNA was further purified using the Qiagen RNeasy Mini-Kit according to the manufacturer’s protocol.  Total RNA yield and purity was assessed with a spectrophotometer and with the model 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA); all samples had A260/A280 ratios of 1.9–2.2 and showed two sharp peaks corresponding to 18S and 28S RNA on the Bioanalyzer electropherograms.

treatment_protocol: Following euthanasia with carbon dioxide, the olfactory epithelium was quickly microdissected, weighed, and snap-frozen in liquid nitrogen.

tag: Genotype

value: +/Y; strain B6CBACa, male, 6 months old, olfactory epithelium


title: A22

growth_protocol: A22 bone marrow aspirate was collected with informed consent. after red blood cells lysis, nucleated cells were counted and 4.7x10(5) cells per square centimeter were plated. cells were cultured in T75 flask (Becton Dickinson) containing 30mL of a growth medium consisting of a-MEM, 2mM L-glutamine, 100U/mL penicillin, 20% fetal bovine serum (FBS, Invitrogen). medium was replaced on day 1 and then twice a week. first passage was performed on days 12-16 when colonies began to merge and cells were replated in T75 flasks at 0.1x10(5) cells/cm(2). (Kuznetsov S.A. et al. JBMR volume 12, number 9, 1997 - "Single-Colony Derived Strains of Human Marrow Stromal Fibroblasts Form Bone After Transplantation In Vivo")


title: 6 month old adult male mutant mouse Hq/Y, biol rep3

description: Gene expression data from olfactory epithelium of Harlequin mutant mice (Hq/Y)

value: Hq/Y; strain B6CBACAw-J/A-Pdcd8-Hq/J; male, 6 months old, olfactory epithelium


title: A27


title: 6 month old adult male littermate control +/Y,  biol rep2


title: A27 treated with PDGF-BB

treatment_protocol: PDGF-BB (R&D Systems) was added to cultures at passage 3 for 1 week (10ng/ml) and the medium was changed every 2 days


title: 6 month old adult male littermate control +/Y,  biol rep3


title: 6 month old adult male mutant mouse Hq/Y, biol rep2


title: CP-A hTERT control_rep 1

status: Public on Dec 05 2007

city: Leeds University, Leeds

first: Clare

last: Donnellan

state: West Yorkshire

address: LIGHT Laboratories

department: Molecular Epidemiology

country: United Kingdom

institute: Leeds University

description: Gene expression data from unexposed cells

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

scan_protocol: GeneChips were scanned using the Afftymetrix Scanner GCS3000

data_processing: The data were analysed using using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: unexposed cells

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

growth_protocol: For the base solution, 1 vial of MCDB 153 (Sigma) was added to 750 ml of sterile water (Sigma).  To this was added 1.2g of NaHCO3 (Sigma) and once dissolved, the pH was adjusted to 7.14 with NaOH 3N (Sigma).  The volume was made up to 1L and was vacuum filtered into a sterile bottle.    To make 1L of complete media, 585 mg of glutamine (Gibco) was added to 50 ml of the base solution and filter sterilised.  This was added to 900 ml of the base solution with 0.4 μg/ml hydrocortisone (Sigma), 20ng/ml epidermal growth factor (Gibco), 0.1nmol/L cholera toxin (Sigma), 20ng/ml adenine (Sigma), 100 units/ml penicillin and streptomycin (Gibco), 0.25ug/ml amphotericin B (Gibco), 5ug/ml insulin, transferrin and selenium (Sigma), 5% FBS (Sigma) and 140ug/ml bovine pituitary extract (Sigma).  Before use, the bovine pituitary extract was transferred to a 15 ml falcon tube (Corning), centrifuged at 180g for 5 minutes, and the supernatant added to the media.  The pellets were then washed with a total of 50 ml of MCDB 153 solution, re-centrifuged and the supernatant added again.

extract_protocol: RNA extraction was performed using the RNEasy mini kit from Qiagen according to manufactuer's instructions

treatment_protocol: Primary bile salt challenge solutions were made by adding to the full media either 100uM glycocholic acid, sodium taurocholic acid, sodium glycocholate and taurochenodeoxycholic acid (all Sigma primary bile acids), or deoxycholic acid alone.  Following this the pH was corrected to pH 4.5 with HCl (Sigma), with just the latter stage for an acidic pH with no bile acids.     Flasks of cells were washed twice with phosphate buffered saline (PBS) and exposed to the relevant challenge conditions for 15 minutes.  At the end of this time, cells were again washed twice with PBS and normal media replaced.  For control flasks, media was also replaced.  Cells were lysed for RNA extraction at 2 and 6 hours.

tag: CP-A hTERT Barrett's oesophagus cell line

tag: Non-dysplastic, immortalised Barrett's oesophagus cell line with no p53 mutations


title: CP-A hTERT-primary bile mixture pH 4.5_6 hours_ rep 1

description: Gene expression data from 6 hours after exposure to a mix of primary bile salts, pH 4.5

source_name: 6 hours after 15 minute exposure to a mix of primary bile salts, pH 4.5


title: CP-A hTERT control_rep 2


title: CP-A hTERT-acid pH 4.5_2 hours_ rep 2

description: Gene expression data from 2 hours after exposure to acid pH 4.5

source_name: 2 hours after 15 minute exposure to acid, pH 4.5


title: CP-A hTERT-primary bile mixture pH 4.5_2 hours_ rep 2

description: Gene expression data from 2 hours after exposure to a mix of primary bile salts, pH 4.5

source_name: 2 hours after 15 minute exposure to a mix of primary bile salts, pH 4.5


title: 6 month old adult male mutant mouse Hq/Y, biol rep1


title: A18

growth_protocol: A18 bone marrow aspirate was collected with informed consent. after red blood cells lysis, nucleated cells were counted and 4.7x10(5) cells per square centimeter were plated. cells were cultured in T75 flask (Becton Dickinson) containing 30mL of a growth medium consisting of a-MEM, 2mM L-glutamine, 100U/mL penicillin, 20% fetal bovine serum (FBS, Invitrogen). medium was replaced on day 1 and then twice a week. first passage was performed on days 12-16 when colonies began to merge and cells were replated in T75 flasks at 0.1x10(5) cells/cm(2). (Kuznetsov S.A. et al. JBMR volume 12, number 9, 1997 - "Single-Colony Derived Strains of Human Marrow Stromal Fibroblasts Form Bone After Transplantation In Vivo")

tag: male, 35 years old


title: CP-A hTERT-acid pH 4.5_2 hours_ rep 1


title: CP-A hTERT-acid pH 4.5_6 hours_ rep 2

description: Gene expression data from 6 hours after exposure to acid pH 4.5

source_name: 6 hours after 15 minute exposure to acid, pH 4.5


title: CP-A hTERT-primary bile mixture pH 4.5_2 hours_ rep 1


title: CP-A hTERT-acid pH 4.5_6 hours_ rep 1


title: CP-A hTERT-deoxycholic acid pH 4.5_2 hours_ rep 1

description: Gene expression data from 2 hours after exposure to deoxycholic acid, pH 4.5

source_name: 2 hours after 15 minute exposure to deoxycholic acid, pH 4.5


title: CP-A hTERT-deoxycholic acid pH 4.5_6 hours_ rep 2

description: Gene expression data from 6 hours after exposure to deoxycholic acid, pH 4.5

source_name: 6 hours after 15 minute exposure to deoxycholic acid, pH 4.5


title: CP-A hTERT-deoxycholic acid pH 4.5_6 hours_ rep 1


title: wild type

city: Shanghai

first: jing

last: zhang

address: No 411 Hefei Road

institute: Institute of Health Sciences,Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS)

description: wild type 4-day-old mouse

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.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner G3000A.

data_processing: RMA algorithm

source_name: wild type 4-day-old mouse dorsal skin

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

value: BALB/cA, Gender:female, Age:4 days, Tissue:dorsal skin


title: uncv null_sample 1

description: uncv null 4-day-old mouse

source_name: uncv null 4-day-old mouse dorsal skin


title: middle flower buds of J10B, biol_rep2

source_name: middle flower buds, fertile plants, J10


title: CP-A hTERT-deoxycholic acid pH 4.5_2 hours_ rep 2


title: brain, Cell line: O5Tm_e_le1

status: Public on Dec 04 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: Transformed postnatal progenitors

source_name: brain, Cell line


title: brain, Cell line: O3Tm_e_le1

description: Transformed postnatal progenitors


title: brain, Cell line: O4Tm_e_le1

description: Transformed postnatal progenitors


title: brain, Cell line: O2Tm_e_le1

description: Transformed postnatal progenitors


title: uncv null_sample 2

description: uncv null 4-day-old mouse


title: Control for GR-REV dex treatment: dexamethasone induced Ler seedlings

city: Palo Alto

first: M. Kathryn

last: Barton

state: CA

address: 260 Panama Street

department: Dept. of Plant Biology

institute: Carnegie Institution

description: Part of experiment to identify immediate downstream targets of Arabidopsis REV HD-ZIPIII transcription factor.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

organism: Arabidopsis thaliana

source_name: Wild-type Ler seedlings , 1 hour after dexamethasone treatment

label_protocol: Twenty micrograms biotinylated cRNA was prepared from the purified total RNA using standard Affymetrix protocols.

growth_protocol: Seedlings were grown in liquid culture, in 50 ml MS salts plus glucose in 250 ml flasks, 100 seeds per flask.  Flasks were shaken gently on a rotator under fluorescent lights (24 hour, 22 degrees).  Seeds were stratified at 4 degrees in water for 2 days prior to adding to culture medium.

extract_protocol: RNA was isolated from 100 mg of tissue using a QIAGEN RNeasy plant miniprep kit.

treatment_protocol: Seedlings were treated with dexamethasone in ethanol to a final concentration of 0.1% ethanol and 50 micrograms per ml dexamethasone for one hour before tissue was harvested and quick frozen.

tag: Wild-type Landsberg erecta seedlings.  Seedlings were 10 days old.


title: Control for GR-REV dex treatment: mock induced transgenic GRREV seedlings

source_name: GR-REV transgenic seedling, 1 hour after dexamethasone treatment

treatment_protocol: Seedlings were mock treated with 0.1% ethanol for one hour before tissue was harvested and quick frozen.

tag: Transgenic GR-REV seedlings, 10 days post germination


title: mouse anatomy: JP_1133_le1

description: monosomy 21 cells

source_name: mouse anatomy


title: brain, Cell line: O5m_e_le1

description: Control postnatal progenitors


title: mouse anatomy: JP_2591_le1

description: monosomy 21 cells


title: brain, Cell line: O3m_e_le1

description: Control postnatal progenitors


title: Control for GR-REV dex treatment: mock induced WT Ler seedlings

source_name: Wt Landsberg erecta seedling, 1 hour after mock treatment

label_protocol: standard Affymetrix protocol

treatment_protocol: Seedlings were mock treated with carrier alone (ethanol) to a final concentration of 0.1% ethanol for one hour before tissue was harvested and quick frozen.

tag: Wild type Landsberg erecta seedlings, 10 days post germination


title: Experiment:Dexamethasone induction of GR-REV transgenic Ler seedlings

source_name: Transgenic Ler seedling carrying GRREV transgene, 1 hour after mock treatment

growth_protocol: Seedlings were grown in liquid culture, in 50 ml MS salts plus glucose in 250 ml flasks, 100 seeds per flask. Flasks were shaken gently on a rotator under fluorescent lights (24 hour, 22 degrees). Seeds were stratified at 4 degrees in water for 2 days prior to adding to culture medium.

tag: Transgenic Ler seedling carrying GRREV transgene. Transgene is a fusion of glucocorticoid receptor to Arabidopsis REVOLUTA protein. Expression is driven by 35S promoter. Seedlings were 10 days old.


title: brain, Cell line: O4m_e_le1

description: Control postnatal progenitors


title: brain, Cell line: G4Tm_e_le1

description:
Transduced embryonic progenitors
Treatment, type=genetic_modification


title: brain, Cell line: O1Tm_e_le1

description: Transformed postnatal progenitors


title: mouse anatomy: JP_1132_le1

description: control cells


title: skin: JP_337_le1

description: Euploid fibroblasts

source_name: skin


title: skin: JP_1663_le1

description: TS21 fibroblasts


title: skin: JP_1514_le1

description: TS21 Fibroblasts


title: brain, Cell line: O2m_e_le1

description: Control postnatal progenitors


title: brain, Cell line: O1m_e_le1

description: Control postnatal progenitors


title: brain, Cell line: G5Fm_e_le1

description: Control embryonic progenitors


title: brain, Cell line: G3Tm_e_le1


title: brain, Cell line: G1Tm_e_le1


title: mouse anatomy: JP_1131_le1

description: control cells


title: skin: JP_848_le1

description: TS21 Fibroblasts


title: skin: JP_847_le1

description: TS21 fibroblasts


title: brain, Cell line: G2Tm_e_le1


title: skin: JP_391_le1

description: Euploid fibroblasts


title: skin: JP_1478_le1

description: TS21 Fibroblasts


title: brain, Cell line: G4Fm_e_le1

description: Control embryonic progenitors


title: brain, Cell line: G2Fm_e_le1

description: Control embryonic progenitors


title: skin: JP_77_le1

description: Euploid fibroblasts


title: skin: JP_115_le1

description: Euploid fibroblasts


title: brain, Cell line: G5Tm_e_le1


title: brain, Cell line: G3Fm_e_le1

description: Control embryonic progenitors


title: ErbDBD rep 6

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: 2 micrograms biotin-labeled, fragmented, single-stranded cDNA were hybridized with each array using the standard Affymetrix protocol with an Affymetrix hybridization oven and Fluidics Station 450.

scan_protocol: After washing and staining with phycoerythrin-streptavidin per the standard Affymetrix protocol, arrays were scanned with an Affymetrix Scanner 3000

data_processing: Cel files were used to perform GCRMA normalization implemented by the Bioconductor gcrma package. Detection calls and detection P values were computed with Gene Chip Operating Software (Affymetrix)

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta mutant defective in binding to ERE; rep6

label_protocol: Biotin-labeled cDNA was prepared from 20 ng total RNA using the NuGen Ovation kit per instructions provided with the kit.

growth_protocol: MDA-MB-231 cells were infected with the recombinant adenovirus bearing no cDNA (CMV) or a cDNA for ERbeta, or ERbeta mutant defective in binding to ERE (ERbDBD) in medium without phenol red and containing 10% CD-FBS for 48h. Cells were then treated with 1 nM estradiol-17beta for 6h.

extract_protocol: Cells were collected by trpsinization, pelleted.  Total RNA was extracted using Qiagen mini RNEasy kit.

treatment_protocol: Infected cells were treated with 17beta-estradiol for 6h


title: ErbDBD rep 4

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta mutant defective in binding to ERE; rep4


title: brain, Cell line: G1Fm_e_le1

description: Control embryonic progenitors


title: ErbDBD rep 5

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta mutant defective in binding to ERE; rep5


title: ErbDBD rep 1

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta mutant defective in binding to ERE; rep1


title: nervous system: HM1 day 6 replicate 1_le1

description: HM1 embryonic stem cells following four days of neuronal differentiation, replicate one.

source_name: nervous system


title: skin: JP_46_le1

description: Euploid fibroblasts


title: ErbDBD rep 3

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta mutant defective in binding to ERE; rep3


title: nervous system: HM1 day 4 replicate 1_le1


title: nervous system: CAG 150 day 4 replicate 2_le1

description: CAG 150 embryonic stem cells following four days of neuronal differentiation, replicate two.


title: ErbDBD rep 2

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta mutant defective in binding to ERE; rep2


title: Erb rep 6

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta; rep6


title: nervous system: HM1 day 6 replicate 3_le1


title: nervous system: HM1 day 4 replicate 3_le1

description: HM1 embryonic stem cells following four days of neuronal differentiation, replicate three.


title: nervous system: HM1 day 6 replicate 2_le1


title: nervous system: CAG 150 day 6 replicate 2_le1

description: CAG 150 embryonic stem cells following six days of neuronal differentiation, replicate one.


title: CMV rep6

source_name: infected with recombinant adenovirus bearing no cDNA

growth_protocol: MDA-MB-231 cells were infected with the recombinant adenovirus bearing no cDNA (CMV) or a cDNA for ERalpha mutant defective in binding to ERE (3411E) in medium without phenol red and containing 10% CD-FBS for 48h. Cells were then treated with 1 nM estradiol-17beta for 6h.

tag: MDA-MB-231 cells


title: nervous system: CAG 150 day 4 replicate 3_le1

description: CAG 150 embryonic stem cells following four days of neuronal differentiation, replicate three.


title: nervous system: CAG 150 day 6 replicate 3_le1


title: nervous system: HM1 day 4 replicate 2_le1

description: HM1 embryonic stem cells following four days of neuronal differentiation, replicate two.


title: Ctrlrv, rep2

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Per Joslin Diabetes Center microarray core facility.

data_processing: RMA

source_name: Tconv cells retrovirally transduced with empty vector

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

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

tag: Genetic background

tag: Age

value: 4-6 wks

tag: Number of mice per chip

tag: Tissue

value: Spleen and LN (cervical, mesenteric)

tag: Sort

tag: Culture

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (empty-GFP) and cultured for an additional 48hrs.

tag: Post-culture sort

value: GFP+ cells


title: Erb rep 5

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta; rep5


title: Erb rep 4

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta; rep4


title: Erb rep 2

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta; rep2


title: nervous system: CAG150 day 4 replicate 1_le1

description: CAG 150 embryonic stem cells following four days of neuronal differentiation, replicate one.


title: Erb rep 1

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta; rep1


title: nervous system: CAG 150 day 6 replicate 1_le1


title: CMV rep5


title: Erb rep 3

source_name: infected with recombinant adenovirus bearing cDNA for ERbeta; rep3


title: Foxp3rv, rep2

scan_protocol: Per Joslin Diabetes Center microarray core facility.

source_name: Tconv cells retroviarally transduced with Foxp3

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (Foxp3-GFP) and cultured for an additional 48hrs.


title: ERa3411 rep5

source_name: infected with recombinant adenovirus bearing cDNA for ERalpha 203/204/211E (3411E)


title: ERa3411 rep4


title: FOXP3rv, rep2

source_name: Tconv cells retrovirally transduced with FOXP3

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (FOXP3-thy1.1) and cultured for an additional 48hrs.

value: Thy1.1+ cells


title: CTRLrv, rep2

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (empty-thy1.1) and cultured for an additional 48hrs.


title: ActCD8TGF, rep3

source_name: CD8 T cells activated in vitro with TGFbeta

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) + TGFbeta (25 ng/ml) for 4 days

value: CD8a hi expressers


title: CMV rep4


title: ERa3411 rep6


title: ERa3411 rep1


title: FOXP3rv, rep3


title: Era_rep6

source_name: infected with recombinant adenovirus bearing cDNA for Eralpha

growth_protocol: MDA-MB-231 cells were infected with the recombinant adenovirus bearing no cDNA (CMV) or a cDNA for Eralpha in medium without phenol red and containing 10% CD-FBS for 48h. Cells were then treated with 1 nM estradiol-17beta for 6h.


title: CMV rep2


title: ActCD8, rep3

source_name: CD8 T cells activated in vitro

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 4 days


title: ActCD8TGF, rep2


title: wtActCD4, rep3

source_name: Tconv cells activated in vitro

value: 10 day old

value: Spleen

value: enriched with anti-CD4 MACS beads


title: CMV rep3


title: CMV rep1


title: ERa3411 rep2


title: sfActCD4TGF, rep2

source_name: Tconv cells activated in vitro with TGFbeta

value: 10 days

value: Enrichment with anti-CD4 MACS beads

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) + TGFbeta (25ng/ml) for 4 days

value: CD4+, CD25 hi expressers (top 45%)


title: ERa3411 rep3


title: CTRLrv, rep3

value: 4-6 wks

value: Spleen and LN (cervical, mesenteric)


title: sfActCD4TGF, rep3


title: ActCD8, rep2


title: Era_rep5


title: Era_rep4


title: sfActCD4, rep3


title: wtActCD4TGF, rep3


title: Era_rep2


title: Era_rep3


title: sfActCD4, rep2


title: wtActCD4TGF, rep2


title: ActCD4TGF, rep2

value: CD25 hi expressors (top 45%)


title: CMV_rep3


title: CMV_rep2


title: CMV_rep6


title: CMV_rep4


title: Era_rep1


title: CMV_rep5


title: ActCD4, rep2

tag: Sorting

value: In vitro activation with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 4 days


title: ActTreg, rep2

source_name: Treg cells activated in vitro

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (2000 U/ml)for 4 days

value: CD25 hi


title: ActCD4, rep3


title: wtActCD4, rep2


title: GSf Neurospheres Hamburg GS-5-2

city: Hamburg

first: Hauke

middle: Simon

last: Guenther

address: Martinistraße 52

department: Neurochirurgie

country: Germany

institute: UKE

description: Gene expression data from glioblastoma derived neurosphere cultures

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: gcRMA package for R Version 2.3.1

extract_protocol: otal RNA was extracted from cells using the RNeasy Protect Mini Kit (Qiagen). Genomic DNA contamination was removed through an on-column DNase digestion step.

tag: GSf


title: GSf Neurospheres Hamburg GS-8-2

source_name: glioblastoma derived neurosphere cultures


title: CMV_rep1

source_name: infected with recombinant adenovirus bearing no cDNA


title: GSf Neurospheres Hamburg GS-9-2


title: ActTreg, rep3


title: ActTregTGF, rep2

source_name: Treg cells activated in vitro with TGFbeta

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (2000 U/ml) + TGFbeta (25ng/ml) for 4 days


title: GSr Neurospheres Hamburg GS-7-2

tag: GSr


title: ActTregTGF, rep3


title: GSr Neurospheres Hamburg GS-4-2


title: Foxp3rv, rep1

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (Foxp3-GFP) and cultured for an additional 48hrs.

value: GFP+ cells


title: Ctrlrv, rep1

source_name: Tconv cells retrovirally transduced with empty vector

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (empty-GFP) and cultured for an additional 48hrs.


title: CTRLrv, rep1

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (empty-thy1.1) and cultured for an additional 48hrs.

value: Thy1.1+ cells


title: ActCD4TGF, rep3


title: GSr Neurospheres Hamburg GS-2-2


title: GSf Neurospheres Hamburg GS-3-2


title: Wt.4-3.0

city: Norwich

first: Michael

last: Lenhard

state: Norfolk

address: Colney Lane

department: Cell & Developmental Biology

institute: John Innes Centre

description: Gene expression data from Arabidopsis inflorescences of untreated control plants.

hyb_protocol: Genechip Expression Analysis Technical Manual 701021 Rev. 5; Section 2, Chapter 2  Eukaryotic Target Hybridisation  (2.2.3)

scan_protocol: Genechip Expression Analysis Technical Manual 701021 Rev. 5; Secton 2, Chapter 3 Eukaryotic Arrays: Washing, Staining and Scanning (2.3.3)

data_processing: background corrected using RMA, quantile normalized, values summarised by median-polish

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLU; klu-2 line 4-3 without EtOH-treatment.

label_protocol: Genechip Expression Analysis Technical Manual 701021 Rev. 5; Section 2, Chapter 1  Eukaryotic Target Preparation (2.1.3)

growth_protocol: Plants were grown in soil at 22˚C with a 16 h light : 8 h dark cycle.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Plant Mini Kit according to the manufacturer's instructions. RNA was then treated with Ambion Turbo DNA-free Kit according to the manufacturer's instructions.

treatment_protocol: Plants were treated with EtOH-vapour for 0 min, 90 min or 240 min.

tag: Homozygous klu-2 mutant; Landsberg erecta background; soil-grown; flowering plants


title: ActCD8TGF, rep1

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) + TGFbeta (25 ng/ml) for 4 days

value: CD8a hi expressers


title: FOXP3rv, rep1

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 48hrs, then spin infected with retrovirus (FOXP3-thy1.1) and cultured for an additional 48hrs.


title: GSf Neurospheres Hamburg GS-8


title: GSr Neurospheres Hamburg GS-1-2


title: ActCD8, rep1

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 4 days


title: GSf Neurospheres Hamburg GS-9


title: GSr Neurospheres Hamburg GS-7


title: sfActCD4, rep1

value: 10 days

value: Spleen

value: Enrichment with anti-CD4 MACS beads

value: CD4+, CD25 hi expressors (top 45%)


title: GSr Neurospheres Hamburg GS-6


title: Wt.3-1.90

description: Gene expression data from Arabidopsis inflorescences overexpressing wild-type KLU protein for 90 min.

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLU; klu-2 line 3-1 treated with EtOH vapour for 90 min.


title: Mut.1-5.240

description: Gene expression data from Arabidopsis inflorescences overexpressing mutant KLU protein for 240 min.

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLUmut; klu-2 line 1-5 treated with EtOH vapour for 240 min.


title: GSf Neurospheres Hamburg GS-5


title: Mut.3-2.240

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLUmut; klu-2 line 3-2 treated with EtOH vapour for 240 min.


title: ActTregTGF, rep1

value: 4-6 wks

value: Spleen and LN (cervical, mesenteric)


title: Wt.3-1.240

description: Gene expression data from Arabidopsis inflorescences overexpressing wild-type KLU protein for 240 min.

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLU; klu-2 line 3-1 treated with EtOH vapour for 240 min.


title: wtActCD4TGF, rep1

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (20 U/ml) + TGFbeta (25ng/ml) for 4 days


title: Wt.4-3.90

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLU; klu-2 line 4-3 treated with EtOH vapour for 90 min.


title: GSr Neurospheres Hamburg GS-4


title: Wt.3-1.0

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLU; klu-2 line 3-1 without EtOH-treatment.


title: wtActCD4, rep1

value: 10 day old

value: enriched with anti-CD4 MACS beads


title: Wt.4-3.240

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLU; klu-2 line 4-3 treated with EtOH vapour for 240 min.


title: sfActCD4TGF, rep1

value: CD4+, CD25 hi expressers (top 45%)


title: Mut.3-2.90

description: Gene expression data from Arabidopsis inflorescences overexpressing mutant KLU protein for 90 min.

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLUmut; klu-2 line 3-2 treated with EtOH vapour for 90 min.


title: ActTreg, rep1

value: Activation in vitro with anti-CD3/-CD28 beads + IL2 (2000 U/ml)for 4 days

value: CD25 hi


title: GSf Neurospheres Hamburg GS-3


title: Mut.1-5.90

source_name: Pooled inflorescence tissue with young flower buds from 35S::AlcR-AlcA::KLUmut; klu-2 line 1-5 treated with EtOH vapour for 90 min.


title: GSr Neurospheres Hamburg GS-1


title: ActCD4, rep1

source_name: Tconv cells activated in vitro

value: In vitro activation with anti-CD3/-CD28 beads + IL2 (20 U/ml) for 4 days

value: CD25 hi expressors (top 45%)


title: ActCD4TGF, rep1

source_name: Tconv cells activated in vitro with TGFbeta

tag: Genetic backgroun


title: PM_mouse_Lung OVA/PM rep1

status: Public on Dec 01 2007

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: Gene expression data from lung tissue of control animal

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse320_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for ABS_Call; Bioconductor GCRMA package for normalization;

source_name: Lung

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

growth_protocol: standard conditions (12h light-dark cycle, 25-27ºC, ~40% humidity)

treatment_protocol: Oval albumin (0.4 mg/kg i.p, day 0) and an intratracheal OVA challenge (30 mg/kg, day 14); 50 µl aliquot of PM suspended in PBS (10 mg/ml) was placed in the back of the oral cavity and aspirated by the animal.

tag: A/J, male

value: 8-10 week


title: PM_mouse_Lung PM rep1

treatment_protocol: 50 µl aliquot of PM suspended in PBS (10 mg/ml) was placed in the back of the oral cavity and aspirated by the animal


title: PM_mouse_Lung OVA rep3

treatment_protocol: Oval albumin (0.4 mg/kg i.p, day 0) and an intratracheal OVA challenge (30 mg/kg, day 14)


title: GSr Neurospheres Hamburg GS-2

source_name: glioblastoma derived neurosphere cultures


title: IV-CLL6-CD8

first: Gullu

last: Gorgun

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: splenic CD8 T cells_Em-Tcl1, 3mo old, Male

hyb_protocol: Following fragmentation, cRNA were hybridized for overnight at 45C on Affymetrix moe430_2.0 microarray chip.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provided the basis of subsequent analysis.

data_processing: The data were analysed using dCHIP (C Li and W Wong, Proc. Natl. Acad. Sci. Vol. 98, 31-36, 2001a. ).

source_name: splenic CD8 T cells

growth_protocol: T cells were isolated from fresh tissues or peripheral blood.

treatment_protocol: CD4 or CD8 T cells were isolated using negative selection magnetic labeled antibody mix.

tag: Em-Tcl1, 3mo old, Male


title: IV-CLL5-CD8

description: splenic CD8 T cells_Em-Tcl1, 3mo old, Female

tag: Em-Tcl1, 3mo old, Female


title: PM_mouse_Lung PM rep3


title: PM_mouse_Lung PM rep2


title: PM_mouse_Lung Control rep1

treatment_protocol: PBS


title: Liver_C_week4

city: Singapore

first: Mei Yen

last: Chan

state: Singapore

address: 5 Lower Kent Ridge Road

department: Pediatrics

country: Singapore

institute: Yong Loo Lin School of Medicine, National University of Singapore

description: Liver tissue from C57BL/6J mice fed on control diet

hyb_protocol: Following fragmentation, the labeled cRNA were hybridized to the Affymetrix GeneChip® Mouse Genome 430 2.0 chip according to the protocol provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner G2500A

data_processing: The GeneChip Operating Software Version 1.2.0.037 (Affymetrix) was used to analyze the scanned image. The normalization target was set to 500.

source_name: Liver, control

label_protocol: Biotinylated cRNA were prepared using the Genechip IVT Labelling Kit (Affymetrix, 900182), according to manufacturer's protocol.

extract_protocol: Total RNA was isolated from the frozen liver tissue of each mouse using Trizol reagent (Life Technologies, 15596-018) and purified using RNeasy Mini Kit (Qiagen, 74104), according to manufacturer's protocol.

treatment_protocol: Liver samples comprising identical lobes were quickly removed from each mouse. The liver samples were immediately snap-frozen in liquid nitrogen and stored at -80°C.

tag: Female mice


title: PM_mouse_Lung OVA/PM rep3


title: Healthy4-CD8

description: splenic CD8 T cells_Em-TCL1, 9mo old, Male, Healthy

tag: Em-TCL1, 9mo old, Male, Healthy


title: PM_mouse_Lung OVA/PM rep2


title: PM_mouse_Lung OVA rep2


title: PM_mouse_Lung Control rep3


title: CLL11-CD8

description: splenic CD8 T cells_Em-TCL1, 12mo old, Male, CLL

tag: Em-TCL1, 12mo old, Male, CLL


title: CLL12-CD8

description: splenic CD8 T cells_Em-TCL1, 15mo old, Female, CLL

tag: Em-TCL1, 15mo old, Female, CLL


title: IV-CLL4-CD8


title: PM_mouse_Lung OVA rep1

tag: Age


title: IV-CLL2-CD8


title: PM_mouse_Lung Control rep2


title: IV-CLL1-CD8

description: splenic CD8 T cells_Em-TCL1, 3mo old, Female

tag: Em-TCL1, 3mo old, Female


title: IV-CLL3-CD8


title: Healthy3-CD8

description: splenic CD8 T cells_Em-TCL1, 4mo old, Male, Healthy

tag: Em-TCL1, 4mo old, Male, Healthy


title: Healthy1-CD8

description: splenic CD8 T cells_Em-TCL1, 4mo old, Female, Healthy

tag: Em-TCL1, 4mo old, Female, Healthy


title: CLL10-CD8

description: splenic CD8 T cells_Em-TCL1, 12mo old, Female, CLL

tag: Em-TCL1, 12mo old, Female, CLL


title: CLL6-CD8

description: splenic CD8 T cells_Em-TCL1, 14.5mo old, Male, CLL

tag: Em-TCL1, 14.5mo old, Male, CLL


title: CLL1-CD8

description: splenic CD8 T cells_Em-Tcl1, 13.5mo old, Female, CLL

tag: Em-Tcl1, 13.5mo old, Female, CLL


title: CLL8-CD8

description: splenic CD8 T cells_Em-TCL1, 18.5mo old, Male, CLL

tag: Em-TCL1, 18.5mo old, Male, CLL


title: CLL7-CD8

description: splenic CD8 T cells_Em-TCL1, 13mo old, Female, CLL

tag: Em-TCL1, 13mo old, Female, CLL


title: Healthy2-CD8

description: splenic CD8 T cells_Em-TCL1, 9mo old, Female, Healthy

tag: Em-TCL1, 9mo old, Female, Healthy


title: WT4-CD8

description: splenic CD8 T cells_B6C3, 5mo old, Female

tag: B6C3, 5mo old, Female


title: CLL3-CD8

description: splenic CD8 T cells_Em-TCL1, 17mo old, Male, CLL

tag: Em-TCL1, 17mo old, Male, CLL


title: CLL5-CD8

description: splenic CD8 T cells_Em-TCL1, 14.5mo old, Female, CLL

tag: Em-TCL1, 14.5mo old, Female, CLL


title: CLL9-CD8

description: splenic CD8 T cells_Em-TCL1, 16mo old, Male, CLL

tag: Em-TCL1, 16mo old, Male, CLL


title: WT3-CD8

description: splenic CD8 T cells_B6C3, 5mo old, Male

tag: B6C3, 5mo old, Male


title: CLL11-CD4

description: splenic CD4 T cells_Em-TCL1, 12mo old, Male, CLL

source_name: splenic CD4 T cells

tag: Em-TCL1, 12mo old, Male, CLL


title: CLL12-CD4

description: splenic CD4 T cells_Em-TCL1, 15mo old, Female, CLL

tag: Em-TCL1, 15mo old, Female, CLL


title: WT6-CD8

description: splenic CD8 T cells_B6C3, 8.5mo old, Male

tag: B6C3, 8.5mo old, Male


title: WT6-CD4

description: splenic CD4 T cells_B6C3, 8mo old, Female

tag: B6C3, 8mo old, Female


title: CLL2-CD8


title: IV-CLL4-CD4

description: splenic CD4 T cells_Em-Tcl1, 3mo old, Male

tag: Em-Tcl1, 3mo old, Male


title: CLL4-CD8


title: IV-CLL5-CD4

description: splenic CD4 T cells_Em-Tcl1, 3mo old, Female

tag: Em-Tcl1, 3mo old, Female


title: IV-CLL6-CD4


title: Healthy4-CD4

description: splenic CD4 T cells_Em-Tcl1, 9mo old, Male, Healthy

tag: Em-Tcl1, 9mo old, Male, Healthy


title: IV-CLL1-CD4

description: splenic CD4 T cells_Em-TCL1, 3mo old, Female

tag: Em-TCL1, 3mo old, Female


title: IV-CLL3-CD4


title: WT5-CD8

description: splenic CD8 T cells_B6C3, 8.5mo old, Female

tag: B6C3, 8.5mo old, Female


title: IV-CLL2-CD4


title: WT1-CD8

description: splenic CD8 T cells_B6C3, 5mo old, Male


title: WT2-CD8


title: Healthy3-CD4

description: splenic CD4 T cells_Em-TCL1, 4mo old, Male, Healthy

tag: Em-TCL1, 4mo old, Male, Healthy


title: CLL10-CD4

description: splenic CD4 T cells_Em-TCL1, 12mo old, Female, CLL

tag: Em-TCL1, 12mo old, Female, CLL


title: Healthy2-CD4

description: splenic CD4 T cells_Em-TCL1, 9mo old, Female, Healthy

tag: Em-TCL1, 9mo old, Female, Healthy


title: CLL3-CD4

description: splenic CD4 T cells_EmTCL1, 17mo old, Male, CLL

tag: EmTCL1, 17mo old, Male, CLL


title: WT5-CD4

description: splenic CD4 T cells_B6C3, 8.5mo old, Female


title: CLL8-CD4

description: splenic CD4 T cells_Em-TCL1, 16mo old, Male, CLL


title: CLL5-CD4

description: splenic CD4 T cells_Em-Tcl1,14.5mo old, Male, CLL

tag: Em-Tcl1,14.5mo old, Male, CLL


title: CLL7-CD4

description: splenic CD4 T cells_Em-TCL1, 18.5mo old, Male, CLL

tag: Em-TCL1, 18.5mo old, Male, CLL


title: Healthy1-CD4

description: splenic CD4 T cells_Em-TCL1-4mo old, Female, Healthy

tag: Em-TCL1-4mo old, Female, Healthy


title: CLL2-CD4

description: splenic CD4 T cells_EmTCL1, 12mo old, Female, CLL

tag: EmTCL1, 12mo old, Female, CLL


title: CLL6-CD4

description: splenic CD4 T cells_Em-TCL1, 13mo old, Female, CLL

tag: Em-TCL1, 13mo old, Female, CLL


title: WT4-CD4

description: splenic CD4 T cells_B6C3, 5mo old, Female

tag: B6C3, 5mo old, Female


title: WT1-CD4

description: splenic CD4 T cells_B6C3, 5mo old, Male

tag: B6C3, 5mo old, Male


title: WT2-CD4

description: splenic CD4 T cells_B6C3,5mo old, Female

tag: B6C3,5mo old, Female


title: CLL1-CD4

description: splenic CD4 T cells_Em-TCL1,13.5mo old, Female, CLL

tag: Em-TCL1,13.5mo old, Female, CLL


title: CLL9-CD4

description: splenic CD4 T cells_Em-TCL1, 14.5mo old, Female, CLL

tag: Em-TCL1, 14.5mo old, Female, CLL


title: CLL4-CD4


title: S4_2, mouse, SW, control (non-infected),  4 day time matched control_rep 2

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Gene expression data from mouse colon

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse genome 430 2.0 according to the standard Affymetrix protocol

data_processing: The data were analyzed with D-chip

source_name: mouse colon

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

growth_protocol: mouse colon

extract_protocol: rna easy extraction

treatment_protocol: mouse colon control

tag: mouse, SW, control (non-infected),  4 day time matched control, replicate 2

tag: mouse colon


title: Si9_2, mouse, SW, infected,  9 days post infection_rep 2

description: Gene expression data from mouse colon

tag: mouse, SW  9 days post infection, replicate 2


title: Si4_1, mouse, SW, infected,  4 days post infection_rep 1

description: Gene expression data from mouse colon

tag: mouse, SW  4 days post infection, replicate 1


title: Si9_1, mouse, SW, infected,  9 days post infection_rep 1

description: Gene expression data from mouse colon

tag: mouse, SW  9 days post infection, replicate 1


title: Fi9_3, mouse, FVB, infected,  9 days post infection_rep 3

description: Gene expression data from mouse colon

tag: mouse, FVB  9 days post infection, replicate 3


title: S9_1, mouse, SW, control (non-infected),  9 day time matched control_rep 1

description: Gene expression data from mouse colon

tag: mouse, SW, control (non-infected),  9 day time matched control, replicate 1


title: Si9_3, mouse, SW, infected,  9 days post infection_rep 3

description: Gene expression data from mouse colon

tag: mouse, SW  9 days post infection, replicate 3


title: Si4_3, mouse, SW, infected,  4 days post infection_rep 3

description: Gene expression data from mouse colon

tag: mouse, SW  4 days post infection, replicate 3


title: WT3-CD4

description: splenic CD4 T cells_B6C3, 5mo old, Male


title: Fi9_2, mouse, FVB, infected,  9 days post infection_rep 2

description: Gene expression data from mouse colon

tag: mouse, FVB  9 days post infection, replicate 2


title: Liver_HF_week4

description: Liver tissue from C57BL/6J mice fed on high-fat diets

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner G2500A.

source_name: Liver, high-fat

tag: Female mice


title: S4_1, mouse, SW, control (non-infected),  4 day time matched control_rep 1

description: Gene expression data from mouse colon

tag: mouse, SW, control (non-infected),  4 day time matched control, replicate 1


title: Si4_2, mouse, SW, infected,  4 days post infection_rep 2

description: Gene expression data from mouse colon

tag: mouse, SW  4 days post infection, replicate 2


title: S9_2, mouse, SW, control (non-infected),  9 day time matched control_rep 2

description: Gene expression data from mouse colon

tag: mouse, SW, control (non-infected),  9 day time matched control, replicate 2


title: Fi9_1, mouse, FVB, infected,  9 days post infection_rep 1

description: Gene expression data from mouse colon

tag: mouse, FVB  9 days post infection, replicate 1


title: Fi4_3, mouse, FVB, infected,  4 days post infection_rep 3

description: Gene expression data from mouse colon

tag: mouse, FVB  4 days post infection, replicate 3


title: F4_2, mouse, FVB, control (non-infected),  4 day time matched control_rep 2

description: Gene expression data from mouse colon

tag: mouse, FVB, control (non-infected),  4 day time matched control, replicate 2


title: Fi4_2, mouse, FVB, infected,  4 days post infection_rep 2

description: Gene expression data from mouse colon

tag: mouse, FVB  4 days post infection, replicate 2


title: F9_3, mouse, FVB, control (non-infected),  9 day time matched control_rep 3

description: Gene expression data from mouse colon

tag: mouse, FVB, control (non-infected),  9 day time matched control, replicate 3

tag: mouse colon


title: F9_2, mouse, FVB, control (non-infected),  9 day time matched control_rep 2

description: Gene expression data from mouse colon

tag: mouse, FVB, control (non-infected),  9 day time matched control, replicate 2


title: Fi4_1, mouse, FVB, infected,  4 days post infection_rep 1

description: Gene expression data from mouse colon

tag: mouse, FVB  4 days post infection, replicate 1


title: F9_1, mouse, FVB, control (non-infected),  9 day time matched control_rep 1

description: Gene expression data from mouse colon

tag: mouse, FVB, control (non-infected),  9 day time matched control, replicate 1


title: AM14 B cells, CpG treated, rep3

city: Minneapolis

first: Jason

middle: W

last: Bauer

state: MN

address: 420 Deleware St SE MMC108

institute: University of Minnesota

description: AM14 B cells, CpG treated

hyb_protocol: Standard Affymetrix protocol (www.affymetrix.com)

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

source_name: Murine AM-14 B cells

label_protocol: Standard Ambion aRNA Message Amp protocols (www.ambion.com)

extract_protocol: Standard Qiagen RNeasy mini kit protocol (www.qiagen.com)

treatment_protocol: CpG phosphorothioate oligo-deoxynucleotide 1826

tag: Splenic B cells from MRL/+ AM14 mice


title: AM14 B cells, CpG treated, rep1

description: AM14 B cells, CpG treated

scan_protocol: Standard Affymetrix protocol (www.affymetrix.com)

label_protocol: Standard EnzoBio protocols (www.enzo.com)


title: AM14 B cells, PL2-3, rep2

description: AM14 B cells, PL2-3 treated

treatment_protocol: PL2-3 (Chromatin IC)


title: AM14 B cells, Media alone, rep1

description: AM14 B cells, media alone


title: AM14 B cells, Media alone, rep2

description: AM14 B cells, media alone


title: AM14 B cells, anti IgM treated, rep3

description: AM14 B cells treated with anti-IgM

treatment_protocol: F(ab?)2 goat anti-mouse IgM (Jackson ImmunoResearch Laboratories)


title: AM14 B cells, anti-IgM+CpG, rep3

description: AM14 B cells, anti-IgM+CpG treated


title: AM14 B cells, anti IgM treated, rep1

description: AM14 B cells treated with anti-IgM


title: AM14 B cells, anti-IgM+CpG, rep2

description: AM14 B cells, anti-IgM+CpG treated


title: F4_1, mouse, FVB, control (non-infected),  4 day time matched control_rep 1

description: Gene expression data from mouse colon

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

tag: mouse, FVB, control (non-infected),  4 day time matched control, replicate 1


title: AM14 B cells, anti-IgM+CpG, rep1

description: AM14 B cells, anti-IgM+CpG treated


title: AM14 B cells, CpG treated, rep2

description: AM14 B cells, CpG treated


title: AM14 B cells, PL2-3, rep3

description: AM14 B cells, PL2-3 treated


title: AM14 B cells, anti IgM treated, rep2

description: AM14 B cells treated with anti-IgM


title: AM14 B cells, Media alone, rep3

description: AM14 B cells, media alone


title: AM14 B cells, PL2-3, rep1

description: AM14 B cells, PL2-3 treated


title: Rapamycin 3

first: Pere

last: Puigserver

address: 1 Jimmy Fund Way

department: Cancer Biology

description: Affymetrix original enzo processing protocol

hyb_protocol: standard affymetrix hybridization protocol

data_processing:
Data were analyzed by RMA (with default settings) in BioConductor 1.2
Global scaling to TGT 150

source_name: rapamycin-treated

label_protocol: standard affymetrix labelling protocol

growth_protocol: TSC2-/- MEFs were cultured in DMEM containing 10%CCS.  Media was changed at time of treatment.

extract_protocol: trizol isolation

treatment_protocol: 14 hour 20nM rapamycin treatment

tag: Mouse embryo fibroblast tsc2--

tag: confluent TSC2-/- MEFs


title: PGC-1alpha 2

treatment_protocol: confluent TSC2-/- MEFs were infected with adenovirus expressing PGC-1alpha for 10 hours, media was changed and cells were harvested 14 hours later.


title: GFP 2

source_name: gfp-infected

treatment_protocol: confluent TSC2-/- MEFs were infected with adenovirus expressing GFP for 10 hours, media was changed and cells were harvested 14 hours later.


title: PGC-1alpha 1


title: GFP 1


title: Rapamycin 1


title: Control 3

source_name: vehicle-treated

treatment_protocol: 14 hour vehicle (DMSO) treatment


title: GFP 3


title: Control 1


title: Control 2