title: FeSO4.7H2O Time Series, 10 minutes, Array 07130

description: FeSO4 (10 minutes) vs. control

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 10 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 10 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 10 minutes


title: 428 - mAdbID:51985

status: Public on May 31 2006

type: RNA

city: Bethesda

first: Sandeep

last: Dave

state: MD

address: 9000 Rockville Pike

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 51985

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on LymphDX Custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Sample Extraction Protocol

tag: Gender

value: male

tag: Age

tag: Tissue

value: lymph node

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL ABC

value: Follow up status:alive

value: Follow up years:11.38

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:5.8

value: Number of nodal sites:1


title: FeSO4.7H2O Time Series, 10 minutes, Array 07128

city: Seattle

first: Michael

middle: Hiroshi

last: Johnson

state: WA

address: 1441 North 34th Street

department: Computational Biology

institute: Institute for Systems Biology

description: control vs. FeSO4 (10 minutes)

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35[optional]

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See the Microarray facility website at ISB for for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. see the Microarray pipeline data management website at ISB for more details

label: Alexa 532

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC-1, control

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium NRC-1 grown in standard growth media

label: Alexa 647


title: 460 - mAdbID:51986

description: mAdb experiment ID: 51986

value: female

value: Final microarray diagnosis:DLBCL UNCLASSIFIED

value: Follow up years:9.02

value: ECOG performance status:3

value: Number of nodal sites:2


title: FeSO4.7H2O Time Series, 25 minutes, Array 07123

description: control vs. FeSO4 (25 minutes)

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 25 minutes

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35[optional]

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 25 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 25 minutes


title: NiSO4.6H2O Stress Response, Array 08356

description: NiSO4.6H2O stress response (0.5mM) vs. control

label: Alexa 546

source_name: Halobacterium NRC-1, NiSO4.6H2O Stress, 0.5mM

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 cultures were exposed for 5 hours to metal concentration.

tag: Halobacterium NRC-1 grown in standard growth media with NiSO4.6H2O at 0.5mM


title: NiSO4.6H2O Stress Response, Array 08357

description: control vs. NiSO4.6H2O stress response (0.5mM)


title: FeSO4.7H2O Time Series, 5 minutes, Array 07131

description: control vs. FeSO4 (5 minutes)

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 5 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 5 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 5 minutes


title: FeSO4.7H2O Time Series, 15 minutes, Array 07120

description: FeSO4 (15 minutes) vs. control

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 15 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 15 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 15 minutes


title: FeSO4.7H2O Time Series, 80 minutes, Array 07115

description: control vs. FeSO4 (80 minutes)

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 80 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 80 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 80 minutes


title: 623 - mAdbID:51984

description: mAdb experiment ID: 51984

value: male

value: Final microarray diagnosis:DLBCL GCB

value: Follow up status:dead

value: Follow up years:2.43

value: LDH ratio:0.46


title: FeSO4.7H2O Time Series, 25 minutes, Array 07122

description: FeSO4 (25 minutes) vs. control


title: FeSO4.7H2O Time Series, 80 minutes, Array 07114

description: FeSO4 (80 minutes) vs. control


title: 491 - mAdbID:51982

description: mAdb experiment ID: 51982

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Follow up years:4.47


title: 1000 - mAdbID:51981

description: mAdb experiment ID: 51981

value: Final microarray diagnosis:DLBCL ABC

value: Follow up years:0.69

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.68


title: 855 - mAdbID:51837

description: mAdb experiment ID: 51837

value: female

value: Final microarray diagnosis:DLBCL UNCLASSIFIED

value: Follow up status:alive

value: Follow up years:1.67

value: ECOG performance status:1

value: LDH ratio:1.2

value: Number of nodal sites:1


title: FeSO4.7H2O Time Series, 320 minutes, Array 07106

description: control vs. FeSO4 (320 minutes)

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 320 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 320 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 320 minutes


title: FeSO4.7H2O Time Series, 20 minutes, Array 07109

description: FeSO4 (20 minutes) vs. control

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 20 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 20 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 20 minutes


title: FeSO4.7H2O Time Series, 20 minutes, Array 07110

description: control vs. FeSO4 (20 minutes)


title: 700 - mAdbID:51835

description: mAdb experiment ID: 51835

value: male

value: lymph node

value: Follow up status:dead

value: Follow up years:5.40


title: FeSO4.7H2O Time Series, 320 minutes, Array 07105

description: FeSO4 (320 minutes) vs. control


title: FeSO4.7H2O Time Series, 40 minutes, Array 07112

description: FeSO4 (40 minutes) vs. control

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 40 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 40 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 40 minutes


title: 550 - mAdbID:51836

description: mAdb experiment ID: 51836

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL GCB

value: Follow up years:21.78

value: ECOG performance status:0

value: LDH ratio:-1

value: Number of nodal sites:0


title: 702 - mAdbID:51834

description: mAdb experiment ID: 51834

value: female

value: Final microarray diagnosis:DLBCL ABC

value: Follow up years:4.13

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.9


title: FeSO4.7H2O Time Series, 160 minutes, Array 07102

description: control vs. FeSO4 (160 minutes)

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 160 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 160 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 160 minutes


title: 730 - mAdbID:51833

description: mAdb experiment ID: 51833

value: male

value: Follow up years:1.03

value: ECOG performance status:1

value: LDH ratio:1.89


title: 731 - mAdbID:51832

description: mAdb experiment ID: 51832

value: lymph node

value: Lymphoma

value: Follow up status:alive

value: Follow up years:10.18

value: LDH ratio:0.64


title: 758 - mAdbID:51831

description: mAdb experiment ID: 51831

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL GCB

value: Follow up status:dead

value: Follow up years:1.10

value: Number of nodal sites:1


title: 676 - mAdbID:51830

description: mAdb experiment ID: 51830

value: female

value: Final microarray diagnosis:DLBCL ABC

value: Follow up years:1.00

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:2

value: LDH ratio:1.47


title: 777 - mAdbID:51827

description: mAdb experiment ID: 51827

value: male

value: lymph node

value: Final microarray diagnosis:DLBCL PMBL

value: Follow up years:4.27

value: LDH ratio:1.6

value: Number of nodal sites:0


title: FeSO4.7H2O Time Series, -1 minutes, Array 07084

description: FeSO4 (-1 minutes) vs. control

source_name: Halobacterium NRC-1, 6.0mM FeSO4, -1 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for -1 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for -1 minutes


title: FeSO4.7H2O Time Series, -1 minutes, Array 07085

description: control vs. FeSO4 (-1 minutes)


title: 698 - mAdbID:51828

description: mAdb experiment ID: 51828

tag: Gender

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Follow up status:alive

value: Follow up years:3.88

value: ECOG performance status:1

value: LDH ratio:0.74


title: 749 - mAdbID:51826

description: mAdb experiment ID: 51826

value: female

tag: Age

value: Final microarray diagnosis:DLBCL GCB

value: Follow up years:10.40

value: ECOG performance status:0

value: LDH ratio:0.78

value: Number of nodal sites:1


title: FeSO4.7H2O Time Series, 160 minutes, Array 07101

description: FeSO4 (160 minutes) vs. control


title: 678 - mAdbID:51829

description: mAdb experiment ID: 51829

tag: Tissue

value: lymph node

value: Final microarray diagnosis:DLBCL ABC

value: Follow up status:dead

value: Follow up years:0.06

value: LDH ratio:-1

value: Number of nodal sites:2


title: ZnSO4.7H2O Stress Response, Array 06730

description: contrl vs. ZnSO4.7H2O stress response (0.02mM)

source_name: Halobacterium NRC-1, ZnSO4.7H2O Stress, 0.02mM

tag: Halobacterium NRC-1 grown in standard growth media with ZnSO4.7H2O at 0.02mM


title: ZnSO4.7H2O Stress Response, Array 06729

description: ZnSO4.7H2O stress response (0.02mM) vs. control


title: ZnSO4.7H2O Stress Response, Array 06726

description: control vs. ZnSO4.7H2O stress response (0.005mM)

source_name: Halobacterium NRC-1, ZnSO4.7H2O Stress, 0.005mM

tag: Halobacterium NRC-1 grown in standard growth media with ZnSO4.7H2O at 0.005mM


title: FeSO4.7H2O Time Series, 0 minutes, Array 07088

description: FeSO4 (0 minutes) vs. control

source_name: Halobacterium NRC-1, 6.0mM FeSO4, 0 minutes

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1 culture grown in standard media, innoculated with 6.0mM FeSO4 for 0 minutes when sample collected

tag: Halobacterium NRC-1 grown in standard growth media, exposed to 6.0mM FeSO4 for 0 minutes


title: 753 - mAdbID:51824

description: mAdb experiment ID: 51824

value: male

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Follow up years:0.04

value: ECOG performance status:4

value: LDH ratio:1.56

value: Number of nodal sites:0


title: 692 - mAdbID:51825

description: mAdb experiment ID: 51825

value: female

value: Follow up status:alive

value: Follow up years:10.53

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:1.37


title: 779 - mAdbID:51822

description: mAdb experiment ID: 51822

value: lymph node

value: Final microarray diagnosis:DLBCL ABC

value: Follow up status:dead

value: Follow up years:0.35

value: Number of nodal sites:1


title: ZnSO4.7H2O Stress Response, Array 06727

description: ZnSO4.7H2O stress response (0.01mM) vs. control

source_name: Halobacterium NRC-1, ZnSO4.7H2O Stress, 0.01mM

tag: Halobacterium NRC-1 grown in standard growth media with ZnSO4.7H2O at 0.01mM


title: CD4+ CD25-_3

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: CD4+ CD25-_3

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Mus musculus

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

growth_protocol: ex vivo

extract_protocol: Qiagen RNAeasy

tag: genetic modification:

tag: tissue

value: T-cells from spleen


title: MnSO4.H2O Stress Response, Array 06724

description: control vs. MnSO4.H2O stress response (1.5mM)

source_name: Halobacterium NRC-1, MnSO4.H2O Stress, 1.5mM

tag: Halobacterium NRC-1 grown in standard growth media with MnSO4.H2O at 1.5mM


title: CD4+ CD25-_1

description: CD4+ CD25-_1


title: CD4+ CD25-_2

description: CD4+ CD25-_2


title: MnSO4.H2O Stress Response, Array 06723

description: MnSO4.H2O stress response (1.5mM) vs. control

tag: Halobacterium NRC-1 grown in standard growth media


title: 792 - mAdbID:51820

description: mAdb experiment ID: 51820

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL GCB

value: Follow up years:5.53

value: ECOG performance status:0


title: CD4+ CD25+_3

description: CD4+ CD25+_3


title: MnSO4.H2O Stress Response, Array 06722

description: control vs. MnSO4.H2O stress response (1.0mM)

source_name: Halobacterium NRC-1, MnSO4.H2O Stress, 1.0mM

tag: Halobacterium NRC-1 grown in standard growth media with MnSO4.H2O at 1.0mM


title: 789 - mAdbID:51821

description: mAdb experiment ID: 51821

value: male


title: 1923 - mAdbID:51712

description: mAdb experiment ID: 51712

value: female

value: Final microarray diagnosis:DLBCL PMBL

value: Follow up status:alive

value: Follow up years:1.60

value: LDH ratio:3.3


title: 1924 - mAdbID:51711

description: mAdb experiment ID: 51711

value: lymph node

value: Follow up years:6.11

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1


title: 21433_Canton S B

city: Raleigh

first: Stephanie

last: Rollmann

state: NC

address: Department of Zoology

institute: North Carolina State University

data_processing: Affymetrix GCOS software

label: biotinylated cRNA probes

organism: Drosophila melanogaster

source_name: Canton S B M rep1

tag: Male

tag: 5-7 days post eclosion


title: 1920 - mAdbID:51710

description: mAdb experiment ID: 51710

tag: Gender

value: Follow up years:1.97

value: LDH ratio:0.6


title: 21434

source_name: Canton S B Male Rep2


title: 1921 - mAdbID:51713

description: mAdb experiment ID: 51713

tag: Age

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:4.16

value: LDH ratio:0.8


title: CD4+ CD25+_2

description: CD4+ CD25+_2

value: T-cells from spleen


title: 872 - mAdbID:51700

description: mAdb experiment ID: 51700

value: male

tag: Tissue

value: Final pathology diagnosis:DLBCL

value: Final microarray diagnosis:DLBCL ABC

value: Follow up years:5.00

value: LDH ratio:1.7

value: Number of nodal sites:0


title: CuSO4.5H2O Stress Response, Array 06718

description: control vs. CuSO4.5H2O stress response (1.0mM)

source_name: Halobacterium NRC-1, control

source_name: Halobacterium NRC-1, CuSO4.5H2O Stress, 1.0mM

tag: Halobacterium NRC-1 grown in standard growth media with CuSO4.5H2O at 1.0mM


title: MnSO4.H2O Stress Response, Array 06719

description: MnSO4.H2O stress response (0.8mM) vs. control

source_name: Halobacterium NRC-1, MnSO4.H2O Stress, 0.8mM

tag: Halobacterium NRC-1 grown in standard growth media with MnSO4.H2O at 0.8mM


title: CD4+ CD25+_1

description: CD4+ CD25+_1


title: MnSO4.H2O Stress Response, Array 06721

description: MnSO4.H2O stress response (1.0mM) vs. control


title: MnSO4.H2O Stress Response, Array 06720

description: control vs. MnSO4.H2O stress response (0.8mM)


title: 21435

source_name: Canton S B F Rep1

tag: Female


title: CuSO4.5H2O Stress Response, Array 06717

description: CuSO4.5H2O stress response (1.0mM) vs. control


title: 858 - mAdbID:51699

description: mAdb experiment ID: 51699

value: female

value: lymph node

tag: Disease state

value: Follow up status:dead

value: Follow up years:3.58

value: LDH ratio:0.85

value: Number of nodal sites:1


title: CuSO4.5H2O Stress Response, Array 06716

description: control vs. CuSO4.5H2O stress response (0.85mM)

source_name: Halobacterium NRC-1, CuSO4.5H2O Stress, 0.85mM

tag: Halobacterium NRC-1 grown in standard growth media with CuSO4.5H2O at 0.85mM


title: 21436_Canton S B

source_name: Canton S B F Rep2


title: CuSO4.5H2O Stress Response, Array 06715

description: CuSO4.5H2O stress response (0.85mM) vs. control


title: CuSO4.5H2O Stress Response, Array 06714

description: control vs. CuSO4.5H2O stress response (0.7mM)

source_name: Halobacterium NRC-1, CuSO4.5H2O Stress, 0.7mM

tag: Halobacterium NRC-1 grown in standard growth media with CuSO4.5H2O at 0.7mM


title: 21437_

source_name: BG02514 M rep1


title: 538 - mAdbID:51698

description: mAdb experiment ID: 51698

value: Lymphoma

tag: Individual

tag: Clinical info

value: Follow up years:0.34

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:3

value: LDH ratio:-1

value: Number of nodal sites:3


title: 1002 - mAdbID:51697

description: mAdb experiment ID: 51697

value: Submitting diagnosis:DLBCL

value: Final pathology diagnosis:DLBCL

value: Follow up years:0.28

value: ECOG performance status:1

value: LDH ratio:16.68


title: 21439_BG02514

source_name: BG02514 F rep1


title: 21438

source_name: BG02514 M Rep2


title: 21444

source_name: BG02257 F Rep2


title: CuSO4.5H2O Stress Response, Array 06713

description: CuSO4.5H2O stress response (0.7mM) vs. control


title: FeSO4.7H2O Stress Response, Array 04779

description: control vs. FeSO4.7H2O stress response (7.0mM)

source_name: Halobacterium NRC-1, FeSO4.7H2O Stress, 7.0mM

tag: Halobacterium NRC-1 grown in standard growth media with FeSO4.7H2O at 7.0mM


title: 459 - mAdbID:51695

description: mAdb experiment ID: 51695

value: male

value: Final microarray diagnosis:DLBCL GCB

value: Follow up status:alive

value: Follow up years:9.65

value: ECOG performance status:2


title: 415 - mAdbID:51696

description: mAdb experiment ID: 51696

value: lymph node

value: Follow up status:dead

value: Follow up years:5.38

value: ECOG performance status:0

value: LDH ratio:1.21

value: Number of nodal sites:1


title: X028JA (HG-U133A)

city: Stockholm

first: Alexander

last: Ploner

department: Medical Epidemiology and Biostatistics

country: Sweden

institute: Karolinska Institutet

description: Series of 159 tumors

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: Breast tumor

label_protocol: Approximately 10ug of total RNA was processed to produce biotynylated cRNA targets

extract_protocol: Qiagen RNeasy Mini Kit

tag: Breast tumor tissue

tag: RELAPSE

tag: DEATH

tag: SUBTYPE

value: Luminal A

tag: ELSTON

tag: See Series GSE1456 record for additional information


title: 434 - mAdbID:51693

description: mAdb experiment ID: 51693

tag: Gender

value: female

tag: Age

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:10.53

value: Chemotherapy:CHOP-Like Regimen


title: 21442_BG02257

source_name: BG02257 M Rep1

tag: Male

tag: 5-7 days post eclosion


title: FeSO4.7H2O Stress Response, Array 04778

description: FeSO4.7H2O stress response (7.0mM) vs. control

tag: Halobacterium NRC-1 grown in standard growth media


title: 21443_BG02257

source_name: BG02257 F Rep1

tag: Female


title: 492 - mAdbID:51694

description: mAdb experiment ID: 51694

value: male

tag: Tissue

tag: Disease state

value: Final pathology diagnosis:DLBCL

value: Follow up years:11.29

value: Number of nodal sites:0


title: 21440_BG02514

source_name: BG02514 Female Rep2


title: CD4+ CD25+_2 (HG-U133A)

extract_protocol: Trizol

tag: genetic modification:

tag: tissue

value: Blood


title: 21441_BG02257


title: FeSO4.7H2O Stress Response, Array 04775

description: FeSO4.7H2O stress response (6.0mM) vs. control

source_name: Halobacterium NRC-1, FeSO4.7H2O Stress, 6.0mM

tag: Halobacterium NRC-1 grown in standard growth media with FeSO4.7H2O at 6.0mM


title: FeSO4.7H2O Stress Response, Array 04776

description: control vs. FeSO4.7H2O stress response (6.0mM)

source_name: Halobacterium NRC-1, control


title: CD4+ CD25-_1 (HG-U133A)


title: CD4+ CD25+_1 (HG-U133A)


title: TH_GFP_2

status: Public on May 30 2006

growth_protocol: stimulated with irradiated  allogenic EBV B-cells, IL-2

extract_protocol: Qiagen, RNAeasy

tag: genetic modification

value: alloreactive TH cells were transduced using pMSCV-based retroviral vector encoding an IRES-driven GFP

value: T-cells


title: CD4+ CD25-_2 (HG-U133A)


title: TH_FOXP3_2

value: alloreactive TH cells were transduced using pMSCV-based retroviral vector encoding the human Foxp3 coupled to an IRES-driven GFP


title: FeSO4.7H2O Stress Response, Array 04771

description: control vs. FeSO4.7H2O stress response (4.0mM)

source_name: Halobacterium NRC-1, FeSO4.7H2O Stress, 4.0mM

tag: Halobacterium NRC-1 grown in standard growth media with FeSO4.7H2O at 4.0mM


title: Transcriptional Profiling of Borrelia burgdorferi Containing a Unique bosR Allele

city: College Station

first: Jenny

middle: A

last: Hyde

state: TX

address: 407 Reynolds Medical Building

department: MMPA

institute: Texas A&M University HSC

description: Brooks et. al. (2003) Global analysis of Borrelia burgdorferi genes regulated by mammalian host-specific signals.  Infection and Immunity. 3371-3383.

hyb_protocol: The nylon macroarray membranes were prehybridized with 10 ml ExpressHyb (Clonetech, Inc; Palo Alto, CA) at 50∞C for 1 hour.  The [33P] labeled probes were hybridized to the macroarray membranes for 18 hours at 50∞C, washed with a low stringency solution (2X SSC, 0.05% SDS) at 37∞C for 10 minutes, and then incubated in a high stringency wash (0.1X SSC, 0.1% SDS) at 50∞C for 10 minutes.

scan_protocol: The membranes were exposed to a phosphor screen (Amersham Pharmacia Biotech, Piscataway, NJ) for 48 hours at room temperature.  Signals were detected using the Storm 860 phosphorimager (Amersham Biosciences).  Macroarray membranes were stripped of probe as per the Strip-EZ RT kit (Ambion, Austin, TX), exposed to a phosphor screen, and analyzed using the Storm 860 phosphoimager to confirm that the signal was removed and then reprobed as described above.

data_processing:
Raw density values were converted into percent density value of the total array.  Data points were averaged for each ORF from three arrays spotted in duplicate.  Density values not exceeded 2 standard deviations above background were removed from the final data set.  The data was analyzed by Student's t-test.
Raw data is included in the supplementary files of Series GSE4856

organism: Borreliella burgdorferi

source_name: Borrelia burgdorferi B31 derivative, CHP100

label_protocol: The purified RNA was converted to ±-[33P] labeled cDNA using Ambion Strip-EZ RT kit together with 5 ºg of pooled total RNA and ±-[33P] dATP (Perkin Elmer, Boston, MA).  The probe was then purified by gel filtration spin column and the specific activity was determined by scintillation counting.  Probes with specific activities greater than 1x106 cpm/ºg were used for hybridization.

growth_protocol: Conventional microaerophilic growth(1% CO2) in 1XBSK II supplemented with 6% normal rabbit serum.

extract_protocol: Gentra RNA kit, Ambion Turbo DNAfree

tag: Clonal noninfectious, high passage B31 derivative designate CHP100.  Lacking 7 plasmids.


title: TH_FOXP3_1


title: TH_GFP_1

value: alloreactive TH cells were transduced using pMSCV-based retroviral vector encoding  IRES-driven GFP


title: Treg_2

growth_protocol: stimulated with irradiated  allogenic EBV B-cells, daily IL2


title: Treg_1


title: TH_2


title: TH_1


title: Transcriptional Profiling of Borrelia burgdorferi containing a unique bosR allele

source_name: Borrelia burgdoreri B31 derivative JS167

tag: Noninfectious, high passage strain of Bb B31, designated JS167, with insertional mutation in the bb0647 loci.  JS167 is missing 8 plasmids that are found in infectious Borrelia burgdorferi.


title: Hog1 ChIP-Chip repeat 2

status: Public on May 26 2006

type: genomic

city: Valencia

first: Markus

last: Proft

address: Camino de Vera s/n

department: Inst. Biol. Molecular Celular de Plantas

country: Spain

institute: Universidad Politecnica Valencia

description: Immunoprecipitated sample value divided by total DNA value

data_processing: Ratio of ChIP sample value to total DNA value

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Hog1-3HA (MAP51) ChIP repeat 2

growth_protocol: YPD + 0.4M NaCl for 5 min

treatment_protocol: Chromatin immunoprecipitated with anti-HA (12CA5) monoclonal antibody, labeled with Cy5

tag: MAP51 cells with genomic 3HA tag at the Hog1 N-terminus, repeat 2

source_name: Hog1-3HA (MAP51) total repeat 2

treatment_protocol: Total chromatin, labeled with Cy3


title: Poly(A)+ MPSS signatures located at in the region of the chromosome 3 centromere

type: MPSS

city: Davis

first: Blake

middle: C.

last: Meyers

state: CA

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

description: MPSS data were obtained from the following samples: young leaves, young roots, young leaves - cold stressed, young roots - cold stressed, young leaves - drought stressed, young roots - drought stressed, young leaves - salt stressed, young roots - salt stressed, mature leaves, mature roots, 10 day old seedlings (dark grown), 3 day old seedlings, immature panicle, meristematic tissue, ovary & mature stigma, pollen, callus.

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the average expression level of the corresponding signatures for the libraries described above. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/rice.

organism: Oryza sativa

source_name: Untreated and abiotic-stress treated rice tissues.

tag: Cultivar

value: Nipponbare


title: Hog1 ChIP-Chip repeat 1

source_name: Hog1-3HA (MAP51) ChIP

tag: MAP 51 cells with genomic 3HA tag at the Hog1 N-terminus

source_name: Hog1-3HA (MAP51) total DNA


title: Small RNA MPSS signatures located in the region of the chromosome 3 centromere.

description:
All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper Lu et al. (Science 2005, 309:1567) .

data_processing: To determine the normalized abundance value for each signature in the library, we separately merged 2-step runs and 3-step runs to create a raw abundance count for each stepper. The average total number of signatures sequenced in all 2-step or for all 3-step runs was calculated within the library. The normalized abundance is the raw abundance count divided by the average total number of signatures for both of the steppers in the library, multiplied by 250,000 to obtain a "transcripts per quarter million" or TPM value. For each signature, only one normalized value is used - either the 2-step or 3-step normalized value, selected based on the higher of the sum of the 2-step or 3-step data across all libraries. The numbers in the VALUE column represent the average expression level of the corresponding signatures in the 2 libraries. More details are available in Meyers et al. (2004, Genome Research 14:1641).

source_name: Immature panicle and seedlings


title: Hog1 ChIP-Chip repeat 3

source_name: Hog1-3HA (MAP51) ChIP repeat 3

tag: MAP51 cells with genomic 3HA tag at the Hog1 N-terminus


title: E13 testis XY replicate 1

status: Public on May 27 2006

city: Bar Harbor

first: Gerrit

middle: J

last: Bouma

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: isolated E13 testes

hyb_protocol: standard Affymetrix procedures with modifications according to NuGEN protocol

scan_protocol: standard Affymetrix procedures

data_processing: RMA

source_name: fetal gonad

label_protocol: Approximately 20ng of total RNA was processed to produce biotinylated cDNA targets using the Ovation Biotin (NuGEN) protocol.

extract_protocol: Total RNA was isolated from 4 XY gonads using the RNAqueousTM-Micro Kit (Ambion, Inc.) according to the manufacturers instructions.

tag: Strain


title: E13 Sertoli cells XY replicate 2

description: sorted E13 Sertoli cells

extract_protocol: Total RNA was isolated from approximately 22,000 EGFP+ sorted XY SSCs using the RNAqueousTM-Micro Kit (Ambion, Inc.) according to the manufacturers instructions.


title: E13 testis XY replicate 2

description: isolated E13 testes


title: E13 ovary XX replicate 1

description: isolated E13 ovaries

extract_protocol: Total RNA was isolated from 4 XX gonads using the RNAqueousTM-Micro Kit (Ambion, Inc.) according to the manufacturers instructions.


title: E13 Sertoli cells XY replicate 1

description: sorted E13 Sertoli cells


title: 711_Spectral

status: Public on May 25 2006

city: Toronto

first: Chung-Hae

last: Lee

state: ON

address: 9th Floor Rm. 717, 610 University Ave

department: Applied Molecular Oncology

country: Canada

institute: Ontario Cancer Institute, Princess Margaret Hospital

description:
Refer to Braude et al. 2006
Large-scale copy number variation (CNV) at 14q12 is associated with the presence of genomic abnormalities in neoplasia.

data_processing: see paper for normalization; log2 ratio provided under VALUE

source_name: Chronic Myeloid Leukemia

tag: Chronic Myeloid Leukemia

tag: microdeletion on the derivative 9 chromosome der(9)

tag: Female age 42

source_name: XY control DNA

tag: pool of male normal DNA (Promega)


title: 228_Spectral

tag: Male age 42


title: OEC_Lp_U34

city: Madrid

first: Erika

last: Pastrana

state: Madrid

address: Cantoblanco

department: Universidad Autonoma de Madrid

institute: Centro de Biologia Molecular Severo Ochoa

description: ONL was dissected from the OBs and cells were dissociated and plated. M3 medium allowed OEC selection. OEC characterization was performed by immunocytochemistry employing typical OEC markers. Over 90% OEC purity was obtained. Cells were serially passed in vitro and cultures that had surpassed 50 population doublings were established as a population of OECs adapted to long-term culture.

label: Affymetrix hybridization

organism: Rattus norvegicus

source_name: Primary culture of Olfactory Ensheathing Cells ONL adapted to long-term culture

growth_protocol: M3 medium: DMEM, 3% FBS, 20ug/ml Bovine Pituitary Extract, 2uM Forskolin

extract_protocol: TRIZOL

value: Wistar

tag: Age

value: 21 days postnatal

tag: Tissue of origin

value: ONL of both OBs

tag: Cells

value: cultured in M3 medium

tag: PDs

value: over 50


title: E13 pre-granulosa cells XX replicate 1

description: sorted E13 pre-granulosa cells

extract_protocol: Total RNA was isolated from approximately 30,000 EGFP+ sorted XX SSCs using the RNAqueousTM-Micro Kit (Ambion, Inc.) according to the manufacturers instructions.


title: 607_Spectral

tag: Male age 53


title: TEG3_U34A

description: ONL was dissected from the OBs and cells were dissociated and plated. OEC characterization was performed by immunocytochemistry employing typical OEC markers. Cultures were transfected with a plasmid coding for LT SV40 antigen. After clonal selection TEG3 cells were characterized and established as a cell line.  TEG3 cells were serially passed in vitro and were established as a population of OECs adapted to long-term culture by genetic immortalization(Moreno-Flores et al. 2003).

source_name: OEC cell line obtained by immortaliztion of a primary culture of OECs by transfection with LTSV40 gene

value: 2 month old (postnatal day 60)


title: 217_Spectral

tag: Female age 58


title: OEC_Ep_U34A

description: ONL was dissected from the OBs and cells were dissociated and plated. M3 medium allowed OEC selection. OEC characterization was performed by immunocytochemistry employing typical OEC cell markers. Over 90% OEC purity was obtained. After one week in culture (less than 3PDs) total RNA was extracted.

source_name: Primary culture of Olfactory Ensheathing Cells from ONL

growth_protocol: M3 medium: DMEM, 3% FBS, 20ug/ml of Bovine Pituitary Extract, 2uM Forskolin

tag: Tissue of Origin

value: less than 3


title: E13 pre-granulosa cells XX replicate 2

description: sorted E13 pre-granulosa cells


title: TEG3_RAE2.0


title: 313_SMRT

tag: NO microdeletion on the derivative 9 chromosome (der(9)

tag: Female age 65


title: OEC_Lp_RAE2.0


title: E13 ovary XX replicate 2

description: isolated E13 ovaries


title: OEC_Ep_RAE2.0


title: 607_SMRT

description:
Refer to Braude et al. 2006
Large scale copy number variation (CNV) at 14q12 is associated with the presence of genomic abnormalities in neoplasia.


title: 711_SMRT


title: 217_SMRT


title: macrophages_stimlpsic_2hours_rep2

city: College Park

first: Justin

last: Edwards

department: CBMG

institute: University of Maryland

description: Protocols and data processing were done using standard methods described by Affymetrix provided litterature. This includes Eukaryotic Sample and Array Processing manual and GeneChip Expression Analysis Data Analysis Fundamentals manual.

hyb_protocol: Followed Affymetrix published Eukaryotic Sample and Array Processing manual.

data_processing: Data processing using Affymetrix Microarray Suite Version 5.0. following GeneChip Expression Analysis Data Analysis Fundamentals manual.

source_name: macrophages, stim. LPS+immune complexes, 2 hours

growth_protocol: Bone marrow derived macrophages with grown from bone marrow precursers in D10 supplemented with 20% L-cell conditioned media (LCM) for 7 days. Prior to stimulation cells were plated out and grown in LCM free media overnight.

extract_protocol: Trizol extraction followed by DNase treatment and RNA cleanup using the RNeasy kit.

treatment_protocol: BMM were IFN gamma primed overnight with 100 U/ml, washed with PBS, then stimulated for 2 hours with LPS (10 ng/ml) +Immune complexes.

tag: Balb/c bone marrow derived macrophages


title: mamma carcinoma T661-IDC HG_U133Plus

status: Public on May 24 2006

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

data_processing: RMAExpress

source_name: mamma carcinoma tumor T661-IDC


title: mamma carcinoma H191-DCIS HG_U133Plus

source_name: mamma carcinoma tumor H191-DCIS


title: mamma carcinoma T808-IDC HG_U133Plus

source_name: mamma carcinoma tumor T808-IDC


title: Flk- 84hr 4

city: Chapel Hill

first: Monte

middle: S

last: Willis

address: 103 Mason Farm Road

department: Pathology & Laboratory Medicine

institute: UNC

description: Flk- 84hr 4

hyb_protocol: Agilent

scan_protocol: Axon / GenePix 2000b

data_processing: non-linear modified quantile normalization

source_name: Total Mouse RNA

label_protocol: Amplification

extract_protocol: GITC of homogenized mouse pups

tag: Total Mouse RNA

source_name: Flk- 84hr 4

extract_protocol: Qiagen RNeasy

tag: ES cells


title: mamma carcinoma T808-DCIS HG_U133Plus

source_name: mamma carcinoma tumor T808-DCIS


title: mamma carcinoma T796-IDC HG_U133Plus

source_name: mamma carcinoma tumor T796-IDC


title: mamma carcinoma T787-DCIS HG_U133Plus

source_name: mamma carcinoma tumor T787-DCIS


title: mamma carcinoma T796-DCIS HG_U133Plus

source_name: mamma carcinoma tumor T796-DCIS


title: IFN gamma Macrophage_LPSstim_2h_rep2

scan_protocol: Followed Affymetrix published Eukaryotic Sample and Array Processing manual.

source_name: Bone marrow derived macrophages, stimulated LPS, 2 hours

growth_protocol: Cells were growth from bone marrow progenitors in complete media (D10) containing 20% L-cell conditioned media for 7 days. Cells were plated out overnight in LCM free prior to stimulation.

extract_protocol: Trizol extraction followed by DNase treatment and RNA cleanup using RNeasy kit.

treatment_protocol: Bone marrow derived macrophages with IFN-gamma primed o/n at 100U/ml. 16 hours later media was removed, cells washed with PBS, then stimulated with 10ng/ml LPS.

tag: Balb/c bone marrow derrived macrophages stimulated overnight, washed, then stimulated 2 hours with 10ng/ml LPS in complete media.


title: mamma carcinoma T661-DCIS HG_U133Plus

source_name: mamma carcinoma tumor T661-DCIS


title: mamma carcinoma tumor T787-DCIS HG-U133A


title: mamma carcinoma T396-DCIS HG_U133Plus

source_name: mamma carcinoma tumor T396-DCIS


title: mamma carcinoma T706-IDC HG_U133Plus

source_name: mamma carcinoma tumor T706-IDC


title: Flk- 84hr 1

description: Flk- 84hr 1

source_name: Flk- 84hr 1


title: Flk- 84hr 2

description: Flk- 84hr 2

source_name: Flk- 84hr 2


title: mamma carcinoma tumor T808-DCIS HG-U133A


title: mamma carcinoma H191-IDC HG_U133Plus

source_name: mamma carcinoma tumor H191-IDC


title: mamma carcinoma T787-IDC HG_U133Plus

source_name: mamma carcinoma tumor T787-IDC


title: mamma carcinoma T706-DCIS HG_U133Plus

source_name: mamma carcinoma tumor T706-DCIS


title: Flk- 84hr 3

description: Flk- 84hr 3

source_name: Flk- 84hr 3


title: mamma carcinoma tumor T787-IDC HG-U133A


title: mamma carcinoma tumor T808-IDC HG-U133A

source_name: mamma carcinoma tumor T808-IDC


title: Flk+ 84hr 4

description: Flk+ 84hr 4

source_name: Total Mouse RNA

source_name: Flk+ 84hr 4


title: mamma carcinoma tumor T661-DCIS HG-U133A


title: mamma carcinoma tumor T661-IDC HG-U133A

source_name: mamma carcinoma tumor T661-IDC


title: mamma carcinoma T396-IDC HG_U133Plus

source_name: mamma carcinoma tumor T396-IDC


title: mamma carcinoma tumor T478-DCIS HG-U133A

source_name: mamma carcinoma tumor T478-DCIS


title: Flk+ 84hr 3

description: Flk+ 84hr 3

source_name: Flk+ 84hr 3


title: Flk+ 84hr 2

description: Flk+ 84hr 2

source_name: Flk+ 84hr 2


title: Flk+ 84hr 1

description: Flk+ 84hr 1

source_name: Flk+ 84hr 1


title: mamma carcinoma tumor T374-DCIS HG-U133A

source_name: mamma carcinoma tumor T374-DCIS


title: mamma carcinoma tumor T374-IDC HG-U133A

source_name: mamma carcinoma tumor T374-IDC


title: Flk+ 95hr 4

description: Flk+ 95hr 4

source_name: Flk+ 95hr 4


title: mamma carcinoma tumor T478-IDC HG-U133A

source_name: mamma carcinoma tumor T478-IDC


title: Flk- 95hr 1

description: Flk- 95hr 1

source_name: Flk- 95hr 1


title: Flk- 95hr 4

description: Flk- 95hr 4

source_name: Flk- 95hr 4


title: Flk- 95hr 2

description: Flk- 95hr 2

source_name: Flk- 95hr 2


title: RUNX2 -/- embryonic humeri at day E14.5, biological rep2 (A)

city: Berlin

first: Jochen

last: Hecht

address: Ihnestr. 73

department: Mundlos

institute: Max Planck Institute for Molecular Genetics

description: Gene expression data from Runx2 -/- mouse embryonic humeri.

hyb_protocol: biotin-labeled cRNA was hybridized at a concentration of 60 ng/µl  for 16 hr at 45C on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G2500A (Agilent Technologies)

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: mouse embryos at day E14.5

label_protocol: 10 µg of total RNA were first reverse transcribed into cDNA (cDNA Synthesis System, Roche). The cDNA was used for in vitro transcription (T7 Megascript Kit, Ambion) and labeling with Biotin-11-CTP and Biotin-16-UTP (Perkin-Elmer, Boston, USA)

extract_protocol: peqGOLD TriFast (peqLab) extraction of total RNA was performed according to the manufacturer's instructions followed by Qiagen RNeasy column purification including an on column Dnase digestion according to manufacturers instructions

treatment_protocol: humeri were disected in RNAlater (Qiagen) and stored in liquid nitrogen until RNA isolation

tag: Genotype

value: Runx2 -/-

value: embryonic stage E14.5


title: wt embryonic humeri at day E14.5, biological rep2 (A)

description: Gene expression data from Runx2 wt mouse embryonic humeri.

value: Runx2 wildtype


title: Flk- 95hr 3

description: Flk- 95hr 3

source_name: Flk- 95hr 3


title: Flk+ 95hr 3

description: Flk+ 95hr 3

source_name: Total Mouse RNA

source_name: Flk+ 95hr 3


title: RUNX2 -/- embryonic humeri at day E14.5, biological rep2 (C)


title: wt embryonic humeri at day E14.5, biological rep1 (A)


title: RUNX2 -/- embryonic humeri at day E14.5, biological rep1 (A)


title: Flk- 8d 4

description: Flk- 8d 4

source_name: Flk- 8d 4


title: Flk+ 95hr 2

description: Flk+ 95hr 2

source_name: Flk+ 95hr 2


title: CC2_14028s_ChIP_WN442_pHNS-HA_antiHA__6D073_1

city: Irvine

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
User - Pcheng
Date_of_Scan = Tue Sep 13 13:42:42 2005

data_processing: Quantarray 3.0, adaptive quantitation, protocol STv6_01_050607.pro

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 14028s gDNA

extract_protocol: SIGMA GenElute bacterial gDNA extraction kit

tag: Salmonella typhimurium 14028s genomic DNA

extract_protocol: IP using anti-HA

tag: Salmonella typhimurium 14028s-rpoSlow-hns mutant complemented with pWN442-pHNS-HA IP'd with anti-HA


title: Flk+ 95hr 1

description: Flk+ 95hr 1

source_name: Flk+ 95hr 1


title: CC2_14028s_ChIP_WN442_pHNS-HA_antiHA__6D073_3


title: Flk- 8d 2

description: Flk- 8d 2

source_name: Flk- 8d 2


title: CC2_14028s_ChIP_WN442_pHNS-HA_antiHA__6D073_2


title: CC2_14028s_ChIP_WN441_pHNS-FLAG_antiHA__6D072_3

description:
User - Pcheng
Date_of_Scan = Tue Sep 13 13:11:04 2005

tag: Salmonella typhimurium 14028s-rpoSlow-hns mutant complemented with pWN441-pHNS-FLAG IP'd with anti-HA


title: Flk- 8d 3

description: Flk- 8d 3

source_name: Flk- 8d 3


title: CC2_14028s_ChIP_WN441_pHNS-FLAG_antiHA__6D072_2


title: CC2_14028s_ChIP_WN441_pHNS-FLAG_antiHA__6D072_1


title: wt embryonic humeri at day E14.5, biological rep2 (C)

tag: Age


title: CC2_14028s_ChIP_WN442_pHNS-HA_antiHA__6D061_3

description:
User - Pcheng
Date_of_Scan = Wed Sep 07 10:24:13 2005


title: Flk- 8d 1

description: Flk- 8d 1

source_name: Flk- 8d 1


title: RUNX2 -/- embryonic humeri at day E14.5, biological rep1 (C)


title: CC2_14028s_ChIP_WN442_pHNS-HA_antiHA__6D061_2


title: Flk+ 8d 4

description: Flk+ 8d 4

source_name: Flk+ 8d 4


title: RUNX2 -/- embryonic humeri at day E14.5, biological rep1 (B)


title: wt embryonic humeri at day E14.5, biological rep1 (C)


title: CC2_14028s_ChIP_WN441_pHNS-FLAG_antiHA__6D059_2

description:
User - Pcheng
Date_of_Scan = Wed Sep 07 11:29:13 2005


title: Flk+ 8d 2

description: Flk+ 8d 2

source_name: Flk+ 8d 2


title: CC2_14028s_ChIP_WN442_pHNS-HA_antiHA__6D061_1


title: CC2_14028s_ChIP_WN441_pHNS-FLAG_antiHA__6D059_3


title: wt embryonic humeri at day E14.5, biological rep2 (B)


title: RUNX2 -/- embryonic humeri at day E14.5, biological rep2 (B)


title: CC2_14028s_ChIP_WN441_pHNS-FLAG_antiHA__6D059_1


title: wt embryonic humeri at day E14.5, biological rep1 (B)


title: Flk+ 8d 1

description: Flk+ 8d 1

source_name: Flk+ 8d 1


title: cow 7187, liver Cy3, day -30 relative to parturition

status: Public on May 23 2006

city: Urbana

first: Juan

middle: J.

last: Loor

state: IL

address: 1207 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

description: Holstein cow fed ad libitum amounts of a moderate-energy diet (1.60 Mcal/kg) during an entire 65 day dry period.  Cow consumed ~120% of NRC (2001) requirements.  The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).

data_processing: array centering and Loess normalization

organism: Bos taurus

source_name: liver, day -30, labelled with Cy3

tag: liver day -30 relative to parturition

source_name: reference standard RNA, labelled with Cy5

tag: mixture of bovine tissues


title: cow 7187, liver Cy5, day 49 relative to parturition

source_name: liver, day 49, labelled with Cy5

tag: liver day 49 relative to parturition

source_name: reference standard RNA, labelled with Cy3


title: cow 7187, liver Cy3, day -14 relative to parturition

source_name: liver, day -14, labelled with Cy3

tag: liver day -14 relative to parturition


title: cow 7187, liver Cy5, day -14 relative to parturition

source_name: liver, day -14, labelled with Cy5


title: cow 7187, liver Cy5, day 14 relative to parturition

source_name: liver, day 14, labelled with Cy5

tag: liver day 14 relative to parturition


title: cow 7187, liver Cy3, day 14 relative to parturition

source_name: liver, day 14, labelled with Cy3


title: cow 7187, liver Cy3, day 1 relative to parturition

source_name: liver, day 1, labelled with Cy3

tag: liver day 1 relative to parturition


title: cow 7187, liver Cy5, day -65 relative to parturition

source_name: liver, day -65, labelled with Cy5

tag: liver day -65 relative to parturition


title: Flk+ 8d 3

description: Flk+ 8d 3

source_name: Total Mouse RNA

source_name: Flk+ 8d 3


title: cow 7187, liver Cy3, day 49 relative to parturition

source_name: liver, day 49, labelled with Cy3


title: cow 7187, liver Cy5, day 1 relative to parturition

source_name: liver, day 1, labelled with Cy5


title: cow 7187, liver Cy5, day 28 relative to parturition

source_name: liver, day 28, labelled with Cy5

tag: liver day 28 relative to parturition


title: cow 7187, liver Cy3, day 28 relative to parturition

source_name: liver, day 28, labelled with Cy3


title: cow 7161, liver Cy5, day -65 relative to parturition


title: cow 7161, liver Cy5, day -14 relative to parturition


title: cow 7161, liver Cy5, day 14 relative to parturition


title: cow 7161, liver Cy3, day -14 relative to parturition


title: cow 7161, liver Cy5, day -30 relative to parturition

source_name: liver, day -30, labelled with Cy5


title: cow 7161, liver Cy3, day -65 relative to parturition

source_name: liver, day -65, labelled with Cy3


title: cow 7161, liver Cy5, day 28 relative to parturition


title: cow 7161, liver Cy3, day 28 relative to parturition

source_name: reference standard RNA, labelled with Cy5


title: cow 7161, liver Cy3, day 49 relative to parturition


title: cow 7161, liver Cy5, day 49 relative to parturition

source_name: liver, day 49, labelled with Cy5


title: cow 7161, liver Cy3, day 14 relative to parturition


title: cow 7161, liver Cy3, day -30 relative to parturition

source_name: liver, day -30, labelled with Cy3


title: cow 7161, liver Cy3, day 1 relative to parturition


title: cow 7187, liver Cy5, day -30 relative to parturition

source_name: reference standard RNA, labelled with Cy3


title: cow 7105, liver Cy3, day -65 relative to parturition

description: Holstein cow fed restricted amounts of a moderate-energy diet (1.60 Mcal/kg) during an entire 65 day dry period.  Cow consumed ~80% of NRC (2001) requirements.  The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).


title: cow 7105, liver Cy5, day 49 relative to parturition


title: cow 7105, liver Cy5, day 14 relative to parturition


title: cow 7105, liver Cy3, day 14 relative to parturition


title: cow 7105, liver Cy3, day 1 relative to parturition


title: cow 7105, liver Cy5, day 28 relative to parturition


title: cow 7161, liver Cy5, day 1 relative to parturition


title: cow 7105, liver Cy3, day 49 relative to parturition


title: cow 7105, liver Cy3, day 28 relative to parturition


title: cow 7050, liver Cy5, day -30 relative to parturition

tag: liver day -30 days relative to parturition


title: cow 7105, liver Cy3, day -30 relative to parturition


title: cow 7105, liver Cy5, day -14 relative to parturition

source_name: liver, day -14, labelled with Cy5


title: cow 7105, liver Cy5, day -30 relative to parturition


title: cow 7105, liver Cy5, day 1 relative to parturition


title: cow 7105, liver Cy3, day -14 relative to parturition

source_name: liver, day -14, labelled with Cy3


title: cow 7050, liver Cy5, day 1 relative to parturition


title: cow 7050, liver Cy3, day 14 relative to parturition

source_name: liver, day 14, labelled with Cy3


title: cow 7050, liver Cy3, day 28 relative to parturition


title: cow 7050, liver Cy5, day 28 relative to parturition


title: cow 7050, liver Cy5, day -14 relative to parturition


title: cow 7050, liver Cy5, day 14 relative to parturition

source_name: liver, day 14, labelled with Cy5


title: cow 7050, liver Cy3, day 1 relative to parturition

source_name: liver, day 1, labelled with Cy3


title: cow 7045, liver Cy5, day -65 relative to parturition

source_name: liver, day -65, labelled with Cy5


title: cow 7045, liver Cy3, day -65 relative to parturition


title: cow 7050, liver Cy3, day -14 relative to parturition


title: cow 7050, liver Cy3, day -30 relative to parturition


title: cow 7105, liver Cy5, day -65 relative to parturition


title: cow 7045, liver Cy5, day -30 relative to parturition

tag: mixture of bovine tissues RNA


title: cow 7187, liver Cy3, day -65 relative to parturition


title: cow 7045, liver Cy3, day -14 relative to parturition


title: cow 7045, liver Cy3, day 49 relative to parturition


title: cow 7045, liver Cy5, day -14 relative to parturition


title: cow 7045, liver Cy5, day 49 relative to parturition


title: cow 7045, liver Cy3, day -30 relative to parturition


title: cow 6952, liver Cy5, day -30 relative to parturition

tag: liver, day -30 relative to parturition


title: cow 6952, liver Cy5, day -14 relative to parturition

tag: Liver, day -14 relative to parturition

tag: Mixture of bovine tissues RNA


title: cow 6952, liver Cy3, day 49 relative to parturition

tag: Liver, day 49 relative to parturition


title: cow 7045, liver Cy5, day 14 relative to parturition

tag: liver, day 14 relative to parturition


title: cow 6952, liver Cy3, day -14 relative to parturition


title: cow 6952, liver Cy5, day 14 relative to parturition

tag: Liver, day 14 relative to parturition


title: cow 7045, liver Cy3, day 1 relative to parturition

tag: liver, day 1 relative to parturition

tag: mixture of bovine tissue RNA


title: cow 6952, liver Cy3, day -30 relative to parturition

tag: Liver, day -30 relative to parturition


title: cow 6952, liver Cy3, day -65 relative to parturition

tag: liver, day -65 relative to parturition


title: cow 6952, liver Cy3, day 28 relative to parturition

tag: Liver, day 28 relative to parturition


title: cow 6952, liver Cy5, day 49 relative to parturition


title: cow 6952, liver Cy3, day 1 relative to parturition

tag: Liver, day 1 relative to parturition


title: cow 7045, liver Cy5, day 28 relative to parturition


title: cow 6952, liver Cy5, day 1 relative to parturition

tag: Mixture of bovine tissues


title: cow 6952, liver Cy3, day 14 relative to parturition


title: cow 7045, liver Cy3, day 14 relative to parturition


title: cow 7045, liver Cy3, day 28 relative to parturition


title: cow 7045, liver Cy5, day 1 relative to parturition


title: cow 6886, liver Cy5, day -14 relative to parturition


title: cow 6886, liver Cy5, day -65 relative to parturition

tag: Liver, day -65 relative to parturition


title: cow 6952, liver Cy5, day 28 relative to parturition


title: cow 6952, liver Cy5, day -65 relative to parturition


title: cow 6886, liver Cy5, day -30 relative to parturition


title: cow 6886, liver Cy3, day -65 relative to parturition


title: cow 6886, liver Cy3, day -14 relative to parturition


title: cow 6886, liver Cy3, day -30 relative to parturition

tag: Mxiture of bovine tissues RNA


title: cow 6886, liver Cy3, day 28 relative to parturition


title: cow 6886, liver Cy5, day 28 relative to parturition


title: cow 6886, liver Cy5, day 1 relative to parturition


title: cow 6886, liver Cy5, day 14 relative to parturition


title: cow 6877, liver Cy3, day -65 relative to parturition

description: Holstein cow fed restricted amounts of a moderate-energy (1.60 Mcal/kg) diet during an entire 65 day dry period.  Cow consumed ~80% NRC (2001) requirements. The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).


title: cow 6886, liver Cy3, day 14 relative to parturition


title: cow 6877, liver Cy5, day 49 relative to parturition

description: Holstein cow fed restricted amounts of a moderate-energy (1.60 Mcal/kg) diet during an entire 65 day dry period.  Cow consumed ~80% of NRC (2001) requirements. The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).


title: cow 6877, liver Cy3, day 28 relative to parturition

description:
Holstein cow fed restricted amounts of a moderate-energy (1.60 Mcal/kg) diet during an entire 65 day dry period.  Cow consumed ~80% of NRC (2001) requirements. The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
Keywords = liver
Keywords = cow
Keywords = lactation
Keywords = microarray


title: cow 6886, liver Cy3, day 1 relative to parturition

description: Holstein cow fed ad libitum amounts of a moderate-energy diet during an entire 65 day dry period.  Cow consumed ~120% of NRC (2001) requirements.  The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).


title: cow 6877, liver Cy3, day 49 relative to parturition

description: Holstein cow fed restricted amounts of a moderate-energy (1.60 Mcal/kg) diet during an entire 65 day dry period.  Cow consumed ~80% of NRC (2001) requirements.  The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).


title: cow 6877, liver Cy3, day -30 relative to parturition


title: cow 6877, liver Cy3, day -14 relative to parturition


title: cow 6877, liver Cy5, day -30 relative to parturition


title: cow 6877, liver Cy5, day -65 relative to parturition


title: cow 6877, liver Cy5, day -14 relative to parturition


title: cow 6877, liver Cy5, day 28 relative to parturition


title: cow 6877, liver Cy5, day 14 relative to parturition

description: Holstein cow fed a restricted amount of a moderate-energy (1.60 Mcal/kg) diet during a 65 day dry period.  Cow consumed ~80% of NRC (2001) requirements.  The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).


title: cow 6877, liver Cy3, day 14 relative to parturition

description:
Holstein cow fed a restricted amount of a moderate-energy (1.60 Mcal/kg) diet during an entire 65 day dry period.  Cow consumed ~80% of NRC (2001) requirements.  The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
Keywords = liver
Keywords = cow
Keywords = lactation
Keywords = microarray

tag: Mixture of bovine tissues total RNA


title: cow 6877, liver Cy5, day 1 relative to parturition

description:
Holstein cow fed a restricted amount of a moderate-energy (1.60 Mcal/kg) diet during a 65 day dry period.  Cow consumed ~80% of NRC (2001) requirements. The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
Keywords = liver
Keywords = cow
Keywords = lactation
Keywords = microarray


title: cow 6877, liver Cy3, day 1 relative to parturition

description:
Holstein cow fed a restricted amount of a moderate-energy (1.60 Mcal/kg) diet during an entire 65 day dry period.   Cow consumed ~80% of NRC (2001) requirements. The cDNA from liver RNA and the reference standard was coupled with Cy3 or Cy5 fluorescent dye and then co-hybridized to the microarray. Fluoresecent images for both dye channels were obtained using a Scanarray 4000 (GSI-Lumonics, Billerica, MA) dual-laser confocal scanner and images were processed using GenePix 4.0 (Axon Instruments, Inc., CA).
Keywords = liver
Keywords = cow
Keywords = lactation
Keywords = microarray

tag: Liver, cow, day 1 relative to parturition

tag: Mixture of bovine tissue RNA


title: H3K4Me3_gastrula_3_Slide2

status: Public on May 22 2006

city: Cambridge

first: Elizabeth

last: Herbolsheimer

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: IPed H3K4Me3 versus Control Whole Cell Extract Replicate 3

data_processing: None; Raw Data files

organism: Danio rerio

source_name: IP H3K4Me3

tag: Zebrafish Gastrula

source_name: Whole Cell Extract

tag: Control Whole Cell Extract


title: IRE1_RNAi_+DTT_B

status: Public on May 20 2006

city: San Francisco

first: Julie

last: Hollien

address: 1700 Fourth Street

department: Cell and Molecular Pharmacology

institute: UCSF

description: This is a sample for a study on the unfolded protein response in Drosophila S2 cells, hybridized with a standard ref. sample used for all associated arrays. We normalized the data using the NOMAD database (http://ucsf-nomad.sourceforge.net/), and filtered to remove spots with low signal intensity (<1.5 fold above background), inconsistent Cy5 to Cy3 signal ratios within the spot (R2 <0.5 for linear relationship between Cy5 vs. Cy3 signal), or obviously defective spots (visual inspection).

hyb_protocol: We hybridized the reference and experimental samples to the arrays at 65 °C overnight.

scan_protocol: Washing and scanning was essentially as described: Z. Bozdech et al., Genome Biol 4, R9 (2003).

data_processing: Normalized with population-based centering and filtered for intensity and quality (see description)

source_name: S2 cells, IRE1 RNAi, +DTT

label_protocol: For experimental samples (channel 1), we used total RNA (16 ug) extracted from S2 cells to synthesize amino-allyl labeled cDNA (Z. Bozdech et al., Genome Biol 4, R9 (2003)) which we then coupled to the fluorescent dye Cy5.

growth_protocol: Drosophila Schneider 2 (S2) cells were grown according to standard protocols at 26 °C in Schneider’s medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics.

extract_protocol: We collected cells by centrifugation and isolated total RNA using Trizol reagent (Invitrogen).

treatment_protocol: We depleted cells of specific transcripts using the general RNAi procedure described previously (J. C. Clemens et al., Proc Natl Acad Sci U S A 97, 6499 (Jun 6, 2000). Briefly, we synthesized dsRNA corresponding to ~400-500 nucleotides of the target mRNAs using T7 RNA polymerase. Drosophila IDs for the targets are: CG4583 (IRE1), CG9415 (XBP-1). We added ~15 ug/mL of the dsRNA to cells in serum-free media for 30-60 minutes then added serum-containing media (10% final serum concentration) to allow recovery. We passaged and re-treated cells with dsRNA after 3-4 days and 6-7 days, and induced the unfolded protein response with DTT (2 mM, 7.4 hours) one day after the third RNA treatment.

tag: S2 cells

tag: Depleted of IRE1 by RNAi

tag: Treated with DTT (2 mM, 7.4 hrs)

tag: replicate B

label_protocol: RNA was used to synthesize amino-allyl labeled cDNA (Bozdech et al., Genome Biol 4, R9 (2003)), which we then coupled to the fluorescent dye Cy3.

extract_protocol: S2 cells were collected by centrifugation and isolated total RNA using Trizol reagent (Invitrogen). RNA from embryos was isolated according to reference: M. N. Arbeitman et al., Science 297, 2270 (Sep 27, 2002).

treatment_protocol: S2 cells were either untreated or treated with DTT (2 mM, 7.4 hours).  embryos were untreated. embryo samples were from equal mixtures of embryos collected 0-8, 8-16, and 16-24 hours after egg lay.

tag: equal mixtures of total RNA purified from:

tag: 1. Drosophila embryos,

tag: 2. DTT-treated S2 cells, and

tag: 3. untreated S2 cells


title: IRE1_RNAi_+DTT_A

tag: replicate A


title: IRE1_RNAi_+DTT_C

tag: replicate C


title: KINECells_Chemokinetic

city: Sydney

first: Lilian

last: Soon

state: NSW

address: LG14, Madsen Building, F09

department: Australian Key Centre for Microscopy and Microanalysis, EMU

country: Australia

institute: The University of Sydney

hyb_protocol: Hybridization, washing and staining were performed in a Fluidics Station according to standard procedures.  Briefly, 15 micrograms of biotinylated cRNA were hybridized to a U133A chip for 16 h, and labeld with anti-streptavidin biotinylated antibody with intermittent washing steps.

scan_protocol: Affymetrix® GeneChip® Scanner3000 was used to scan the chip with preset pixel resolution and wavelength values.

data_processing: Affymetrix MAS 5.0 Scaling Protocol.  Original signal values are scaled to a mean of 1000.

label: Biotin

label_protocol: cRNA was labeled with biotin using the Affymetrix Enzo Kit according to the manufacturer's protocol.

growth_protocol: Cells grown were in complete medium (DMEM + 5% FBS).  No antibiotics were used for the experiment.  Cells were cultured for 24 h prior to harvesting for RNA extraction.

extract_protocol: Standard RNA extraction procedure using RNAeasy Mini kit (Qiagen).

treatment_protocol: Cells were selected for behaviour under chemokinetic conditions (no gradient of chemoattractant [1.5%FBS]) using Boyden chambers.

tag: H460 Lung Cancer Cells Selected for highly chemokinetic trait.


title: XBP_RNAi_+DTT_C

source_name: S2 cells, XBP-1 RNAi, +DTT

tag: Depleted of XBP-1 by RNAi


title: IRE1_RNAi_-DTT_C

source_name: S2 cells, IRE1 RNAi, -DTT

tag: untreated with DTT (control)


title: IRE1_RNAi_-DTT_A


title: IRE1_RNAi_-DTT_B


title: XBP_RNAi_-DTT_B

description: This is a control sample for a study on the unfolded protein response in Drosophila S2 cells, hybridized with a standard ref. sample used for all associated arrays.  We normalized the data using the NOMAD database (http://ucsf-nomad.sourceforge.net/), and filtered to remove spots with low signal intensity (<1.5 fold above background), inconsistent Cy5 to Cy3 signal ratios within the spot (R2 <0.5 for linear relationship between Cy5 vs. Cy3 signal), or obviously defective spots (visual inspection).

source_name: S2 cells, XBP-1 RNAi, -DTT

treatment_protocol: We depleted cells of specific transcripts using the general RNAi procedure described previously (J. C. Clemens et al., Proc Natl Acad Sci U S A 97, 6499 (Jun 6, 2000). Briefly, we synthesized dsRNA corresponding to ~400-500 nucleotides of the target mRNAs using T7 RNA polymerase. Drosophila IDs for the targets are: CG4583 (IRE1), CG9415 (XBP-1). We added ~15 ug/mL of the dsRNA to cells in serum-free media for 30-60 minutes then added serum-containing media (10% final serum concentration) to allow recovery. We passaged and re-treated cells with dsRNA after 3-4 days and 6-7 days, and induced the unfolded protein response with DTT (2 mM, 7.4 hours) one day after the third RNA treatment. As this is a control sample, DTT treatments were mock.

tag: Not treated with DTT (control)

treatment_protocol: S2 cells were either untreated or treated with DTT (2 mM, 7.4 hours). embryos were untreated. embryo samples were from equal mixtures of embryos collected 0-8, 8-16, and 16-24 hours after egg lay.


title: XBP_RNAi_+DTT_B


title: H3K4Me3_gastrula_1_Slide2

description: IPed H3K4Me3 versus Control Whole Cell Extract Replicate 1


title: control_+DTT_C

description:
This is a control sample for a study on the unfolded protein response in Drosophila S2 cells, hybridized with a standard ref. sample used for all associated arrays.
We normalized the data using the NOMAD database
(http://ucsf-nomad.sourceforge.net/), and filtered to remove spots with low signal intensity (<1.5 fold above background), inconsistent Cy5 to Cy3 signal ratios within the spot (R2 <0.5 for linear relationship between Cy5 vs. Cy3 signal), or obviously defective spots (visual inspection).

source_name: S2 cells, no RNAi, +DTT

label_protocol:
For experimental samples (channel 1), we used total RNA (16 g) extracted from S2 cells to synthesize amino-allyl labeled cDNA (1), which we then coupled to the fluorescent dye Cy5.
1.	Z. Bozdech et al., Genome Biol 4, R9 (2003).

growth_protocol:
Drosophila Schneider 2 (S2) cells were grown according to standard protocols (1) at 26 °C in Schneider’s medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics.
1.	J. C. Clemens et al., Proc Natl Acad Sci U S A 97, 6499 (Jun 6, 2000).

treatment_protocol:
We depleted cells of specific transcripts using the general RNAi procedure described previously (1). Briefly, we synthesized dsRNA corresponding to ~400-500 nucleotides of the target mRNAs using T7 RNA polymerase. Drosophila IDs for the targets are: CG4583 (IRE1), CG9415 (XBP-1). We added ~15 ug/mL of the dsRNA to cells in serum-free media for 30-60 minutes then added serum-containing media (10% final serum concentration) to allow recovery. We passaged and re-treated cells with dsRNA after 3-4 days and 6-7 days, and induced the unfolded protein response with DTT (2 mM, 7.4 hours) one day after the third RNA treatment. As this is a control sample, RNAi treatments were mock.
1.	J. C. Clemens et al., Proc Natl Acad Sci U S A 97, 6499 (Jun 6, 2000).

tag: untreated for RNAi (control)

tag: treated with DTT (2 mM, 7.4 hrs)

label_protocol:
RNA was used to synthesize amino-allyl labeled cDNA (1), which we then coupled to the fluorescent dye Cy3.
1.	Z. Bozdech et al., Genome Biol 4, R9 (2003).

extract_protocol:
S2 cells were collected by centrifugation and isolated total RNA using Trizol reagent (Invitrogen).
RNA from embryos was isolated according to reference:
1.	M. N. Arbeitman et al., Science 297, 2270 (Sep 27, 2002).

treatment_protocol:
S2 cells were either untreated or treated with DTT (2 mM, 7.4 hours).
embryos were untreated.
embryo samples were from equal mixtures of embryos collected 0-8, 8-16, and 16-24 hours after egg lay.


title: CONCells_Chemotactic

treatment_protocol: Untreated control cells.

tag: Cell Line

value: H460 Lung Cancer Cells

tag: Type

value: Non-Small-Cell-Lung-Cancer

tag: Treatment

value: Unselected control


title: XBP_RNAi_-DTT_C

tag: S2 cells


title: control_-DTT_C

source_name: S2 cells, no RNAi, -DTT

label_protocol:
For experimental samples (channel 1), we used total RNA (16 ug) extracted from S2 cells to synthesize amino-allyl labeled cDNA (1), which we then coupled to the fluorescent dye Cy5.
1.	Z. Bozdech et al., Genome Biol 4, R9 (2003).

treatment_protocol:
We depleted cells of specific transcripts using the general RNAi procedure described previously (1). Briefly, we synthesized dsRNA corresponding to ~400-500 nucleotides of the target mRNAs using T7 RNA polymerase. Drosophila IDs for the targets are: CG4583 (IRE1), CG9415 (XBP-1). We added ~15 ug/mL of the dsRNA to cells in serum-free media for 30-60 minutes then added serum-containing media (10% final serum concentration) to allow recovery. We passaged and re-treated cells with dsRNA after 3-4 days and 6-7 days, and induced the unfolded protein response with DTT (2 mM, 7.4 hours) one day after the third RNA treatment. As this is a control sample, all treatments were mock (no dsRNA, no DTT).
1.	J. C. Clemens et al., Proc Natl Acad Sci U S A 97, 6499 (Jun 6, 2000).

extract_protocol:
S2 cells were collected by centrifugation and isolated total RNA using Trizol reagent (Invitrogen).
RNA from embryos was isolated accoring to reference:
1.	M. N. Arbeitman et al., Science 297, 2270 (Sep 27, 2002).


title: control_+DTT_B

tag: replicate B


title: control_+DTT_A

tag: equal mixtures of total RNA purified from:


title: XBP_RNAi_+DTT_A

tag: Treated with DTT (2 mM, 7.4 hrs)

tag: 1. Drosophila embryos,


title: H3K4Me3_gastrula_2_Slide2

description: IPed H3K4Me3 versus Control Whole Cell Extract Replicate 2

tag: Zebrafish Gastrula

tag: Control Whole Cell Extract


title: XBP_RNAi_-DTT_A

tag: replicate A

tag: 2. DTT-treated S2 cells, and

tag: 3. untreated S2 cells


title: control_-DTT_B

description:
This is a control sample for a study on the unfolded protein response in Drosophila S2 cells, hybridized with a standard ref. sample used for all associated arrays.

We normalized the data using the NOMAD database
(http://ucsf-nomad.sourceforge.net/), and filtered to remove spots with low signal intensity (<1.5 fold above background), inconsistent Cy5 to Cy3 signal ratios within the spot (R2 <0.5 for linear relationship between Cy5 vs. Cy3 signal), or obviously defective spots (visual inspection).

tag: untreated with DTT (control)


title: H3K4Me3_gastrula_3_Slide1


title: H3K4Me3_gastrula_1_Slide1


title: H3K4Me3_gastrula_2_Slide1


title: PBMC treated_CT-8-hr-Trial-2

status: Public on May 19 2006

city: Silver Spring

first: Rasha

last: Hammamieh

address: 503 Robert Grant Ave

department: Molecular Pathology

institute: Walter Reed Army Institute of Research

description: RNA isolated from PBMC

data_processing: Local background correction and intrachip LOWESS normalization was accomplished by Genespring® 7.0 (Agilent Tech., CA).

source_name: PBMC treated with CT

tag: treated with CT


title: PBMC treated_CT-8-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC treated_CT-4-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC treated_CT-72-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC treated_CT-48hr-A

description: RNA isolated from PBMC


title: PBMC treated_CT-16-hr-Trial-1

description: RNA isolated from PBMC


title: control_-DTT_A

tag: untreated for RNAi (control)


title: PBMC treated_CT-4-hr-Trial-2

description: RNA isolated from PBMC


title: PBMC treated_Brucella6hsB2-120401sum

description: RNA isolated from PBMC

source_name: PBMC treated with brucella

tag: treated with brucella


title: PBMC treated_Brucella2hsB2-112701sum

description: RNA isolated from PBMC


title: PBMC treated_CT-16-hr-Trial-2

description: RNA isolated from PBMC


title: PBMC treated_CT-1-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC treated_Brucella6hsB3-122601sum

description: RNA isolated from PBMC


title: PBMC treated_CT-1-hr-Trial-2

description: RNA isolated from PBMC


title: PBMC treated_brucella6hsA1080701sum16bit

description: RNA isolated from PBMC


title: PBMC treated_Brucella6hsB1-120401sum

description: RNA isolated from PBMC


title: PBMC treated_Brucella2hsB1-112701sum

description: RNA isolated from PBMC


title: PBMC treated_brucella24hsB1121101sum

description: RNA isolated from PBMC


title: PBMC treated_brucella24hsB2-121101sum

description: RNA isolated from PBMC


title: PBMC treated_Brucella24hsB3-122601sum

description: RNA isolated from PBMC


title: PBMC treated_brucella2hsA1080701sum16bit

description: RNA isolated from PBMC


title: PBMC treated_bot6hr1B111401sum

description: RNA isolated from PBMC

source_name: PBMC treated with Bot

tag: treated with Bot


title: Salmonella typhimurium 14028 Hns ChIP-Chip rep 2

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

description: The array was hybridized with genomic DNA and hns-bound DNA from a chromatin immunoprecipitation.

data_processing: Using R program and limma pacakge, raw intensities were normalized by the median intensity in each channel and the ratios were calculated by log base 2 (hns-bound DNA / genomic DNA) after the normalization.

organism: Salmonella

source_name: Salmonella typhimurium 14028

tag: Salmonella typhimurium 14028 Genomic DNA

tag: Salmonella typhimurium 14028 Hns ChIP DNA sample


title: PBMC treated_bot6hr1A111401sum

description: RNA isolated from PBMC


title: PBMC treated_Bot2hr1B110701sum

description: RNA isolated from PBMC


title: PBMC treated_Anthrax8hr1A12

description: RNA isolated from PBMC

source_name: PBMC treated with anthrax

tag: treated with anthrax


title: PBMC treated_bot24hr1B111401sum

description: RNA isolated from PBMC


title: PBMC treated_Anthrax4hsA1030901sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_Anthrax8hs030901B1sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_Bot2hr1A110701sum

description: RNA isolated from PBMC


title: PBMC treated_Anthrax4hr2A12

description: RNA isolated from PBMC


title: Salmonella typhimurium 14028 Hns ChIP-Chip rep 1


title: PBMC treated_Anthrax4hs030901B1sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_Anthrax4hr1B110101sum

description: RNA isolated from PBMC


title: PBMC treated_bot24hr1A111401sum

description: RNA isolated from PBMC


title: PBMC treated_Anthrax8hsA1030901sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_anthrax2hsA1030901sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_Anthrax2hs030901-B1sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_Anthrax2hr1A12

description: RNA isolated from PBMC


title: PBMC treated_Anthrax4hr1A110101sum

description: RNA isolated from PBMC


title: PBMC untreated_SEB_12H_2A_110701_Sum

description: RNA isolated from PBMC

source_name: PBMC controls

tag: untreated


title: PBMC untreated_VEE-4h-Array I-exp-1-globa-sum-Jan 24-01

description: RNA isolated from PBMC


title: PBMC untreated_VEE-1h-Array I-Exp2-global-sum-Nov 01

description: RNA isolated from PBMC


title: PBMC untreated_VEE-8h-Array I-Exp1A-global sum-Nov1-01

description: RNA isolated from PBMC


title: PBMC untreated_VEE-4h-Exp2-Array I-global-sum-Nov 01-01

description: RNA isolated from PBMC


title: PBMC untreated_SEB_12H_1A_082500_Sum

description: RNA isolated from PBMC


title: PBMC untreated_VEE-8h-Array I-Exp1B-Global -sum-Nov1-01

description: RNA isolated from PBMC


title: PBMC untreated_SEB_18H_1A_083100_Sum

description: RNA isolated from PBMC


title: PBMC untreated_SEB_06H_2A_110801_Sum

description: RNA isolated from PBMC


title: PBMC untreated_VEE-1h-Array I-exp-1-sum- Jan24-01

description: RNA isolated from PBMC


title: PBMC untreated_SEB_18H_2A_110701_Sum

description: RNA isolated from PBMC


title: PBMC untreated_Plague4hr1B121301Sum

description: RNA isolated from PBMC


title: PBMC untreated_plague8hr1B111901Sum

description: RNA isolated from PBMC


title: PBMC untreated_Plague8hr1A111901Sum

description: RNA isolated from PBMC


title: PBMC untreated_SEB_03H_2A_110801_Sum

description: RNA isolated from PBMC


title: PBMC untreated_SEB_06H_1A_071100_Sum

description: RNA isolated from PBMC


title: PBMC untreated_SEB_03H_1A_083100_Sum

description: RNA isolated from PBMC


title: PBMC untreated_Plague2hr2B0110801Sum

description: RNA isolated from PBMC


title: PBMC untreated_Plague4hr1A121301Sum

description: RNA isolated from PBMC


title: PBMC untreated_Plague2hr1A080601Sum

description: RNA isolated from PBMC


title: PBMC untreated_DEN-8h-ArrayI-Exp1A-global-sum-May-01

description: RNA isolated from PBMC


title: PBMC untreated_Plague1hr1A092801Sum

description: RNA isolated from PBMC


title: PBMC untreated_Plague1hr1B121101Sum

description: RNA isolated from PBMC


title: PBMC untreated_DEN-4h-Array I-global-sum-Exp1A-May-01

description: RNA isolated from PBMC


title: PBMC untreated_Plague2hr2A0110801Sum

description: RNA isolated from PBMC


title: PBMC untreated_DEN-24h-Array I-exp1A-global-sum-Sept-01

description: RNA isolated from PBMC


title: PBMC untreated_DEN-4h-Array I-global-sum-Exp1B-July16-01

description: RNA isolated from PBMC


title: PBMC untreated_CT-72-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC untreated_CT-48hr-A

description: RNA isolated from PBMC


title: PBMC untreated_DEN-24h-ArrayI-exp1B-global-sum-Oct-01

description: RNA isolated from PBMC


title: PBMC untreated_CT-8-hr-Trial-2

description: RNA isolated from PBMC


title: PBMC untreated_CT-4-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC untreated_DEN-8h-Array I-exp1B-global-sum-July-01

description: RNA isolated from PBMC


title: PBMC untreated_CT-16-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC untreated_CT-1-hr-Trial-2

description: RNA isolated from PBMC


title: PBMC untreated_CT-16-hr-Trial-2

description: RNA isolated from PBMC


title: PBMC untreated_CT-4-hr-Trial-2

description: RNA isolated from PBMC


title: PBMC untreated_CT-1-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC untreated_Brucella6hsB2-120401sum

description: RNA isolated from PBMC


title: PBMC untreated_Brucella6hsB3-122601sum

description: RNA isolated from PBMC


title: PBMC untreated_Brucella2hsB1-112701sum

description: RNA isolated from PBMC


title: PBMC untreated_Brucella2hsB2-112701sum

description: RNA isolated from PBMC


title: PBMC untreated_brucella6hsA1080701sum16bit

description: RNA isolated from PBMC


title: PBMC untreated_Brucella24hsB3-122601sum

description: RNA isolated from PBMC


title: PBMC untreated_bot6hr1B111401sum

description: RNA isolated from PBMC


title: PBMC untreated_Brucella6hsB1-120401sum

description: RNA isolated from PBMC


title: PBMC untreated_CT-8-hr-Trial-1

description: RNA isolated from PBMC


title: PBMC untreated_Bot2hr1B110701sum

description: RNA isolated from PBMC


title: PBMC untreated_bot24hr1B111401sum

description: RNA isolated from PBMC


title: PBMC untreated_bot6hr1A111401sum

description: RNA isolated from PBMC


title: PBMC untreated_bot24hr1A111401sum

description: RNA isolated from PBMC


title: PBMC untreated_brucella24hsB2-121101sum

description: RNA isolated from PBMC


title: PBMC untreated_brucella24hsB1121101sum

description: RNA isolated from PBMC


title: PBMC untreated_brucella2hsA1080701sum16bit

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax8hr1A12

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax4hsA1030901sum 16bit

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax4hs030901B1sum 16bit

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax8hsA1030901sum 16bit

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax4hr2A12

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax4hr1A110101sum

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax4hr1B110101sum

description: RNA isolated from PBMC


title: PBMC untreated_Bot2hr1A110701sum

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax2hs030901-B1sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_VEE-8h-Array I-Exp1A-global sum-Nov1-01

description: RNA isolated from PBMC

source_name: PBMC treated with VEE

tag: treated with VEE


title: PBMC treated_VEE-8h-Array I-Exp1B-Global -sum-Nov1-01

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax2hr1A12

description: RNA isolated from PBMC


title: PBMC untreated_anthrax2hsA1030901sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_VEE-1h-Array I-Exp2-global-sum-Nov 01

description: RNA isolated from PBMC


title: PBMC treated_VEE-4h-Exp2-Array I-global-sum-Nov 01-01

description: RNA isolated from PBMC


title: PBMC treated_SEB_18H_2A_110701_Sum

description: RNA isolated from PBMC

source_name: PBMC treated with SEB

tag: treated with SEB


title: PBMC treated_SEB_12H_2A_110701_Sum

description: RNA isolated from PBMC


title: PBMC treated_SEB_18H_1A_083100_Sum

description: RNA isolated from PBMC


title: PBMC treated_VEE-1h-Array I-exp-1-sum- Jan24-01

description: RNA isolated from PBMC


title: PBMC treated_SEB_03H_2A_110801_Sum

description: RNA isolated from PBMC


title: PBMC treated_SEB_12H_1A_082500_Sum

description: RNA isolated from PBMC


title: PBMC treated_VEE-4h-Array I-exp-1-globa-sum-Jan 24-01

description: RNA isolated from PBMC


title: PBMC untreated_Anthrax8hs030901B1sum 16bit

description: RNA isolated from PBMC


title: PBMC treated_plague8hr1B111901Sum

description: RNA isolated from PBMC

source_name: PBMC treated with plague

tag: treated with plague


title: PBMC treated_Plague8hr1A111901Sum

description: RNA isolated from PBMC


title: PBMC treated_Plague4hr1A121301Sum

description: RNA isolated from PBMC


title: PBMC treated_SEB_06H_2A_110801_Sum

description: RNA isolated from PBMC


title: PBMC treated_SEB_06H_1A_071100_Sum

description: RNA isolated from PBMC


title: PBMC treated_Plague4hr1B121301Sum

description: RNA isolated from PBMC


title: PBMC treated_Plague1hr1A092801Sum

description: RNA isolated from PBMC


title: PBMC treated_Plague2hr2A0110801Sum

description: RNA isolated from PBMC


title: PBMC treated_DEN-8h-ArrayI-Exp1A-global-sum-May-01

description: RNA isolated from PBMC

source_name: PBMC treated with DEN

tag: treated with DEN


title: PBMC treated_Plague2hr1A080601Sum

description: RNA isolated from PBMC


title: PBMC treated_DEN-8h-Array I-exp1B-global-sum-July-01

description: RNA isolated from PBMC


title: PBMC treated_DEN-4h-Array I-global-sum-Exp1A-May-01

description: RNA isolated from PBMC


title: PBMC treated_DEN-24h-ArrayI-exp1B-global-sum-Oct-01

description: RNA isolated from PBMC


title: PBMC treated_DEN-4h-Array I-global-sum-Exp1B-July16-01

description: RNA isolated from PBMC


title: PBMC treated_Plague2hr2B0110801Sum

description: RNA isolated from PBMC


title: PBMC treated_Plague1hr1B121101Sum

description: RNA isolated from PBMC


title: PBMC treated_DEN-24h-Array I-exp1A-global-sum-Sept-01

description: RNA isolated from PBMC


title: set1htz1sir2_array3

status: Public on May 17 2006

first: Shivkumar

last: Venkatasubrahmanyam

department: Biochemistry

description: set1htz1sir2 vs wild-type

data_processing: log2 of set1htz1sir2/WT ratio, normalized for total signal in each channel

molecule: polyA RNA

tag: set1htz1sir2, log phase, YPAD, 30C

source_name: wild-type

tag: wild-type, log phase, YPAD, 30C


title: set1htz1sir2_array4

description: set1htz1sir2 vs wild-type


title: H3K4A_array1

description: H3K4A vs wild-type

data_processing: log2 of H3K4A/WT ratio, normalized for total signal in each channel

tag: H3K4A, log phase, YPAD, 30C


title: H3K4A_array2

description: H3K4A vs wild-type


title: H3K4A_array4

description: H3K4A vs wild-type


title: set1htz1_array2

description: set1htz1 vs wild-type

data_processing: log2 of set1htz1/WT ratio, normalized for total signal in each channel

tag: set1htz1, log phase, YPAD, 30C


title: set1htz1_array4

description: set1htz1 vs wild-type


title: set1_array2

description: set1 vs wild-type

data_processing: log2 of set1/WT ratio, normalized for total signal in each channel

tag: set1, log phase, YPAD, 30C


title: set1htz1_array3

description: set1htz1 vs wild-type


title: H3K4A_array3

description: H3K4A vs wild-type


title: set1_array3

description: set1 vs wild-type


title: set1htz1_array1

description: set1htz1 vs wild-type


title: set1htz1sir2_array1

description: set1htz1sir2 vs wild-type


title: set1htz1sir2_array2

description: set1htz1sir2 vs wild-type


title: set1_array1

description: set1 vs wild-type


title: set1_array4

description: set1 vs wild-type


title: Tet-A673/EF-2-RNAi, 0 hours, induced, run 2

city: Salt Lake City

first: Stephen

last: Lessnick

state: UT

address: 2000 Circle of Hope

department: Center for Children

institute: Huntsman Cancer Institute

description: Inducible-rescue A673 experiment

data_processing: Mas5.0, scaled

label: biotinylated CTP and UTP

source_name: A673 Ewing's sarcoma cells

tag: A673 Ewing's sarcoma cells, with inducible EWS/FLI cDNA, harboring the EF-2-RNAi retrovirus, induced for the indicated time period.


title: Tet-A673/EF-2-RNAi, 72 hours, uninduced, run 2

description: Inducible-rescue A673 experiment

tag: A673 Ewing's sarcoma cells, with inducible EWS/FLI cDNA, harboring the EF-2-RNAi retrovirus, left uninduced for the indicated time period.


title: Tet-A673/EF-2-RNAi, 24 hours, uninduced, run 2

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 72 hours, induced, run 2

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 48 hours, induced, run 2

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 12 hours, induced, run 2

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 6 hours, induced, run 2

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 24 hours, induced, run 2

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 72 hours, uninduced, run 1

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 72 hours, induced, run 1

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 48 hours, induced, run 1

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 24 hours, induced, run 1

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 12 hours, induced, run 1

description: Inducible-rescue A673 experiment


title: Tet-A673/EF-2-RNAi, 6 hours, induced, run 1

description: Inducible-rescue A673 experiment


title: Distribution of Spo13 during Meiosis I

status: Public on May 16 2006

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: Spo13 distribution in Meiosis I.

data_processing: The protocol provided by Affymetrix (GCOS ver1.4) was used.

source_name: Chromatin-immunoprecipitated DNA

tag: Spo13 was tagged by 3XFLAG. Strain SK1 was used.


title: A673 EF-2-RNAi replicate 2

description: A673 EF-2-RNAi replicate 2

data_processing: MAS5.0, normalized

label: Biotinylated UTP and CTP

tag: A673 Ewing's sarcoma cells harboring the EF-2-RNAi retrovirus


title: A673 luc-RNAi, replicate 3

description: A673 luc-RNAi replicate 3

tag: A673 Ewing's sarcoma cells harboring the luc-RNAi retrovirus.


title: Tet-A673/EF-2-RNAi, 0 hours, induced, run 1

description: Inducible-rescue A673 experiment


title: A673 EF-2-RNAi, replicate 4

description: A673 EF-2-RNAi replicate 4

tag: A673 Ewing's sarcoma cells harboring the EF-2-RNAi retrovirus.


title: A673 luc-RNAi replicate 1

description: A673 luc-RNAi replicate 1

tag: A673 Ewing's sarcoma cells containing luc-RNAi retrovirus


title: A673 luc-RNAi, replicate 7

description: A673 luc-RNAi replicate 7


title: Pt.2 PB-CTL NKG2C+

status: Public on May 15 2006

city: Chicago

first: Bana

last: Jabri

address: 5841 S Maryland Ave, S354

department: Department of Pathology

institute: University of Chicago

description: Gene expression data from PB-CTLs from adult CMV seropositive patient.

data_processing: Data analyses were preformed using DNA-Chip Analyzer 1.3 (dChip) with the *.CEL files obtained from GeneChip Operating System 1.3 (GCOS 1.3). A PM-only model was used to estimate gene expression level and the invariant set approach was used for normalization.

source_name: Peripheral Blood Lymphocytes

tag: TCRab+ CD8+ NKG2C+ PB-CTL from CMV seropositive patient.


title: macrophages_stimlpsic_2hours_rep1

description: Protocols and data processing were done using standard methods described by Affymetrix provided litterature. This includes Eukaryotic Sample and Array Processing manual and GeneChip Expression Analysis Data Analysis Fundamentals manual.

data_processing: Data processing using Affymetrix Microarray Suite Version 5.0. following GeneChip Expression Analysis Data Analysis Fundamentals manual.

source_name: macrophages, stim. LPS+immune complexes, 2 hours

label_protocol: Followed Affymetrix published Eukaryotic Sample and Array Processing manual.

tag: Balb/c bone marrow derived macrophages


title: Pt.3 PB-CTL NKG2C+

description: Gene expression data from PB-CTLs from adult celiac patient.

tag: TCRab+ CD8+ NKG2C+ PB-CTL from active celiac disease patient.


title: A673 EF-4-RNAi, replicate 8

description: A673 EF-4-RNAi replicate 8

tag: A673 Ewing's sarcoma cells harboring the EF-4-RNAi retrovirus.


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_6.5hB_#7471

status: Public on May 14 2006

city: Saint Louis

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

description: BT3172-deficient Bacteroides thetaiotaomicron grown in a batch culture fermenter in rich media (1% tryptone, 0.5%yeast extract, 0.2%glucose; TYG); harvested at 6.5 hours

data_processing: MAS5; scaling = 500

organism: Bacteroides thetaiotaomicron

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 6.5hB


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_8.8hB_#7473

description: BT3172-deficient Bacteroides thetaiotaomicron grown in a batch culture fermenter in rich media (1% tryptone, 0.5%yeast extract, 0.2%glucose; TYG); harvested at 8.8 hours

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 8.8hB


title: Pt.7 IE-CTL NKG2C-

description: Gene expression data from IE-CTLs from adult celiac patient.

source_name: Intraepithelial Lymphocytes

tag: TCRab+ CD8+ NKG2C- IE-CTL from active celiac disease patient.


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_8.8h_#7472

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 8.8hA


title: Pt.3 PB-CTL NKG2C-

tag: TCRab+ CD8+ NKG2C- PB-CTL from active celiac disease patient.


title: Pt.8 PB-CTL NKG2C+


title: Pt.6 IE-CTL NKG2C+

tag: TCRab+ CD8+ NKG2C+ IE-CTL from active celiac disease patient.


title: A673 EF-4-RNAi, replicate 6

description: A673 EF-4-RNAi replicate 6


title: Pt.6 IE-CTL NKG2C-


title: IFN gamma Macrophage_LPSstim_2h_rep1

source_name: Bone marrow derived macrophages, stimulated LPS, 2 hours

tag: Balb/c bone marrow derrived macrophages stimulated overnight, washed, then stimulated 2 hours with 10ng/ml LPS in complete media.


title: Pt.8 PB-CTL NKG2C-


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_6.5hA_#7470

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 6.5hA


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_5.5hA_#7468

description: BT3172-deficient Bacteroides thetaiotaomicron grown in a batch culture fermenter in rich media (1% tryptone, 0.5%yeast extract, 0.2%glucose; TYG); harvested at 5.5 hours

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 5.5hA


title: A673 luc-RNAi, replicate 5

description: A673 luc-RNAi replicate 5


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_5.5hB_#7469

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 5.5hB


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_3.5hA_#7466

description: BT3172-deficient Bacteroides thetaiotaomicron grown in a batch culture fermenter in rich media (1% tryptone, 0.5%yeast extract, 0.2%glucose; TYG); harvested at 3.5 hours.

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 3.5h


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_GSchow_10d_5_#8501

description: BT3172-deficient Bacteroides thetaiotaomicron monoassociated in gnotobiotic NMRI mice on a glucose-sucrose polysaccharide-deficient (GS) diet, harvested from the cecum after 10 days.

source_name: Bacteroides thetaiotaomicron(BT3172::pGERM), monoassociation, cecum NMRI mice, 10days


title: Bthetaiotaomicron(BT3172::pGERM)_TYG_3.5hB_#7467

description: BT3172-deficient Bacteroides thetaiotaomicron grown in a batch culture fermenter in rich media (1% tryptone, 0.5%yeast extract, 0.2%glucose; TYG); harvested at 3.5 hours

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), TYG, 3.5hB


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_GSchow_10d_3_#8499

tag: Bacteroides thetaiotaomicron(BT3172::pGERM), monoassociation, cecum NMRI mice, 10days


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_GSchow_10d_4_#8500


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_GSchow_10d_2_#8498


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_PRchow_10d_2_#8425

description: BT3172-deficient Bacteroides thetaiotaomicron monoassociated in gnotobiotic NMRI mice on a standard polysaccharide-rich (PR)diet, harvested from the cecum after 10 days.


title: Pt.2 PB-CTL NKG2C-

tag: TCRab+ CD8+ NKG2C- PB-CTL from CMV seropositive patient.


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_PRchow_10d_3_#8426


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_PRchow_10d_4_#8427


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_PRchow_10d_5_#8428


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_GSchow_10d_1_#8497


title: Bthetaiotaomicron_NMRIcecum_PRchow_10d_1_#8429

description: Bacteroides thetaiotaomicron monoassociated in gnotobiotic NMRI mice on a standard polysaccharide-rich (PR)diet, harvested from the cecum after 10 days.

source_name: Bacteroides thetaiotaomicron, monoassociation, cecum NMRI mice, 10days


title: Bthetaiotaomicron_NMRIcecum_PRchow_10d_5_#8433

tag: Bacteroides thetaiotaomicron, monoassociation, cecum NMRI mice, 10days


title: Bthetaiotaomicron(BT3172::pGERM)_NMRIcecum_PRchow_10d_1_#8424


title: Bthetaiotaomicron_NMRIcecum_PRchow_10d_2_#8430


title: Bthetaiotaomicron_NMRIcecum_PRchow_10d_4_#8432


title: S1P replicate 3

status: Public on May 13 2006

first: Chris

middle: D

last: McCabe

address: 2430 N Halsted

department: Neurobiology

institute: Children's Memorial Hospital

description: Sphingosine 1-phosphate treated glioblastoma cell line

data_processing: MAS 5.0

source_name: glioblastoma cell line

treatment_protocol: Sphingosine 1-phosphate treatment in vitro

tag: glioblastoma cell line, replicate 3, Sphingosine 1-phosphate treatment