title: prostate cancer/normal reference-18

status: Public on Sep 26 2008

type: genomic

city: Shanghai

first: Mei

last: Jiang

address: Handan Road

department: Institute of Genetics

country: China

institute: Fudan University

description: prostate cancer versus normal reference

hyb_protocol: Resultant cDNA was purified and hybridized to the microarray provided by United Gene Holdings Group Co., Ltd. Microarrays were pre-hybridized with hybridization solution containing 0.5 mg/ml denatured salmon sperm DNA at 42℃ for 6 hr. Fluorescent probe mixtures were denatured at 95℃ for 5 min, and the denatured probe mixtures were applied onto the pre-hybridized chip. And then put a cover glass on it. Chips were hybridized at 42℃ for 15–17 hr. The hybridized chips were then washed at 60℃ for 10 min each in solutions of 2ХSSC and 0.2% SDS, 0.1ХSSC and 0.2% SDS, and 0.1ХSSC, and then dried at room temperature.

scan_protocol: Every slide was scanned by ScanArray 4000B scanner (General Scanning, Watertown, MA). The fluorescent images of Cy5 and Cy3 were scanned separately and saved for further image analysis.

data_processing:
The acquired images were analyzed with GenePix Pro 3.0 software (Axon Instruments, Inc., Union City, CA).
VALUE is log2 ratio of the median of Channel 1 (635 nm) to Channel 2 (532 nm)

molecule: genomic DNA

organism: Homo sapiens

source_name: prostate cancer

label_protocol: For labeling, genomic DNA was digested with EcoRⅠ and HindⅢ (Sango, Shanghai, China) and then purified by extraction with phenol:chloroform and ethanol precipitation. Tumor and normal reference DNA were labeled with Cy5-dCTP and Cy3-dCTP (Amersham Pharmacia Biotech, Piscataway, NJ), respectively, by means of nick translation as described by Pollack et al.. The two color probes were then mixed, precipitated with ethanol, and dissolved in 20μl of hybridization solution [5ХSSC (0.75 M NaCl and 0.075 M sodium citrate), 0.4% SDS, 50% formamide, and 5ХDenhardt’s Solution (0.1% Ficoll, 0.1% polyvinylpyrrolidone, and 0.1% BSA)].

tag: Tumor

value: prostate cancer Gender:male Sample assession number:No.32

source_name: normal reference

tag: Tissue

value: kidney Gender:male


title: prostate cancer/common reference-25

type: RNA

description: prostate cancer versus common reference

data_processing: VALUE is log2 ratio of the median of Channel 1 (635 nm) to Channel 2 (532 nm)

molecule: total RNA

value: prostate cancer Gender:male Sample assession number:No.25

source_name: common reference

tag: a pool of RNA from mixed human embryo tissues


title: prostate cancer/normal reference-13

description: prostate cancer versus normal reference

extract_protocol: Tumor and normal reference DNA were labeled with Cy5-dCTP and Cy3-dCTP (Amersham Pharmacia Biotech, Piscataway, NJ), respectively, by means of nick translation as described by Pollack et al.. The two color probes were then mixed, precipitated with ethanol, and dissolved in 20μl of hybridization solution [5ХSSC (0.75 M NaCl and 0.075 M sodium citrate), 0.4% SDS, 50% formamide, and 5ХDenhardt’s Solution (0.1% Ficoll, 0.1% polyvinylpyrrolidone, and 0.1% BSA)].

value: prostate cancer Gender:male Sample assession number:No.27


title: prostate cancer/common reference-15

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.15


title: prostate cancer/normal reference-14

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.28


title: prostate cancer/normal reference-17

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.31


title: prostate cancer/common reference-11

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.11


title: prostate cancer/normal reference-15

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.29


title: prostate cancer/normal reference-10

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.23


title: prostate cancer/common reference-12

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.12


title: prostate cancer/common reference-24

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.24


title: prostate cancer/common reference-16

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.16


title: prostate cancer/common reference-20

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.20


title: prostate cancer/common reference-23

description: prostate cancer versus common reference


title: prostate cancer/common reference-19

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.19


title: prostate cancer/normal reference-9

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.21


title: prostate cancer/normal reference-5

description: prostate cancer versus normal reference


title: prostate cancer/normal reference-16

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.30


title: prostate cancer/common reference-21

description: prostate cancer versus common reference


title: prostate cancer/normal reference-6

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.17


title: prostate cancer/normal reference-12

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.26

value: kidney Gender:male


title: prostate cancer/common reference-22

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.22


title: prostate cancer/common reference-18

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.18


title: prostate cancer/normal reference-7

description: prostate cancer versus normal reference


title: prostate cancer/normal reference-11

description: prostate cancer versus normal reference


title: prostate cancer/common reference-17

description: prostate cancer versus common reference


title: prostate cancer/common reference-14

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.14


title: prostate cancer/normal reference-4

description: prostate cancer versus normal reference


title: prostate cancer/normal reference-8

description: prostate cancer versus normal reference


title: prostate cancer/common reference-10

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.10


title: prostate cancer/common reference-5

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.05


title: prostate cancer/common reference-13

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.13


title: Replicate 1 of the comparsion of crc/Mb101 at 5 hr

status: Public on Sep 11 2008

city: San Diego

first: Hongfan

last: Jin

state: CA

address: 5501 Oberlin Drive

department: Biotechnology

country: USA

institute: The Dow Chemical Company

description: this is the replicate 1 of the comparsion of crc/Mb101 at 5 hr

data_processing: log2 ratio of lowess normalized data

organism: Pseudomonas fluorescens

source_name: 5hr crc_cy3

tag: crc mutant strain at 5 hr sample

source_name: 5hr MB_cy5

tag: P. fluorescens strain MB101 at 5hr sample


title: prostate cancer/common reference-9

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.09


title: prostate cancer/common reference-1

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.01


title: prostate cancer/normal reference-3

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.6


title: Nomal prostate/common reference-1

description: normal prostate tissue versus common reference

source_name: normal prostate tissue

tag: normal prostate tissue

source_name: Common reference


title: prostate cancer/common reference-4

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.04


title: Replicate 2 of the comparsion of crc/Mb101 at 9 hr

description: this is the replicate 2 of the comparsion of crc/Mb101 at 9 hr

source_name: 9hr MB_cy3

tag: P. fluorescens strain MB101 at 9hr sample

source_name: 9hr crc_cy5

tag: crc mutant strain at 9 hr sample


title: Replicate 2 of the comparsion of crc/Mb101 at 7 hr

description: this is the replicate 2 of the comparsion of crc/Mb101 at 7 hr

source_name: 7hr MB_Cy3

tag: P. fluorescens strain MB101 at 7hr sample

source_name: 7hr crc_cy5

tag: crc mutant strain at 7 hr sample


title: Nomal prostate/common reference-3


title: Replicate 2 of the comparsion of crc/Mb101 at 5 hr

description: this is the replicate 2 of the comparsion of crc/Mb101 at 5 hr

source_name: 5hr MB_cy3

source_name: 5hr crc_cy5


title: Nomal prostate/common reference-2


title: prostate cancer/common reference-2

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.02


title: Replicate 1 of the comparsion of crc/Mb101 at 6 hr

description: this is the replicate 1 of the comparsion of crc/Mb101 at 6 hr

source_name: 6hr crc_cy3

tag: crc mutant strain at 6 hr sample

source_name: 6hr MB_cy5

tag: P. fluorescens strain MB101 at 6hr sample


title: Replicate 1 of the comparsion of crc/Mb101 at 7 hr

description: this is the replicate 1 of the comparsion of crc/Mb101 at 7 hr

source_name: 7hr crc_cy3

source_name: 7hr MB_cy5


title: prostate cancer/common reference-6

description: prostate cancer versus common reference

source_name: prostate cancer

value: prostate cancer Gender:male Sample assession number:No.06


title: Replicate 1 of the comparsion of crc/Mb101 at 8 hr

description: this is the replicate 1 of the comparsion of crc/Mb101 at 8 hr

hyb_protocol: not supplied

scan_protocol: not supplied

source_name: 8hr crc_cy3

label_protocol: not supplied

extract_protocol: not supplied

tag: crc mutant strain at 8 hr sample

source_name: 8hr MB_cy5

tag: P. fluorescens strain MB101 at 8hr sample


title: prostate cancer/common reference-8

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.08

source_name: common reference


title: Replicate 1 of the comparsion of crc/Mb101 at 9 hr

description: this is the replicate 1 of the comparsion of crc/Mb101 at 9 hr

source_name: 9 hr crc_cy3

source_name: 9 hr MB_cy5


title: prostate cancer/normal reference-1

description: prostate cancer versus normal reference

label_protocol: For labeling, genomic DNA was digested with EcoRⅠ and HindⅢ (Sango, Shanghai, China) and then purified by extraction with phenol:chloroform and ethanol precipitation.

value: prostate cancer Gender:male Sample assession number:No.2

source_name: normal reference


title: Replicate 2 of the comparsion of crc/Mb101 at 8 hr

description: this is the replicate 2 of the comparsion of crc/Mb101 at 8 hr

source_name: 8hr MB-Cy3

source_name: 8hr crc_cy5


title: prostate cancer/normal reference-2

description: prostate cancer versus normal reference

value: prostate cancer Gender:male Sample assession number:No.4


title: Replicate 2 of the comparsion of crc/Mb101 at 6 hr

description: this is the replicate 2 of the comparsion of crc/Mb101 at 6 hr

source_name: 6hr MB_cy3

source_name: 6hr crc_cy5


title: prostate cancer/common reference-3

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.03


title: prostate cancer/common reference-7

description: prostate cancer versus common reference

value: prostate cancer Gender:male Sample assession number:No.07


title: sep-3

status: Public on Sep 01 2008

city: Stony Brook

first: Wei

last: Zeng

state: NY

institute: SUNY at Stony Brook

description: This human melanoma LOX cell was transfected with pGUS vector expressing GFP and siRNA targeting mRNA of seprase/FAP alpha.

source_name: Human melanoma LOX cell


title: alpha3-1

description: This human fibrosarcoma cell HT1080 was transfected with pGUS vector expressing GFP and siRNA targeting mRNA of integrin alpha3.

source_name: Human fibrosarcoma cell line HT1080


title: alpha3-2


title: MT1-2

description: This human fibrosarcoma cell HT1080 was transfected with pGUS vector expressing GFP and siRNA targeting mRNA of MT1-MMP.


title: HT1080-GUS-1

description: This human fibrosarcoma cell HT1080 was transfected with mock pGUS vector expressing GFP only.


title: GUS-1

description: This melanoma LOX cell line was transfected with mock pGUS vector expressing GFP.


title: HT1080-GUS-2


title: MT1-1


title: sep-2

description: This melanoma LOX cell line was transfected with pGUS vector expressing GFP and siRNA targeting mRNA of seprase/FAP alpha.


title: 3588

city: Redwood City

first: Jordan

last: Hiller

address: 1400 Seaport Blvd.

institute: PDL BioPharma

description:
xenograft: x_V703
pdl_hyb_id: 3588
Xenograft_source: colon stage 2 cell line

source_name: colon stage 2 cell line


title: GUS-2


title: 3716

description:
primary tumor
pdl_hyb_id: 3716
sex: F
age_at_diagnosis: 77
stage: 3
Site_in_colon: rectum/cecum synchr

source_name: rectum/cecum synchr


title: GUS-3


title: 3740

description:
xenograft: x_V9P
pdl_hyb_id: 3740
Xenograft_source: colon stage 3 cell line

source_name: colon stage 3 cell line


title: 3710

description:
primary tumor
pdl_hyb_id: 3710
sex: M
age_at_diagnosis: 62
stage: 2
Site_in_colon: descending colon

source_name: descending colon


title: 3595

description:
xenograft: x_V6
pdl_hyb_id: 3595
Xenograft_source: colon stage 3 cell line


title: 3598

description:
xenograft: x_V10M
pdl_hyb_id: 3598
Xenograft_source: Liver Met cell line

source_name: Liver Met cell line


title: 3735

description:
cell line: V394
pdl_hyb_id: 3735
Cell_line_source: Liver Met

source_name: Liver Met


title: 3593

description:
xenograft: x_V5
pdl_hyb_id: 3593
Xenograft_source: colon stage 3 cell line


title: 3709

description:
primary tumor
pdl_hyb_id: 3709
sex: F
age_at_diagnosis: 82
stage: 2
Site_in_colon: cecum

source_name: cecum


title: 3737

description:
xenograft: x_V8
pdl_hyb_id: 3737
Xenograft_source: Liver Met cell line


title: 3715

description:
primary tumor
pdl_hyb_id: 3715
sex: F
age_at_diagnosis: 76
stage: 3
Site_in_colon: rectosigmoid

source_name: rectosigmoid


title: 3741

description:
xenograft: x_V411
pdl_hyb_id: 3741
Xenograft_source: colon stage 1 cell line

source_name: colon stage 1 cell line


title: 3586

description:
xenograft: x_V576
pdl_hyb_id: 3586
Xenograft_source: Liver Met cell line


title: 3736

description:
cell line: V10M
pdl_hyb_id: 3736
Cell_line_source: Liver Met


title: 3582

description:
xenograft: x_V400
pdl_hyb_id: 3582
Xenograft_source: Liver Met cell line


title: 3738

description:
xenograft: x_V451
pdl_hyb_id: 3738
Xenograft_source: Lymph Node Met cell line

source_name: Lymph Node Met cell line


title: 3960

description:
liver met
pdl_hyb_id: 3960
sex: F
age_at_diagnosis: 73
stage: 4
Site_in_colon: rectosigmoid junction

source_name: rectosigmoid junction


title: 3591

description:
xenograft: x_V9M
pdl_hyb_id: 3591
Xenograft_source: Liver Met cell line


title: 3589

description:
xenograft: x_V784
pdl_hyb_id: 3589
Xenograft_source: Liver Met cell line


title: 3580

description:
xenograft: x_V241
pdl_hyb_id: 3580
Xenograft_source: colon stage 4 cell line

source_name: colon stage 4 cell line


title: 3742

description:
liver met
pdl_hyb_id: 3742
sex: M
age_at_diagnosis: 59
stage: 4
Site_in_colon: unknown

source_name: unknown


title: 3576

description:
xenograft: x_566
pdl_hyb_id: 3576
Xenograft_source: primary colon tumor, stage 2

source_name: primary colon tumor, stage 2


title: 3584

description:
xenograft: x_V481
pdl_hyb_id: 3584
Xenograft_source: colon stage 2 cell line


title: 3578

description:
xenograft: x_586
pdl_hyb_id: 3578
Xenograft_source: primary Liver Met

source_name: primary Liver Met


title: 3577

description:
xenograft: x_585
pdl_hyb_id: 3577
Xenograft_source: primary colon tumor, stage 2


title: 3573

description:
xenograft: x_452
pdl_hyb_id: 3573
Xenograft_source: primary colon tumor, stage 3

source_name: primary colon tumor, stage 3


title: 3583

description:
xenograft: x_V429
pdl_hyb_id: 3583
Xenograft_source: colon stage 2 cell line


title: 3574

description:
xenograft: x_480
pdl_hyb_id: 3574
Xenograft_source: primary colon tumor, stage 3


title: 3579

description:
xenograft: x_595
pdl_hyb_id: 3579
Xenograft_source: primary colon tumor, stage 2


title: 3569

description:
cell line: V389
pdl_hyb_id: 3569
Cell_line_source: primary colon tumor, stage 4

source_name: primary colon tumor, stage 4


title: 3565

description:
cell line: V489
pdl_hyb_id: 3565
Cell_line_source: primary colon tumor, stage 3


title: 3567

description:
cell line: V411
pdl_hyb_id: 3567
Cell_line_source: primary colon tumor, stage 1

source_name: primary colon tumor, stage 1


title: 3570

description:
cell line: V400
pdl_hyb_id: 3570
Cell_line_source: Liver Met


title: 3563

description:
cell line: V576
pdl_hyb_id: 3563
Cell_line_source: Liver Met


title: 3575

description:
xenograft: x_528
pdl_hyb_id: 3575
Xenograft_source: primary colon tumor, stage 4


title: sep-1

description: This melanoma LOX cell line was transfected with pGUS vector expressing GFP and siRNA targeting mRNA of seprase/FAP alpha.

source_name: Human melanoma LOX cell


title: 3561

description:
cell line: V456
pdl_hyb_id: 3561
Cell_line_source: unknown


title: 3564

description:
cell line: V235
pdl_hyb_id: 3564
Cell_line_source: primary colon tumor, stage 1


title: 3562

description:
cell line: V503
pdl_hyb_id: 3562
Cell_line_source: Liver Met


title: 3571

description:
cell line: V9M
pdl_hyb_id: 3571
Cell_line_source: Liver Met


title: 3566

description:
cell line: V241
pdl_hyb_id: 3566
Cell_line_source: Liver Met


title: 3560

description:
cell line: V410
pdl_hyb_id: 3560
Cell_line_source: Liver Met


title: 3568

description:
cell line: V206
pdl_hyb_id: 3568
Cell_line_source: Liver Met


title: 3550

description:
primary tumor
pdl_hyb_id: 3550
sex: M
age_at_diagnosis: 42
stage: 4
Site_in_colon: sigmoid

source_name: sigmoid


title: 3559

description:
cell line: V429
pdl_hyb_id: 3559
Cell_line_source: primary colon tumor, stage 2


title: 3558

description:
cell line: V330
pdl_hyb_id: 3558
Cell_line_source: primary colon tumor, stage 1


title: 3557

description:
cell line: V364
pdl_hyb_id: 3557
Cell_line_source: Liver Met


title: 3549

description:
primary tumor
pdl_hyb_id: 3549
sex: F
age_at_diagnosis: 42
stage: 4
Site_in_colon: sigmoid


title: 3551

description:
primary tumor
pdl_hyb_id: 3551
sex: F
age_at_diagnosis: 55
stage: 4
Site_in_colon: descending colon

source_name: descending colon


title: 3544

description:
primary tumor
pdl_hyb_id: 3544
sex: F
age_at_diagnosis: 83
stage: 3
Site_in_colon: sigmoid


title: 3543

description:
primary tumor
pdl_hyb_id: 3543
sex: F
age_at_diagnosis: 45
stage: 3
Site_in_colon: descending colon


title: 3548

description:
primary tumor
pdl_hyb_id: 3548
sex: F
age_at_diagnosis: 26
stage: 3
Site_in_colon: sigmoid


title: 3497

description:
cell line: FET
pdl_hyb_id: 3497
Cell_line_source: other

source_name: other


title: 3542

description:
primary tumor
pdl_hyb_id: 3542
sex: M
age_at_diagnosis: 64
stage: 3
Site_in_colon: ascending colon

source_name: ascending colon


title: 3488

description:
cell line: V457
pdl_hyb_id: 3488
Cell_line_source: Liver Met

source_name: Liver Met


title: 3494

description:
cell line: V703
pdl_hyb_id: 3494
Cell_line_source: primary colon tumor, stage 2


title: 3495

description:
cell line: HCT116
pdl_hyb_id: 3495
Cell_line_source: other


title: 3496

description:
cell line: RKO
pdl_hyb_id: 3496
Cell_line_source: other


title: 3490

description:
cell line: V5
pdl_hyb_id: 3490
Cell_line_source: primary colon tumor, stage 3


title: 3487

description:
cell line: sw480
pdl_hyb_id: 3487
Cell_line_source: other


title: 3492

description:
cell line: V432
pdl_hyb_id: 3492
Cell_line_source: primary colon tumor, stage 2


title: 3547

description:
primary tumor
pdl_hyb_id: 3547
sex: F
age_at_diagnosis: 84
stage: 3
Site_in_colon: cecum

source_name: cecum


title: 3545

description:
primary tumor
pdl_hyb_id: 3545
sex: F
age_at_diagnosis: 63
stage: 3
Site_in_colon: ascending colon


title: 3493

description:
cell line: V481
pdl_hyb_id: 3493
Cell_line_source: primary colon tumor, stage 2


title: 3541

description:
primary tumor
pdl_hyb_id: 3541
sex: M
age_at_diagnosis: 55
stage: 3
Site_in_colon: ascending colon


title: 3491

description:
cell line: V6
pdl_hyb_id: 3491
Cell_line_source: primary colon tumor, stage 3


title: 3546

description:
primary tumor
pdl_hyb_id: 3546
sex: M
age_at_diagnosis: 69
stage: 3
Site_in_colon: transverse colon

source_name: transverse colon


title: 3486

description:
cell line: V531
pdl_hyb_id: 3486
Cell_line_source: primary colon tumor, stage 2


title: 3485

description:
cell line: V478
pdl_hyb_id: 3485
Cell_line_source: primary colon tumor, stage 3


title: 3484

description:
cell line: V9P
pdl_hyb_id: 3484
Cell_line_source: primary colon tumor, stage 3


title: 3480

description:
cell line: V425
pdl_hyb_id: 3480
Cell_line_source: Liver Met


title: 3469

description:
normal colon
pdl_hyb_id: 3469
sex: F
age_at_diagnosis: 84
Site_in_colon: cecum


title: 3481

description:
cell line: V451
pdl_hyb_id: 3481
Cell_line_source: nodal Met

source_name: nodal Met


title: 3478

description:
xenograft: x_727
pdl_hyb_id: 3478
Xenograft_source: primary Liver Met


title: 3482

description:
cell line: V8
pdl_hyb_id: 3482
Cell_line_source: primary colon tumor, stage 4


title: 3489

description:
cell line: V670
pdl_hyb_id: 3489
Cell_line_source: nodal Met


title: 3483

description:
cell line: V441
pdl_hyb_id: 3483
Cell_line_source: primary colon tumor, stage 4


title: 3479

description:
cell line: V786
pdl_hyb_id: 3479
Cell_line_source: Liver Met


title: 3464

description:
primary tumor
pdl_hyb_id: 3464
sex: M
age_at_diagnosis: 75
stage: 4
Site_in_colon: sigmoid


title: 3465

description:
normal colon
pdl_hyb_id: 3465
sex: F
age_at_diagnosis: 64
Site_in_colon: sigmoid


title: 3468

description:
normal colon
pdl_hyb_id: 3468
sex: F
age_at_diagnosis: 68
Site_in_colon: rectum

source_name: rectum


title: 3453

description:
liver met
pdl_hyb_id: 3453
sex: M
age_at_diagnosis: 76
stage: 4
Site_in_colon: ascending colon


title: 3463

description:
liver met
pdl_hyb_id: 3463
sex: F
age_at_diagnosis: 63
stage: 4
Site_in_colon: cecum


title: 3467

description:
normal colon
pdl_hyb_id: 3467
sex: unk
age_at_diagnosis: unk
Site_in_colon: unknown


title: 3452

description:
liver met
pdl_hyb_id: 3452
sex: M
age_at_diagnosis: 49
stage: 4
Site_in_colon: ascending colon


title: 3451

description:
primary tumor
pdl_hyb_id: 3451
sex: F
age_at_diagnosis: 57
stage: 2
Site_in_colon: transverse

source_name: transverse


title: 3454

description:
liver met
pdl_hyb_id: 3454
sex: M
age_at_diagnosis: 76
stage: 4
Site_in_colon: ascending colon


title: 3446

description:
primary tumor
pdl_hyb_id: 3446
sex: M
age_at_diagnosis: 83
stage: 2
Site_in_colon: ascending colon


title: 3444

description:
primary tumor
pdl_hyb_id: 3444
sex: M
age_at_diagnosis: 66
stage: 2
Site_in_colon: ascending colon


title: 3466

description:
normal colon
pdl_hyb_id: 3466
sex: F
age_at_diagnosis: 84
Site_in_colon: unknown

source_name: unknown


title: 3449

description:
primary tumor
pdl_hyb_id: 3449
sex: F
age_at_diagnosis: 79
stage: 2
Site_in_colon: descending colon


title: 3443

description:
primary tumor
pdl_hyb_id: 3443
sex: M
age_at_diagnosis: 45
stage: 2
Site_in_colon: sigmoid


title: 3448

description:
primary tumor
pdl_hyb_id: 3448
sex: F
age_at_diagnosis: 69
stage: 2
Site_in_colon: cecum


title: 3445

description:
primary tumor
pdl_hyb_id: 3445
sex: F
age_at_diagnosis: 74
stage: 2
Site_in_colon: ascending colon


title: 3450

description:
primary tumor
pdl_hyb_id: 3450
sex: F
age_at_diagnosis: 73
stage: 2
Site_in_colon: sigmoid


title: 3442

description:
primary tumor
pdl_hyb_id: 3442
sex: F
age_at_diagnosis: 65
stage: 2
Site_in_colon: sigmoid


title: 3462

description:
liver met
pdl_hyb_id: 3462
sex: F
age_at_diagnosis: 45
stage: 4
Site_in_colon: cecum


title: 3447

description:
primary tumor
pdl_hyb_id: 3447
sex: F
age_at_diagnosis: 58
stage: 2
Site_in_colon: sigmoid


title: 3441

description:
primary tumor
pdl_hyb_id: 3441
sex: M
age_at_diagnosis: 73
stage: 2
Site_in_colon: sigmoid


title: 3440

description:
primary tumor
pdl_hyb_id: 3440
sex: M
age_at_diagnosis: 55
stage: 2
Site_in_colon: cecum


title: 3435

description:
primary tumor
pdl_hyb_id: 3435
sex: M
age_at_diagnosis: 68
stage: 2
Site_in_colon: ascending colon


title: 3436

description:
primary tumor
pdl_hyb_id: 3436
sex: F
age_at_diagnosis: 71
stage: 2
Site_in_colon: ascending colon


title: 3430

description:
liver met
pdl_hyb_id: 3430
sex: M
age_at_diagnosis: 79
stage: 4
Site_in_colon: sigmoid


title: 3431

description:
liver met
pdl_hyb_id: 3431
sex: M
age_at_diagnosis: 48
stage: 4
Site_in_colon: descending colon


title: 3429

description:
liver met
pdl_hyb_id: 3429
sex: F
age_at_diagnosis: 87
stage: 4
Site_in_colon: cecum


title: 3434

description:
primary tumor
pdl_hyb_id: 3434
sex: F
age_at_diagnosis: 81
stage: 2
Site_in_colon: sigmoid


title: 3439

description:
primary tumor
pdl_hyb_id: 3439
sex: F
age_at_diagnosis: 84
stage: 2
Site_in_colon: ascending colon


title: 3428

description:
liver met
pdl_hyb_id: 3428
sex: M
age_at_diagnosis: 66
stage: 4
Site_in_colon: unknown


title: 3438

description:
primary tumor
pdl_hyb_id: 3438
sex: M
age_at_diagnosis: 81
stage: 2
Site_in_colon: ascending colon


title: 3399

description:
liver met
pdl_hyb_id: 3399
sex: M
age_at_diagnosis: 61
stage: 4
Site_in_colon: rectum


title: 3397

description:
liver met
pdl_hyb_id: 3397
sex: F
age_at_diagnosis: 66
stage: 4
Site_in_colon: rectum


title: 3405

description:
liver met
pdl_hyb_id: 3405
sex: M
age_at_diagnosis: 53
stage: 4
Site_in_colon: ascending colon (cecum)

source_name: ascending colon (cecum)


title: 3402

description:
liver met
pdl_hyb_id: 3402
sex: M
age_at_diagnosis: 57
stage: 4
Site_in_colon: rectum


title: 3406

description:
liver met
pdl_hyb_id: 3406
sex: M
age_at_diagnosis: 71
stage: 4
Site_in_colon: cecum arising in a villous adenoma

source_name: cecum arising in a villous adenoma


title: 3401

description:
liver met
pdl_hyb_id: 3401
sex: M
age_at_diagnosis: 39
stage: 4
Site_in_colon: ascending colon


title: 3400

description:
liver met
pdl_hyb_id: 3400
sex: F
age_at_diagnosis: 70
stage: 4
Site_in_colon: rectum


title: 3411

description:
primary tumor
pdl_hyb_id: 3411
sex: M
age_at_diagnosis: 59
stage: 4
Site_in_colon: transverse colon


title: 3407

description:
liver met
pdl_hyb_id: 3407
sex: F
age_at_diagnosis: 77
stage: 4
Site_in_colon: unknown


title: 3396

description:
liver met
pdl_hyb_id: 3396
sex: F
age_at_diagnosis: 67
stage: 4
Site_in_colon: rectum


title: 3395

description:
liver met
pdl_hyb_id: 3395
sex: F
age_at_diagnosis: 66
stage: 4
Site_in_colon: unknown


title: 3393

description:
liver met
pdl_hyb_id: 3393
sex: M
age_at_diagnosis: 51
stage: 4
Site_in_colon: unknown


title: 3398

description:
liver met
pdl_hyb_id: 3398
sex: M
age_at_diagnosis: 55
stage: 4
Site_in_colon: descending colon


title: 3556

description:
primary tumor
pdl_hyb_id: 3556
sex: M
age_at_diagnosis: 79
stage: 2
Site_in_colon: ascending colon


title: 3391

description:
liver met
pdl_hyb_id: 3391
sex: M
age_at_diagnosis: 59
stage: 4
Site_in_colon: transverse colon


title: 3404

description:
liver met
pdl_hyb_id: 3404
sex: F
age_at_diagnosis: 63
stage: 4
Site_in_colon: descending colon


title: 3412

description:
normal colon
pdl_hyb_id: 3412
sex: M
age_at_diagnosis: 59
Site_in_colon: transverse colon


title: 3392

description:
liver met
pdl_hyb_id: 3392
sex: M
age_at_diagnosis: 75
stage: 4
Site_in_colon: sigmoid


title: 3389

description:
liver met
pdl_hyb_id: 3389
sex: M
age_at_diagnosis: 69
stage: 4
Site_in_colon: sigmoid


title: 3437

description:
primary tumor
pdl_hyb_id: 3437
sex: F
age_at_diagnosis: 85
stage: 2
Site_in_colon: cecum


title: 3394

description:
liver met
pdl_hyb_id: 3394
sex: M
age_at_diagnosis: 69
stage: 4
Site_in_colon: unknown


title: 3390

description:
liver met
pdl_hyb_id: 3390
sex: M
age_at_diagnosis: 68
stage: 4
Site_in_colon: sigmoid


title: Tumor_13d_1

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

country: Germany

institute: Karlsruhe Institute of Technology

description: Gene expression during biotrophic growth

hyb_protocol: Affymetrix EukGE-WS2 on a GeneChip Fluidics Station 400

scan_protocol: Affymetrix GCS2500

label: biotin/phycoerythrin

organism: Mycosarcoma maydis

source_name: Ustilago maydis infected corn plant

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, except for a reaction temperature of 50°C for first-strand cDNA synthesis.

growth_protocol: Corn plants (Sweet corn variety Early Golden Bantam) were grown in soil "Fruehstorfer Erde Typ T" in a Conviron E15 phytochamber, 10 h 20°C dark, 14 h at 28°C with light (four lamps type M400U and  fourlamps type LU400). 7 d old plants were infected with a mixture of strains FB1 and FB2, as described in "Brachmann, A., Weinzierl, G., Kämper, J. & Kahmann, R. Identification of genes in the bW/bE regulatory cascade in Ustilago maydis. Mol Microbiol 42, 1047-63. (2001)". Tumours were harvested at day 13 post infection.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer’s instructions. RNA samples were further column purified (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

tag: Tumors induced in corn plants by an infection with the two wildtype Ustilago maydis strains FB1 and FB2 to measure the gene expression in U. maydis during biotrophic growth


title: 3386

description:
liver met
pdl_hyb_id: 3386
sex: M
age_at_diagnosis: 53
stage: 4
Site_in_colon: descending colon


title: 3388

description:
liver met
pdl_hyb_id: 3388
sex: F
age_at_diagnosis: 80
stage: 4
Site_in_colon: descending colon


title: FB1_MM_2

description: Gene expression in axenic culture

source_name: Ustilago maydis

growth_protocol: FB1 was grown to an OD600 of 0.5 at 28°C in liquid array medium: 6.25 % (w/v) Holiday salt solution, 30 mM L-glutamine, 1 % (w/v) glucose, pH 7.0 (filter-sterilized).

tag: Strain FB1


title: tumor_13d_2


title: 3385

description:
primary tumor
pdl_hyb_id: 3385
sex: F
age_at_diagnosis: 58
stage: 2
Site_in_colon: sigmoid


title: 3387

description:
liver met
pdl_hyb_id: 3387
sex: M
age_at_diagnosis: 48
stage: 4
Site_in_colon: cecum


title: 3383

description:
primary tumor
pdl_hyb_id: 3383
sex: M
age_at_diagnosis: 89
stage: 2
Site_in_colon: splenic flexure

source_name: splenic flexure


title: 3376

description:
normal colon
pdl_hyb_id: 3376
sex: F
age_at_diagnosis: 82
Site_in_colon: cecum


title: 2787

description:
normal colon
pdl_hyb_id: 2787
sex: M
age_at_diagnosis: 65
Site_in_colon: sigmoid


title: FB1_MM_1

description: Gene expression in axenic culture


title: 3375

description:
normal colon
pdl_hyb_id: 3375
sex: F
age_at_diagnosis: 79
Site_in_colon: descending colon


title: 3374

description:
normal colon
pdl_hyb_id: 3374
sex: F
age_at_diagnosis: 88
Site_in_colon: ascending colon


title: 3377

description:
normal colon
pdl_hyb_id: 3377
sex: M
age_at_diagnosis: 77
Site_in_colon: cecum


title: 3380

description:
normal colon
pdl_hyb_id: 3380
sex: F
age_at_diagnosis: 67
Site_in_colon: ascending colon


title: 3382

description:
normal colon
pdl_hyb_id: 3382
sex: F
age_at_diagnosis: 87
Site_in_colon: sigmoid


title: 3379

description:
normal colon
pdl_hyb_id: 3379
sex: M
age_at_diagnosis: 61
Site_in_colon: rectum


title: 3381

description:
normal colon
pdl_hyb_id: 3381
sex: F
age_at_diagnosis: 83
Site_in_colon: sigmoid


title: S1_d3SBb2

status: Public on May 01 2008

city: BORDEAUX

first: Helene

last: BOEUF

country: France

description:
S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000 cells/ml in ES cell medium without LIF in the presence of 10 uM SB203580. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74Av2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed 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 the array was arbitrarily set to 300.

hyb_protocol: Detailed procedure in Duval et al, 2006, Cell Death and Differentiation, 13- 564-575.

label: Biotin

organism: Mus musculus

source_name: Embryonic stem cell line

extract_protocol: Total RNAs were extracted from adherent ES cells with the Qiagen column kit and treated with DNAse, 5u/100 microgrammes, Sigma.


title: 2788

description:
normal colon
pdl_hyb_id: 2788
sex: M
age_at_diagnosis: 69
Site_in_colon: ascending colon


title: 2758

description:
normal colon
pdl_hyb_id: 2758
sex: F
age_at_diagnosis: 52
Site_in_colon: unknown


title: 2792

description:
normal colon
pdl_hyb_id: 2792
sex: F
age_at_diagnosis: 79
Site_in_colon: rectum


title: 2789

description:
normal colon
pdl_hyb_id: 2789
sex: M
age_at_diagnosis: 52
Site_in_colon: splenic flexure


title: S1_d3SB

description:
S1 ES cell line, feeder free, derived as described (Hogan BL et al. 1994. Manipulating the mouse embryo. A laboratory manual, second edition. Cold Spring Harbor Laboratory Press, pp255-272), was grown in DMEM, high glucose supplemented with 0.1 mM beta mercaptoethanol, 10% FCS, 400 ug/ml gentamycin and 500 pM Leukaemia Inhibitory Factor (LIF). For microarray experiments, ES cells were diluted at
10 000 cells/ml in ES cell medium without LIF in the presence of 10 uM SB203580. Cell medium was changed every day and cells were lysed after 3 days. Total RNA from adherent cells were extracted using Qiagen RNeasy kit and treated with DNAse. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 1999, Affymetrix). Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on murine MG_U74A GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and further scanned using the Hewlett-Packard GeneArray Scanner G2500A. The image data were analysed 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 the array was arbitrarily set to 300.

hyb_protocol: Detailed procedure in Duval et al, 2006. Cell Death and Differentiation, 13,564-575.

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocole (Expression Analysis Technical manual, 1999).

extract_protocol: Total RNAs from adherent ES cells were prepared with the Qiagen column kit and treated with Dnase, 5u/100 microgrames (Sigma).


title: S1_d3SBb1

scan_protocol: Detailed procedure in Duval et al, 2006, Cell Death and Differentiation, 13- 564-575.

label: biotin

extract_protocol: Total RNAs from adherent ES cells were prepared with the Qiagen column kit and treated with Dnase, 5u/100microgrames


title: CS101 rgg dec

status: Public on Feb 01 2008

city: Kansas City

first: Alexander

middle: V

last: Dmitriev

state: KS

address: 3901 Rainbow Boulevard

institute: Kansas University Medical Center

description: End-terminus biotin-labeled cDNA (1.86 µg) was hybridized to S. pyogenes GeneChip genome arrays following the prokaryotic hybridization protocol recommended in the Affymetrix GeneChip Expression Analysis Technical Manual available at the Affymetrix website.

hyb_protocol: The GeneChips were hybridized with 1.86 ug of biotin end-terminus labeled cDNA in 1X hybridization buffer [100 mM Mes, 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20 (Pierce Chemical, Rockford, IL), 50 pM control oligonucleotide B2 (Affymetrix), 20 ug herring sperm DNA (Promega, Madison, WI), 100 ug acetylated bovine serum albumin (Invitrogen)] for 16 h at 45°C on a rotisserie at 60 r.p.m. Following hybridization, the hybridization cocktail was removed and the GeneChip filled with non-stringent buffer A [0.9 M sodium chloride, 60 mM sodium phosphate, 6 mM EDTA, and 0.01% Tween 20]. GeneChips were post-processed on the automated Affymetrix GeneChip Fluidics Station 450 using the following protocol: Wash 1: 10 cycles of 2 mixes/cycle with non-stringent buffer A at 25°C; Wash 2: 4 cycles of 15 mixes/cycles with stringent buffer B [100 mM Mes, 0.1 M NaCl, and 0.01% Tween 20] at 45°C; First stain: stain probe array for 10 min at 25°C in streptavidin-phycoerythrin (SAPE) solution [1x Mes stain buffer (100 mM Mes, 1 M NaCl, and 0.05% Tween 20), 2 mg/ml acetylated BSA, and 10 ug/ml SAPE (Molecular Probes, Eugene, OR)] post stain: wash 10 cycles of 4 mixes/cycle with non-stringent buffer A at 300C; second stain: stain probe array for 10 min in antibody solution [1x Mes stain buffer, 2 mg/ml acetylated BSA, 0.1 mg/ml normal goat IgG (Sigma-Aldrich, St. Louis, MO), and 3 ug/ml biotinylated antibody (Vector Laboratories, Burlingame, CA); third stain: stain probe array for 10 min in SAPE solution at 25°C; final wash: 15 cycles of 4 mixes/cycle with non-stringent buffer A at 30°C.

scan_protocol: The probed arrays were scanned at 570 nm at a resolution of 1.56 µm using a confocal GC3000 laser scanner (Affymetrix)

data_processing: Gene expression levels were calculated with GeneSpring 7 software (Silicon Genetics, Redwood City, CA)

organism: Streptococcus pyogenes

source_name: Streptococcus pyogenes, CS101 rgg mutant, post-exponential phase of growth

label_protocol: The 3' terminus of the fragmented cDNA was labeled with Biotin-N6-ddATP (ENZO, New York, NY) at 37°C for 2 h using 50 U of terminal deoxynucleotide transferase (New England Biolabs, Ipswich, MA)

extract_protocol: RNA was isolated using RNeasy Mini Kit (QIAGEN, Valencia, CA). cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Carsbad, CA)

tag: Strain

value: CS101 rgg mutant


title: MGAS5005 rgg Em

source_name: Streptococcus pyogenes, MGAS5005 rgg mutant, post-exponential phase of growth

value: MGAS5005 rgg mutant


title: MGAS5005 rgg dec


title: 2757

description:
normal colon
pdl_hyb_id: 2757
sex: F
age_at_diagnosis: 77
Site_in_colon: rectum


title: CS101 wt Em

source_name: Streptococcus pyogenes, CS101 wild-type strain, post-exponential phase of growth

value: CS101 wild-type


title: with signs of rejection 6 10-2

status: Public on Mar 12 2008

city: worcester

first: Georg

last: Elias

state: MA

address: 377 plantation St/ Biotech 4

department: Surgery/ Transplant

institute: UMASSMED

description:
Intestine, 6 weeks post transplant  under immunosuppressant rep2.
Gene expression data from transplanted intestinal mucosa, when there are signs and symptoms of rejection.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized on 45 C on Affymetrix HG-U133_Plus_2 human GeneChip, GeneChips were washed and stained in the Affymetrix Fluidics according to their protocol, EukGE-WS2v4_450

scan_protocol: GeneChips were scanned using Pixel Size 1.56,  Filter 570, Scanner ID    50208790,   Scanner Type   M10

data_processing: All microarray data analysis was done using the Genespring 6.1 software package Agilent Technologies, Palo Alto, CA, USA.  Gene lists generated, were evaluated for GO biological functions and pathway analysis using David 2.0  NIH, Bethesda, MD, USA and Pathway Assist 3.0 Stratagene, La Jolla, CA,

source_name: Intestinal mucosal biopsy from the donor graft 6 weeks post transplant

label_protocol: Biotinylated cRNA were prepared according to the standard  BioArray RNA IVT labeling kit Enzo Life Science, Farmingdale, NY, USA

extract_protocol: RNeasy micro kit Qiagen, Valencia, CA, USA  Cat No 75142 according to the manufacturer's instructions.

tag: Female, 22 year old doter donate a small bowel to her mother 45 year old, the biopsy from the transplanted intestine 6 weeks post transplant, with signs of rejection


title: CS101 wt dec


title: with signs of rejection 6 10-3

description:
Intestine, 6 weeks post transplant  under immunosuppressant rep3.
Gene expression data from transplanted intestinal mucosa, when there are signs and symptoms of rejection.


title: 3378

description:
normal colon
pdl_hyb_id: 3378
sex: M
age_at_diagnosis: 82
Site_in_colon: sigmoid

source_name: sigmoid


title: SF370 wt dec

source_name: Streptococcus pyogenes, SF370 wild-type strain, post-exponential phase of growth

value: SF370 wild-type


title: SF370 rgg dec

source_name: Streptococcus pyogenes, SF370 rgg mutant, post-exponential phase of growth

value: SF370 rgg mutant


title: SF370 rgg nov


title: without rejection 5 10-3

description:
Intestine, 2 weeks post transplant  under immunosuppressant rep3.
Gene expression data from transplanted intestinal mucosa, before signs and symptoms of rejection.

source_name: Intestinal mucosal biopsy from the donor graft 2 weeks post transplant

tag: Female, 22 year old doter donate a small bowel to her mother 45 year old, the biopsy from the transplanted intestine 2 weeks post transplant, no signs for rejection


title: SF370 wt nov


title: NP+B220iCD138-_d3_rep1

status: Public on Jan 01 2008

city: Birmingham

first: Kai-Michael

last: Toellner

address: Medical School

department: Immunity and Infection

country: United Kingdom

institute: University of Birmingham

description: FACS sorted splenic B cells 3 days after immunization with NP-Ficoll

data_processing: Data was processed using SDS 2.1 software (Applied Biosystems, Foster City, CA), and the Ct value (threshold cycle, the fractional cycle number at which the fluorescence passes the threshold for a given gene within a sample) was determined using auto-baseline and a threshold of 0.25. B2m was chosen as the reference gene and each sample CT was subtracted from B2m CT to give the log2 difference (delta CT). The normalized value was calculated as 2exp(delta Ct). For delta CT calculations, a CT value of 40 was used for any replicate that had CT > 40.

label: FAM

source_name: B cell

label_protocol: Each TaqMan assay was run from total RNA on TaqMan low density arrays. Assays were run with Qiagen Quantitect Probe RT-PCR kit on Applied Biosystems 7900 Fast Real-Time PCR System using universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

extract_protocol: RNeasy Mini columns (Qiagen, Hilden, Germany)

treatment_protocol: 3 days after intraperitoneal immunization with NP-Ficoll

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220intermediate, CD138neg lymphocytes.


title: NP+B220iCD138-_d3_rep3


title: NP+B220iCD138-_d3_rep2


title: NP+B220+CD138-_d3_rep5

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220high, CD138neg lymphocytes.


title: CS101 rgg Em


title: with signs of rejection 6 10-1

description:
Intestine, 6 weeks post transplant  under immunosuppressant rep1.
Gene expression data from transplanted intestinal mucosa, when there are signs and symptoms of rejection.


title: without rejection 5 10-1

description:
Intestine, 2 weeks post transplant  under immunosuppressant rep1.
Gene expression data from transplanted intestinal mucosa, before signs and symptoms of rejection.


title: NP+B220+CD138-_d3_rep4


title: without rejection 5 10-2

description:
Intestine, 2 weeks post transplant  under immunosuppressant rep2.
Gene expression data from transplanted intestinal mucosa, before signs and symptoms of rejection.


title: MGAS5005 wt Em

source_name: Streptococcus pyogenes, MGAS5005 wild-type strain, post-exponential phase of growth

value: MGAS5005 wild-type


title: MGAS5005 wt dec


title: NP+B220+CD138-_d3_rep1


title: NP+B220i_d2_rep4

description: FACS sorted splenic B cells 2 days after immunization with NP-Ficoll

treatment_protocol: 2 days after intraperitoneal immunization with NP-Ficoll

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220intermediate lymphocytes.


title: NP+B220+CD138-_d3_rep3


title: NP+B220+CD138-_d3_rep2


title: NP+B220i_d2_rep3


title: NP+B220i_d2_rep1


title: NP+B220i_d2_rep2


title: NP+B220iCD138+_d3_rep2

description: FACS sorted splenic plasmablasts 3 days after immunization with NP-Ficoll

source_name: plasmablast

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220-intermediate, CD138pos lymphocytes.


title: NP+B220+_d1_rep2

description: FACS sorted splenic B cells 1 day after immunization with NP-Ficoll

treatment_protocol: 1 day after intraperitoneal immunization with NP-Ficoll

tag: C57BL/6 mice with one knockin of NP-specific immunoglobulin heavy chain from quasimonoclonal (QM) mice. FACS sorted NP-binding, B220pos lymphocytes.


title: NP+B220+_d1_rep3


title: NP+B220iCD138+_d3_rep3


title: Control_shRNA-MDA-MB-231_2D

status: Public on Jan 31 2008

city: Berkeley

first: Terumi

last: Kohwi-shigematsu

address: 1 Cyclotron road

department: Life Science

institute: LBNL

description: Gene expression data from MDA-MB-231-control_shRNA cultured on plastic dishes

hyb_protocol: Following fragmentation, 10 ?g of cRNA were hybridized for 18 hr at 37°C.

scan_protocol: Bioarrays were scanned according to manufacturer's instructions using GenePix4000B scanner

data_processing: Probe set based gene expression measurements were generated with CodeLink Expression Analaysis software (GE healthcare) and further using  the GeneSpring software (SiLicon Genetics).

source_name: Parental MDA-MB231 cells grown on 2D culture

label_protocol: Biotinylated cRNA were prepared according to the standard  protocol from 2 ?g total RNA

growth_protocol: grown on plastic culture dish (2D culture)

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

treatment_protocol: Parental MDA-MB-231 cells with pSUPER_control-shRNA transfection

tag: Aggressive human breast cancer cell line


title: Control_shRNA-MDA-MB-231_3D

source_name: Parental MDA-MB231 cells grown on 3D culture

growth_protocol: grown on matrigel coated dish (3D culture)

tag: SATB1-knocked down (by shRNA) human breast cancer cell line


title: SATB1_shRNA1-MDA-MB-231_2D

description: Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on plastic dishes

source_name: SATB1-shRNA trasnfected MDA-MB-231 cells grown on 2D culture

treatment_protocol: MDA-MB-231 cells stably trasnfected with pSUPER_ SATB1-shRNA1 was cloned.


title: NP+B220+_d1_rep1


title: B. fragilis IB397 5%O2-b2

status: Public on Dec 30 2007

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

description: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.

data_processing: data processed using quantile normalization and RMA algorithm

organism: Bacteroides fragilis

source_name: IB397 wild type strain stressed in 5% oxygen

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397

tag: (wild-type) grown in BHIS complex media and then stressed by shaking in a stoppered

tag: bottle with 5% oxygen atmosphere for 30 min.


title: LA_TP1_repl3

status: Public on Dec 15 2007

city: Vancouver

first: Mickael

last: Le Gac

address: University Boulevard

country: Canada

institute: University of British Columbia

hyb_protocol: 80 pmol of the labelled cDNA were combined. The combined cDNA were speed vacuum concentrated, resuspended in 4µL 10mM EDTA and denaturated at 95°C during 1min before adding 76µL of Ambion Hybridization buffer #2 (Ambion). After 2min of denaturation at 95°C, the hybridization solution was placed on a microarray slide and covered by cover glass. The slides were assembled with hybridization chambers (Corning) and hybridized for 20h at 42°C inside a waterbath. The slides were washed 3 times in 0.5X SSC, 0.5% SDS during 5 min and then 3 times in 0.5X SSC, and were dried by centrifugation.

scan_protocol: The hybridized slides were scanned with a ScanArray Express scanner (Perkin-Elmer). ImageGene v5.0 was used to quantify the spot intensities.

data_processing:
Statistical preprocessing steps were conducted with ArrayPipe (version 1.7), a web-based software designed for processing of microarray data (www.pathogenomics.ca/arraypipe, Hokamp et al. 2004). The following pre-processing steps were applied: 1) flagging of markers and control spots, 2) subgrid-wise background correction, using the median of the lower 10% foreground intensity as an estimate for the background noise, 3) data-shifting, 4) limma’s LOESS normalization by print tip, 5) merging of duplicate spots.
VALUEs are calculated as log2-transformed (test/ref) ratios after background correction and limma's LOESS normalization

organism: Escherichia coli

source_name: L, TP1

label_protocol: cDNA was cleaned using QIAquick purification kit (Qiagen) and labelled with either Cy3 or Cy5 following manufacturer's instructions (Amersham Pharmacia)

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 3.5 hours 37°C, 250rpm. Extraction was performed just after.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit. DNA was removed using Ambion DNA-free kit. RNA quality was assessed using 2% agarose gels and OD260/OD280 ratio. Amino-allyl dUTP was used to label 5µg of RNA during reverse transcription. The reverse transcription was performed at 42°C during 50 min using 600 units of superscript RT II (Invitrogen), 3 µg of random hexamers, 0.6mM dATP, dCTP and dGTP, 0.2mM dTTP, and 0.4mM amino-allyl dUTP (Ambion). RNA was then degraded by incubation at 65°C, for 15 min, after adding 10µL of 0.5M EDTA and 10µL of 1M NaOH.

tag: A pool of 3 E. coli clones forming large colonies when plated on TTagar and derived from E. coli B REL606 after 150 days of seasonal evolution experiment in 18mm test tubes in DMga medium.

source_name: A, TP1

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 4 hours 37°C, 250rpm. Extraction was performed just after.

tag: Ancestral E. coli B REL606 strain


title: SATB1_shRNA1-MDA-MB-231_3D

description: Gene expression data from MDA-MB-231-SATB1_shRNA1 cultured on matrigel coated dishes

source_name: SATB1-shRNA trasnfected MDA-MB-231 cells grown on 3D culture


title: LA_TP1_repl5


title: LA_TP3_repl2

source_name: L, TP3

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 12 hours 37°C, 250rpm. Extraction was performed just after.

source_name: A, TP3

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 12hours 37°C, 250rpm. Extraction was performed just after.


title: LA_TP1_repl4


title: SA_TP1_repl2

source_name: S, TP1

tag: A pool of 3 E. coli clones forming small colonies when plated on TTagar and derived from E. coli B REL606 after 150 days of seasonal evolution experiment in 18mm test tubes in DMga medium.

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 4hours 37°C, 250rpm. Extraction was performed just after.


title: B. fragilis IB397 5%O2-a2

description:
For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and
then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were
individually hybridized to the microarray according to the NimbleGen standard operating
procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex
according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm
resolution using an Axon 4000B.

source_name: IB397 wild type strain stressed with 5% oxygen


title: LA_TP1_repl1


title: SA_TP4_repl5

source_name: S, TP4

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18 hours 37°C, 250rpm. Extraction was performed just after.

source_name: A, TP4

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 18hours 37°C, 250rpm. Extraction was performed just after.


title: SA_TP1_repl3


title: LA_TP4_repl5

source_name: L, TP4


title: SA_TP1_repl1


title: LA_TP4_repl4


title: SA_TP3_repl4

source_name: S, TP3


title: SA_TP3_repl5


title: LA_TP3_repl4


title: LA_TP3_repl5


title: LA_TP1_repl2


title: SA_TP1_repl5


title: LA_TP3_repl3


title: SA_TP4_repl2


title: LA_TP3_repl1


title: SA_TP4_repl1


title: LA_TP4_repl3


title: SA_TP4_repl4


title: LA_TP4_repl2


title: LA_TP4_repl1


title: SA_TP1_repl4


title: SA_TP3_repl2


title: SA_TP3_repl3


title: B. fragilis IB397 5%O2-a1

hyb_protocol: For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were individually hybridized to the microarray according to the NimbleGen standard operating procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm resolution using an Axon 4000B.

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397 (wild-type) grown in BHIS complex media and then stressed by shaking in a stoppered bottle with 5% oxygen atmosphere for 30 min.


title: SA_TP4_repl3


title: SA_TP2_repl3

source_name: S, TP2

growth_protocol: Frozen bacteria were grown overnight in 18mm test tubes containing DMga medium, 500µL of culture was transferred to 50mL of fresh DMga in 500mL flasks and grown for 7hours 37°C, 250rpm. Extraction was performed just after.

source_name: A, TP2


title: SA_TP2_repl2


title: SA_TP2_repl4


title: SA_TP3_repl1


title: LA_TP2_repl4

source_name: L, TP2


title: SA_TP2_repl5


title: LA_TP2_repl3


title: LA_TP2_repl1


title: LA_TP2_repl5


title: SA_TP2_repl1


title: LA_TP2_repl2


title: K3_Slide8B_16Cy3_22Cy5

status: Public on Dec 03 2007

city: Jouy en Josas

first: Laurence

last: Flori

address: Domaine de Vilvert

department: Génétique Animale

institute: INRA

description: slide 13309369

hyb_protocol: The slides were pre-soaked, prehybridized and hybridized with the same quantity of Cy3 and Cy5 labelled cDNAs : 20 pmoles of each labelled cDNAs (Pronto Kit, Corning). After 16 hours hybridization at 42-b°C, the slides were washed according to commercial protocol (Pronto kit, Corning) and dried by centrifugation (1500 rpm, 3 min).

scan_protocol: Slides were scanned on the Scanarray scanner (Perkin Elmer). Signals were quantified with the Imagene 5.1 software (Biodiscovery).

data_processing: The normalisation steps was performed using scripts written with R software. Raw data were log2 transformed, normalized by lowess (f=0.3) and the median of each block spotted on slide was substracted.

organism: Sus scrofa

source_name: Porcine epithelial cells (PK15)

label_protocol: Five µg of each RNA were reverse-transcribed and labelled with Cy3 and Cy5 (reagents: Pronto kit, Corning and Amersham, Biosciences). Labelled targets were quantified (Nanodrop, Nyxor Biotech), evaporated and the pellets were resuspended in hybridization buffer (Pronto Kit, Corning) at a final concentration of 2 pmoles/µl. Control RNA (Spikes, Lucidea Universal Scorecard, Amersham Biosciences) specific of control spots on the SLA slides were labelled together with total RNA.

extract_protocol: RNAs were extracted using Trizol (Invitrogen)-chlorofrom method.

tag: Time (h) post-infection

tag: Replicate

tag: Status

value: PrV-Infected

value: Mock-Infected


title: K3_Slide6B_18Cy3_24Cy5

description: slide 13289558


title: K3_Slide3B_4Cy3_10Cy5

description: slide 13291297


title: K3_Slide9A_22Cy3_21Cy5

description: slide 13291313


title: K3_Slide5A_5Cy3_6Cy5

description: slide 13309374


title: K3_Slide7B_23Cy3_17Cy5

description: slide 13309365


title: K3_Slide8A_17Cy3_16Cy5

description: slide 13309369


title: K3_Slide7A_24Cy3_23Cy5

description: slide 13309365


title: K3_Slide24B_25Cy3_31Cy5

description: slide 13291314


title: K3_Slide9B_21Cy3_15Cy5

description: slide 13291313


title: K3_Slide4A_10Cy3_11Cy5

description: slide 13309382


title: K3_Slide4B_11Cy3_5Cy5

description: slide 13309382


title: K3_Slide22B_27Cy3_33Cy5

description: slide 13291310


title: K3_Slide23A_33Cy3_32Cy5

description: slide 13309381


title: K3_Slide5B_6Cy3_12Cy5

description: slide 13309374


title: K3_Slide3A_3Cy3_4Cy5

description: slide 13291297


title: K3_Slide2B_9Cy3_3Cy5

description: slide 13309378


title: K3_Slide21B_34Cy3_28Cy5

description: slide 13291309


title: K3_Slide2A_8Cy3_9Cy5

description: slide 13309378


title: K3_Slide22A_28Cy3_27Cy5

description: slide 13291310


title: K3_Slide23B_32Cy3_26Cy5

description: slide 13309381


title: K3_Slide6A_12Cy3_18Cy5

description: slide 13289558


title: K3_Slide24A_26Cy3_25Cy5

description: slide 13291314


title: K3_Slide21A_35Cy3_34Cy5

description: slide 13291309


title: K3_Slide20B_29Cy3_35Cy5

description: slide 13309366


title: K3_Slide19B_36Cy3_30Cy5

description: slide 13309612


title: K3_Slide20A_30Cy3_29Cy5

description: slide 13309366


title: K3_Slide17A_40Cy3_41Cy5

description: slide 13309364


title: K3_Slide16B_46Cy3_40Cy5

description: slide 13289561


title: K3_Slide18B_48Cy3_42Cy5

description: slide 13309377


title: K3_Slide1A_1Cy3_2Cy5

description: slide 13291304


title: K3_Slide18A_47Cy3_48Cy5

description: slide 13309377


title: K3_Slide19A_42Cy3_36Cy5

description: slide 13309612


title: K3_Slide14A_43Cy3_44Cy5

description: slide 13291301


title: K3_Slide17B_41Cy3_47Cy5

description: slide 13309364


title: K3_Slide16A_45Cy3_46Cy5

description: slide 13289561


title: K3_Slide11A_20Cy3_19Cy5

description: slide 13291295


title: K3_Slide13A_31Cy3_37Cy5

description: slide 13309376


title: K3_Slide11B_19Cy3_13Cy5

description: slide 13291295


title: Cy3: Glucose concentration 0 mg/L time 0h Cy5: Glucose concentration 0 mg/L time 0h

status: Public on Dec 02 2007

city: Bremen

first: Christine

last: Klockow

address: Celsiusstr. 1

institute: Max Planck Institute for Marine Microbiology

description:
further data processing:
Spots flagged as „bad“ were deleted from data set, signal values for spots marked “empty” were set to a value of 1, an array-to-array standardisation was carried out by global scaling; Cy3 and Cy5 values belonging to the same sample were added

hyb_protocol: The differently labeled cDNAs of both samples are hybridized (42°C over night) simultaneously in one experiment to the same array ( MWG PAN Yeast II array, MWG Ebersberg, Germany). After hybridization, the unbound and unspecific fixed cDNA is removed by stringent washing from the array (2 x SSC, 0.1 % SDS; 1 x SSC; 0.5 x SSC).

scan_protocol: scanned with Affymetrix 428 Fluorescence Laser Scanner (Affymetrix, St. Clara, USA), seperatetly for each dye

data_processing: Median (local Background) was subtracted from Median (Signal)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae, grown stirred tank reactor with a mineral medium and starved for 4 hours

label_protocol: First-strand cDNA synthesis was performed in a total volume of 50 µl, where 40 µg of total RNA were reverse transcribed using LabelStar reverse transcriptase (Qiagen, Hilden, Germany), 5 pmol oligo(dT)18 primer and 0.02 mM cyanine 3-dCTP or cyanine 5-dCTP. In total, 120 µg RNA were used for each dye, divided in three preparations and labeled seperately.

growth_protocol: Cells were stored on agar at 10°C; Cultivation  in a 100 mL shaking flask in a mineral medium (120 rpm, 30°C, 24 h); transfer to 2.5 L stirred tank reactor 30°C, 1200 rpm, airflow 300 L/h); batch cultivation with a mineral medium (until glucose was used up, approximately 15 h)

extract_protocol: The cell disruption was carried out with FastPrep FP120 (Bio101, ThermoSavant, Waltham, USA). Total RNA was isolated using Qiagen RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: cells were starved for 4 hours

tag: Strain

value: wild type, H620

treatment_protocol: Cells were starved for 4 hours


title: K3_Slide1B_2Cy3_8Cy5

description: slide 13291304


title: K3_Slide12A_13Cy3_7Cy5

description: slide 13291302


title: K3_Slide15A_38Cy3_39Cy5

description: slide 13291306


title: K3_Slide14B_44Cy3_38Cy5

description: slide 13291301


title: K3_Slide13B_37Cy3_43Cy5

description: slide 13309376


title: Cy3: Glucose conc. 100 mg/L time 7.5 Cy5: Glucose concentration 70 mg/L time 6 h

description:
Further data processing:
Spots flagged as „bad“ were deleted from data set, signal values for spots marked “empty” were set to a value of 1, an array-to-array standardisation was carried out by global scaling; Cy3 and Cy5 values belonging to the same sample were added

hyb_protocol: The differently labelled cDNAs of both samples are hybridized (42°C over night) simultaneously in one experiment to the same array ( MWG PAN Yeast II array, MWG Ebersberg, Germany). After hybridization, the unbound and unspecific fixed cDNA is removed by stringent washing from the array (2 x SSC, 0.1 % SDS; 1 x SSC; 0.5 x SSC).

scan_protocol: The array is scanned with an Affymetrix 428 Fluorescence Laser Scanner (Affymetrix, St. Clara, USA) for the two distinct fluorescent dyes (Cy3 and Cy5) of the cDNA derived from differently treated cells.

data_processing: Median (local Background) was subtracted from Median (Signal

source_name: Saccharomyces cerevisiae, grown in fed batch cultivation with a mineral medium at different glucose concentrations

label_protocol: First-strand cDNA synthesis was performed in a total volume of 50 µl, where 40 µg of total RNA were reverse transcribed using LabelStar reverse transcriptase (Qiagen, Hilden, Germany), 5 pmol oligo(dT)18 primer and 0.02 mM cyanine 3-dCTP or cyanine 5-dCTP. In total, 120 µg RNA were used for each dye, divided in three preparations and labeled separately.

growth_protocol: Cells were stored on agar at 10°C; Cultivation  in a 100 mL shaking flask in a mineral medium (120 rpm, 30°C, 24 h); transfer to 2.5 L stirred tank reactor 30°C, 1200 rpm, airflow 300 L/h); batch cultivation with a mineral medium (until glucose was used up, approximately 15 h); 4 hours starvation time without glucose; fed batch cultivation with constant glucose concentration

treatment_protocol: Cells were grown at a constant glucose concentration for several hours (see growth protocol)


title: K3_Slide12B_7Cy3_1Cy5

description: slide 13291302


title: K3_Slide15B_39Cy3_45Cy5

description: slide 13291306


title: K3_Slide10A_15Cy3_14Cy5

description: slide 13289559


title: K3_Slide10B_14Cy3_20Cy5

description: slide 13289559


title: Cy3: Glucose conc. 500 mg/L time 10 Cy5: Glucose concentration 500 mg/L time 6.3 h

description:
further data processing:
 Spots flagged as „bad“ were deleted from data set, signal values for spots marked “empty” were set to a value of 1, an array-to-array standardisation was carried out by global scaling; Cy3 and Cy5 values belonging to the same sample were added

growth_protocol: Cells were stored on agar at 10°C; Cultivation  in a 100 mL shaking flask in a mineral medium (120 rpm, 30°C, 24 h); transfer to 2.5 L stirred tank reactor 30°C, 1200 rpm, airflow 300 L/h); batch cultivation with a mineral medium (until glucose was used up, approximately 15 h); fed batch cultivation with constant glucose concentration


title: Tcells_PLNDCs_rep3

status: Public on Oct 31 2007

city: New York

first: Jeremy

last: Grubin

address: 411 East 67th Street Rm K425

institute: Memorial Sloan Kettering Cancer Center

description: We stimulated B10.BR T cells with dendritic cells derived from different C57BL/6 organs for four days and then performed array experiments on the T cells.

data_processing: GCOS1.1 target intensity to 500

label: Invitrogen Labeling

source_name: B10.BR T cells, C57BL/6 PLN DCs

tag: T cell strain

tag: Organ-derived DC strain

tag: Stimulation time

value: 4 days


title: Cy3: Glucose concentration 50 mg/L time 7.5 h Cy5: Glucose concentration 50 mg/L time 7.5 h

treatment_protocol: cells were grown at a glucose concentration of 50 mg/L


title: Tcells_PLNDCs_rep4


title: Tcells_SpleenDCs_rep3

source_name: B10.BR T cells, C57BL/6 Spleen DCs


title: Cy3: Glucose concentration 70 mg/L time 3 h Cy5: Glucose concentration 70 mg/L time 3 h

treatment_protocol: cells were grown at a glucose concentration of 70 mg/L


title: Cy3:Glucose concentration 70 mg/L time 6 h Cy5: glucose conc. 100 mg/L time 7.5 h


title: Tcells_LiverDCs_rep2

source_name: B10.BR T cells, C57BL/6 Liver DCs


title: Cy3: Glucose conc. 500 mg/L time 6.3 Cy5: Glucose concentration 500 mg/L time 10 h


title: HCT116, mock, 72hr vs. HCT116, luc, 10nM, 72hr

status: Public on Nov 01 2007

city: Carlsbad

first: Aimee

last: Jackson

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

description: Transcripts regulated over time by LIN54 esiRNA transfected into HCT116 cells

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: HCT116, mock, 72hr

tag: HCT116, luc, 10nM, 72hr


title: Tcells_SpleenDCs_rep4


title: HCT116, mock, 24hr vs. HCT116, luc, 10nM, 24hr

tag: HCT116, mock, 24hr

tag: HCT116, luc, 10nM, 24hr


title: Tcells_LiverDCs_rep4


title: HCT116, mock, 24hr vs. HCT116, LIN54 esiRNA 1, 10nM, 24hr

tag: HCT116, LIN54 esiRNA 1, 10nM, 24hr


title: stphcy3plogcy5slide581norm

status: Public on Oct 20 2007

city: Pittsburgh

first: Graham

last: Hatfull

state: PA

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

description: Gene Expression Data from stationary phase planktonic culture compared against Planktonic log phase culture

hyb_protocol: Using the instruction provided by PFGRC, TIGR at http://pfgrc.tigr.org/protocols/protocols.shtml

scan_protocol: Using the Axon4200 Dual Channel Scanner

data_processing: The data were processed and using GenePix Pro 4.1. The method of global intensity normalization was used.

organism: Mycolicibacterium smegmatis

source_name: Log phase planktonic culture of M.smegmatis

growth_protocol: Grown in modified M63 media at 30C on a platform shaker

extract_protocol: Using the Ambion's Ribopure RNA extraction kit

treatment_protocol: Harvested log phase planktonic culture at optical density of 0.2 and processed for RNA extraction

source_name: Stationary Phase planktonic culture of M. smegmatis

growth_protocol: Grown in modified M63 media at 30C on a shaker

treatment_protocol: Harvested stationary phase planktonic culture at optical density of 2.0 and processed for RNA extraction


title: 4dbfcy5plogcy3slide901norm

description: Gene Expression Data from 4 day biofilm culture compared against Planktonic log phase culture

source_name: 4 day biofilm culture of M.smegmatis

label_protocol: Using the instruction provided by PFGRC, TIGR at http://pfgrc.tigr.org/protocols/protocols.shtml

growth_protocol: Grown in modified M63 media at 30C without shaking

treatment_protocol: Harvested at 4 day biofilm stage and processed for RNA extraction

source_name: Log Phase planktonic culture of M. smegmatis

treatment_protocol: Harvested at optical density of 0.2 and processed for RNA extraction


title: Tcells_LiverDCs_rep3


title: Plogcy5plogcy3slide110norm

description: Gene Expression Data from Planktonic log phase culture compared against itself

source_name: Log phase Planktonic culture of M. smegmatis

growth_protocol: Grown in modified M63 media at 30C on a plantform shaker

source_name: Log Phase Planktonic culture of M.smegmatis


title: Tcells_MLNDCs_rep3

source_name: B10.BR T cells, C57BL/6 MLN DCs


title: stphcy5plogcy3slide487norm

source_name: Stationary phase culture of M.smegmatis


title: HCT116, mock, 72hr vs. HCT116, LIN54 esiRNA 1, 10nM, 72hr

tag: HCT116, LIN54 esiRNA 1, 10nM, 72hr


title: stphcy5plogcy3slide580norm


title: HCT116, mock, 48hr vs. HCT116, LIN54 esiRNA 1, 10nM, 48hr

tag: HCT116, mock, 48hr

tag: HCT116, LIN54 esiRNA 1, 10nM, 48hr


title: 3dbfcy5plogcy3slide603norm

description: Gene Expression Data from 3 day biofilm culture compared against Planktonic log phase culture

source_name: 3 day biofilm culture of M. smegmatis

treatment_protocol: Harvested biofilm at 3day stage and processed for RNA extraction


title: Tcells_PLNDCs_rep2


title: 3dbfcy3plogcy5slide607norm


title: Plogcy5plogcy3slide113norm


title: B6J12-7.vs.B6J-1_rep1_hyb1

status: Public on Oct 28 2007

city: Cold Spring Harbor

first: Ira

middle: M

last: Hall

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

hyb_protocol: Hybs were performed in 25 uL of solution consisting of 37.5% formamide, 4x SSC, and O.1% SDS.  Samples were denatured at 95° for 5 min, pre-annealed for 30 min at 37° with 1 µg of mouse COT1 DNA, applied to the microarray, and hybridized under a coverslip at 42°C for 14-18 h.  Slides were washed for 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC,  30 sec in 0.05x SSC, and dried by centrifugation.

scan_protocol: Microarrays were scanned with an Axon GenePix 4000B scanner with pixel size set to 5um. GenePix Pro 4.0 software was used for gridding and quantitation of intensities.

data_processing: Measured intensities without background subtraction were used to calculate ratios.  Data were normalized using an intensity-based lowess curve fitting algorithm similar to that described in Yang et al (Nucleic Acids Research, 30 e15, Feb 15, 2002).

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse

label_protocol: 1.5 µg of DNA from genomic representations were differentially labeled with Cy5-dCTP or Cy3-dCTP dyes using the Amersham-Pharmacia Megaprime kit. Labeled DNA was purified with Microcon columns (Millipore) with lowTE.

extract_protocol:
DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.
1.5 µg of DNA was digested with the Bgl II restriction enzyme for 8-12 hrs at 37°C.  Fragments were column-purified (Qiagen Minielute kit), and universal adaptors were added to fragments by overnight ligation with T4 ligase at 16º C.  After 22 cycles of PCR amplification with the universal primer, resulting genomic representations were predominantly composed of fragments 100-1200 bp in length.  Representations were then column-purified (Qiagen PCR purification kit).

tag: DNA prep ID

tag: Tissue

value: tail

tag: Age

value: 4-8 weeks

tag: Gender

value: Female

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse

value: liver


title: B6J12-F.vs.B6J-1 _rep1_hyb2

growth_protocol: DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.

value: 6-10 months

value: Male


title: B6J12-6.vs.B6J-1_rep1_hyb2


title: B6J12-F.vs.B6J-1 _rep1_hyb1

value: 7 months


title: B6J12-8.vs.B6J-1_rep1_hyb2


title: B6J12-M.vs.B6J-1_rep1_hyb2


title: Tcells_MLNDCs_rep2


title: Frontal_cerebrocortex_Deltamethrin_3mg/kg_6hr_rep6

status: Public on Oct 15 2007

city: Research Triangle Park

first: Joshua

middle: A

last: Harrill

address: 109 TW Alexander Drive

department: Curriculum in Toxicology

institute: University of North Carolina

description: This sample is part of a data set examining dose-related effects of pyrethroid insectcides on gene expression in the mammalian nervous system.

hyb_protocol: Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021). Breifly, fragmented biotin-labeled cRNA was diluted in a hybridization cocktail containing hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20), 0.5 mg/mL acetylated BSA, 0.1 mg/mL herring sperm DNA, 50 pM of control oligonucleotide B2, and 1.5, 5, 25 and 100 pM of BioB, BioC, BioD and Cre eukaryotic hybridization controls, respectively.  Hybridization cocktails were incubated for 5 min at 99°C followed by incubation for 5 min at 45°C and then injected into the GeneChip® arrays.  Loaded GeneChips® were then incubated in an Affymetrix hybridization oven for 16 hours at 45°C and 60 RPM.  GeneChips® were then washed under a series of non-stringent (buffer A: 0.9 M NaCl,  0.06 M NaH2PO4,  6 mM EDTA, 0.01% Tween-20 at 25°C) and stringent (buffer B: 100 mM MES, 0.1 M NaCl, 0.05% Tween-20 at 50°C) conditions on an Affymetrix fluidics module using the EukGE-WS2v4-450 fluidics script.  GeneChips® were then stained with SAPE solution (100 mM MES, 1 M NaCl, 0.05 % Tween-20, 10 µg/mL streptavidin-phycoerythrin, 2 mg/mL acetylated BSA) and subjected to another series of washes in buffer A.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the Affymetrix GCOS v1.2 software package.

data_processing: Signal intensities calculated using RMA algorithm

organism: Rattus norvegicus

source_name: Frontal cerebrocortex, deltamethrin (3 mg/kg), 6 hours

label_protocol: First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021).  Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol.  Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol.  Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer.

growth_protocol: Test subjects housed 2 per cage in polycarbonate hanging cages (45cm X 24 cm X 20 cm) with heat sterilized pine shaving for bedding.  Subjects maintained on a 12h:12h photoperiod (06:00-18:00) and allowed a 5-7 day period of acclimation to holding suite prior to treatment.  Holding suite maintained at 22.0 +/- 2.0 C with a relative humidity of 55 +/- 20%.  Purina 5001 Rat Chow and tap water were provided ad libitum.

extract_protocol: Total RNA was isolated from cortical tissue using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) per manufacturer's instructions.  Following TRI Reagent extraction, total RNA suspended in DEPC-H20 was treated with 16 units of RNase-free DNase I (Ambion, Inc., Austin, TX) and incubated at 37 C for 1 hour.  DNase I was inactivated with 1 volume of 5:1 acid-phenol:chloroform, pH=4.7.  Samples were vortexed for 60s, stored at 25 C for 15 min and centrifuged for 15 min.  Aqueous phase was removed, supplemented with 1 volume of chloroform, vortexed for 60 s, stored at 25 C for 15 min and centrifuged for 15 min.  Aqueous phase was removed and total RNA precipitated overnight with 0.1 volumes of 3 M sodium acetate (pH = 5.2) and 2.5 volumes of 100 % ethanol following by centrifugation for 15 min.  Precipitated pellets samples were washed with 75% ethanol and resuspended in DEPC H2O.

treatment_protocol:
Test Compound:  Deltamethrin
Test Compound CAS#:  52918-63-5
Isomer Composition:  100 % (1R, 3R, alpha-S)
Purity:  98.9 %
Vehicle:  Corn Oil
Vehicle CAS #:  8001-30-07
Administration Route:  Oral Gavage
Test Compound Concentration:  3 mg/mL
Delivery Volume:  1 mL / kg body weight
Expsoure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure

value: Long-Evans

value: Adult (PND62-PND64)

value: Cerebrocortex


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep8

hyb_protocol: Hybridization of Affymetrix Rat 230 2.0 GeneChips was performed according to manufacturer's instructions (Affymetrix pub #701021).

source_name: Frontal cerebrocortex, deltamethrin (1 mg/kg), 6 hours

treatment_protocol:
Test Compound:  Deltamethrin
Test Compound CAS#:  52918-63-5
Isomer Composition:  100 % (1R, 3R, alpha-S)
Purity:  98.9 %
Vehicle:  Corn Oil
Vehicle CAS #:  8001-30-07
Administration Route:  Oral Gavage
Test Compound Concentration:  1 mg/mL
Delivery Volume:  1 mL / kg body weight
Expsoure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure


title: B6J12-8.vs.B6J-1_rep1_hyb1


title: Plogcy5plogcy3slide111norm


title: Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep4


title: Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep5


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep6

source_name: Frontal Cerebrocortex, deltamethrin (1 mg/kg), 6 hours


title: 4dbfcy5plogcy3slide480norm


title: Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep7


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep3


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep4


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep7

source_name: Frontal cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours

treatment_protocol:
Test Compound:  Deltamethrin
Test Compound CAS#:  52918-63-5
Isomer Composition:  100 % (1R, 3R, alpha-S)
Purity:  98.9 %
Vehicle:  Corn Oil
Vehicle CAS #:  8001-30-07
Administration Route:  Oral Gavage
Test Compound Concentration:  0.3 mg/mL
Delivery Volume:  1 mL / kg body weight
Expsoure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure


title: Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep1


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep6


title: B6J12-6.vs.B6J-1_rep1_hyb1


title: Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep8


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep4


title: Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep3


title: HCT116, mock, 48hr vs. HCT116, luc, 10nM, 48hr

tag: HCT116, luc, 10nM, 48hr


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep2

tag: Strain


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep8

source_name: Frontal cerebrocortex, permethrin (100 mg/kg), 6 hours

treatment_protocol:
Test Compound:  Permethrin
Test Compound CAS#:  52645-53-1
Isomer Composition:  40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
Purity:  92.0 %
Vehicle:  Corn Oil
Vehicle CAS #:  8001-30-07
Administration Route:  Oral Gavage
Test Compound Concentration:  100 mg/mL
Delivery Volume:  1 mL/kg body weight
Expsoure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep5


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep7


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep1


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep5

source_name: Frontal cerebrocortex, permethrin (10 mg/kg), 6 hours

treatment_protocol:
Test Compound:  Permethrin
Test Compound CAS#:  52645-53-1
Isomer Composition:  40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
Purity:  92.0 %
Vehicle:  Corn Oil
Vehicle CAS #:  8001-30-07
Administration Route:  Oral Gavage
Test Compound Concentration:  10 mg/mL
Delivery Volume:  1 mL/kg body weight
Expsoure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep3


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep4

source_name: Frontal Cerebrocortex, permethrin (100 mg/kg), 6 hours


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep2


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep7

source_name: Frontal Cerebrocortex, permethrin (10 mg/kg), 6 hours


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep5


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep2


title: Tcells_MLNDCs_rep4

tag: T cell strain


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep1


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep8


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep8

source_name: Frontal Cerebrocortex, permethrin (1 mg/kg), 6 hours

treatment_protocol:
Test Compound:  Permethrin
Test Compound CAS#:  52645-53-1
Isomer Composition:  40%-cis, 60%-trans, 1:1 ratio of 1R, 1S
Purity:  92.0 %
Vehicle:  Corn Oil
Vehicle CAS #:  8001-30-07
Administration Route:  Oral Gavage
Test Compound Concentration:  1 mg/mL
Delivery Volume:  1 mL/kg body weight
Expsoure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep3


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep1


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep6


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep4

source_name: Frontal cerebrocortex, permethrin (1 mg/kg), 6 hours


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep5


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep2


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep6

source_name: Frontal Cerebrocortex, permethrin (10mg/kg), 6 hours


title: Frontal_Cerebrocortex_Deltamethrin_3mg/kg_6hr_rep2


title: B6J12-M.vs.B6J-1_rep1_hyb1


title: Frontal_Cerebrocortex_Deltamethrin_1mg/kg_6hr_rep5


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep6


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep3


title: Frontal_Cerebrocortex_Deltamethrin_0.3mg/kg_6hr_rep8

source_name: Frontal Cerebrocortex, deltamethrin (0.3 mg/kg), 6 hours


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep7


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep3


title: Frontal_Cerebrocortex_Permethrin_10mg/kg_6hr_rep4


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep7


title: 4dbfcy3plogcy5slide903norm

source_name: Log Phase Planktonic culture of M.smegmatis

source_name: 4 day biofilm culture of M. smegmatis

treatment_protocol: Harvested biofilm at 4 day stage and processed for RNA extraction


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep2

source_name: Frontal cerebrocortex, Permethrin (1 mg/kg), 6 hours


title: Frontal_Cerebrocortex_Vehicle_6hr_rep11

source_name: Frontal cerebrocortex, vehicle control (corn oil), 6 hours

treatment_protocol:
Test Compound: Corn Oil
CAS #:  8001-30-07
Administration Route:  Oral Gavage
Delivery Volume:  1mL/kg
Exposure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure


title: Frontal_Cerebrocortex_Permethrin_100mg/kg_6hr_rep1

source_name: Frontal cerebrocortex, permethrin 100 mg/kg, 6 hours


title: 3dbfcy5plogcy3slide601norm

source_name: 3 day biofilm culture of M. smegmatis

treatment_protocol: Harvested biofilm at 3day stage


title: Frontal_Cerebrocortex_Vehicle_6hr_rep12


title: Frontal_Cerebrocortex_Vehicle_6hr_rep10


title: Frontal_Cerebrocortex_Permethrin_1mg/kg_6hr_rep1

source_name: Frontal cerebrocortex, permethrin (1mg/kg), 6 hours


title: Frontal_Cerebrocortex_Vehicle_6hr_rep8


title: B6J12-7.vs.B6J-1_rep1_hyb2

source_name: Bgl II genomic representation of DNA isolated from the liver of a C57BL/6J inbred mouse

source_name: Bgl II genomic representation of DNA isolated from the tail of a C57BL/6J inbred mouse


title: Frontal_Cerebrocortex_Vehicle_6hr_rep5


title: Frontal_Cerebrocortex_Vehicle_6hr_rep2

source_name: Frontal Cerebrocortex, vehicle control (corn oil), 6 hours


title: Frontal_Cerebrocortex_Vehicle_6hr_rep3


title: Frontal_Cerebrocortex_Vehicle_6hr_rep4


title: Frontal_Cerebrocortex_Vehicle_6hr_rep9


title: Frontal_Cerebrocortex_Vehicle_6hr_rep6


title: Frontal_Cerebrocortex_Vehicle_6hr_rep7


title: Cj 960094 replicate 1

status: Public on Oct 01 2007

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

institute: National Research Council

description: Campylobacter jejuni,  strain 960094, genomic DNA

hyb_protocol: overnight hybridization at 37 deg in DIG-easy hyb solution (Roche). Washes performed as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

scan_protocol: scans acquired using Scanarray chipreader (BioRad) as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

data_processing: Features were extracted using ArrayPro Analyzer version 4.5 and imported into the BioArray Software Environment (BASE version 1.2). Spots flagged due to poor spot morphology or low signal intensity (less than 5 X local background) were filtered out. After print-tip Loess normalization, data was used to calculate the average log ratio [log2(Signal Tester / Signal Control)]

organism: Campylobacter jejuni

source_name: 960094 genomic DNA

label_protocol: Approximately 2 µg of genomic DNA was labeled by chemical coupling to Label IT Cy dye as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

extract_protocol: Approximately 10^10 cells were harvested from cells grown overnight under microaerophilic conditions in Mueller Hinton plates. Genomic DNA extracted by modified lysis/phenol extraction protocol as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

tag: strain 960094

source_name: NCTC11168 genomic DNA

tag: strain NCTC11168 (control)


title: Cj GB24 replicate 1

description: Campylobacter jejuni,  strain GB24, genomic DNA

source_name: GB24 genomic DNA

tag: strain GB24


title: Cj 961090 replicate 1

description: Campylobacter jejuni,  strain 961090, genomic DNA

source_name: 961090 genomic DNA

tag: strain 961090


title: Cj 961163 replicate 1

description: Campylobacter jejuni,  strain 961163, genomic DNA

source_name: 961163 genomic DNA

tag: strain 961163


title: Cj 961089 replicate 1

description: Campylobacter jejuni,  strain 961089, genomic DNA

source_name: 961089 genomic DNA

tag: strain 961089


title: Cj 990520 replicate 1

description: Campylobacter jejuni,  strain 990520, genomic DNA

source_name: 990520 genomic DNA

tag: strain 990520


title: Cj MF08 replicate 1

description: Campylobacter jejuni,  strain MF08, genomic DNA

source_name: MF08 genomic DNA

tag: strain MF08


title: Cj 981087 replicate 1

description: Campylobacter jejuni,  strain 981087, genomic DNA

source_name: 981087 genomic DNA

tag: strain 981087


title: Cj 961095 replicate 1

description: Campylobacter jejuni,  strain 961095, genomic DNA

source_name: 961095 genomic DNA

tag: strain 961095


title: Cj CURA276 replicate 1

description: Campylobacter jejuni,  strain CURA276, genomic DNA

source_name: CURA276 genomic DNA

tag: strain CURA276


title: Cj CURA117 replicate 1

description: Campylobacter jejuni,  strain CURA117, genomic DNA

source_name: CURA117 genomic DNA

tag: strain CURA117


title: Cj GB14 replicate 1

description: Campylobacter jejuni,  strain GB14, genomic DNA

source_name: GB14 genomic DNA

tag: strain GB14


title: Cj GB22 replicate 1

description: Campylobacter jejuni,  strain GB22, genomic DNA

source_name: GB22 genomic DNA

tag: strain GB22


title: Cj MF07 replicate 1

description: Campylobacter jejuni,  strain MF07, genomic DNA

source_name: MF07 genomic DNA

tag: strain MF07


title: Frontal_Cerebrocortex_Vehicle_6hr_rep1

source_name: Frontal cerebrocortex, vehicle control (corn oil), 6 hours

label_protocol: First and second strand cDNA synthesis, RNase H digestion and (ds)cDNA isolation were performed according to Affymetrix protocol (Affymetrix pub #701021).  Biotin-labeled cRNA was synthesized with BioArray HighYeild RNA transcript labeling kit (Enzo Life Sciences, Farmingdale, NY) using manufacturer's protocol.  Clean up was performed with Qiagen RNeasy spin columns (Spoorstraat, Netherlands) according to manufacturer's protocol.  Biotin-labeled cRNA was fragmented using Affymetrix 5X fragmentation buffer (200mM Tris acetate - pH = 8.1, 100 mM KOAc, 150 mM MgOAc).

treatment_protocol:
Test compound:  Corn Oil
CAS: 8001-30-07
Administration Route:  Oral Gavage
Delivery Volume:  1 mL/kg
Exposure Duration:  Single, Acute
Sampling Time:  6 Hours post-exposure

tag: Strain

tag: Gender

tag: Age

tag: Tissue


title: Cj 9072 replicate 1

description: Campylobacter jejuni,  strain 9072, genomic DNA

source_name: 9072 genomic DNA

tag: strain 9072

tag: strain NCTC11168 (control)


title: Cj 9123 replicate 1

description: Campylobacter jejuni,  strain 9123, genomic DNA

source_name: 9123 genomic DNA

tag: strain 9123


title: Cj 98706 replicate 1

description: Campylobacter jejuni,  strain 98706, genomic DNA

source_name: 98706 genomic DNA

tag: strain 98706

source_name: NCTC11168 genomic DNA


title: Cj GB19 replicate 1

description: Campylobacter jejuni,  strain GB19, genomic DNA

source_name: GB19 genomic DNA

tag: strain GB19


title: Cj 9140 replicate 1

description: Campylobacter jejuni,  strain 9140, genomic DNA

source_name: 9140 genomic DNA

tag: strain 9140


title: Cj 990521 replicate 1

description: Campylobacter jejuni,  strain 990521, genomic DNA

source_name: 990521 genomic DNA

tag: strain 990521


title: Cj GB23 replicate 1

description: Campylobacter jejuni,  strain GB23, genomic DNA

source_name: GB23 genomic DNA

tag: strain GB23


title: Cj 9126 replicate 1

description: Campylobacter jejuni,  strain 9126, genomic DNA

source_name: 9126 genomic DNA

tag: strain 9126


title: Cj 9146 replicate 1

description: Campylobacter jejuni,  strain 9146, genomic DNA

source_name: 9146 genomic DNA

tag: strain 9146


title: Cj 9141 replicate 1

description: Campylobacter jejuni,  strain 9141, genomic DNA

source_name: 9141 genomic DNA

tag: strain 9141


title: Cj GB02 replicate 1

description: Campylobacter jejuni,  strain GB02, genomic DNA

source_name: GB02 genomic DNA

tag: strain GB02


title: Cj GB15 replicate 1

description: Campylobacter jejuni,  strain GB15, genomic DNA

source_name: GB15 genomic DNA

tag: strain GB15


title: Cj GB18 replicate 1

description: Campylobacter jejuni,  strain GB18, genomic DNA

source_name: GB18 genomic DNA

tag: strain GB18


title: Cj GB26 replicate 1

description: Campylobacter jejuni,  strain GB26, genomic DNA

source_name: GB26 genomic DNA

tag: strain GB26


title: Cj GB04 replicate 1

description: Campylobacter jejuni,  strain GB04, genomic DNA

source_name: GB04 genomic DNA

tag: strain GB04


title: Cj CURA170 replicate 1

description: Campylobacter jejuni,  strain CURA170, genomic DNA

source_name: CURA170 genomic DNA

tag: strain CURA170


title: Cj GB25 replicate 1

description: Campylobacter jejuni,  strain GB25, genomic DNA

source_name: GB25 genomic DNA

tag: strain GB25


title: Cj GB17 replicate 1

description: Campylobacter jejuni,  strain GB17, genomic DNA

source_name: GB17 genomic DNA

tag: strain GB17

tag: strain NCTC11168 (control)


title: Cj CURA034 replicate 1

description: Campylobacter jejuni,  strain CURA034, genomic DNA

source_name: CURA034 genomic DNA

tag: strain CURA034


title: Cj GB27 replicate 1

description: Campylobacter jejuni,  strain GB27, genomic DNA

source_name: GB27 genomic DNA

tag: strain GB27

source_name: NCTC11168 genomic DNA


title: Cj GB11 replicate 1

description: Campylobacter jejuni,  strain GB11, genomic DNA

source_name: GB11 genomic DNA

tag: strain GB11


title: Cj CURA181 replicate 1

description: Campylobacter jejuni,  strain CURA181, genomic DNA

source_name: CURA181 genomic DNA

tag: strain CURA181


title: Cj GB13 replicate 1

description: Campylobacter jejuni,  strain GB13, genomic DNA

source_name: GB13 genomic DNA

tag: strain GB13


title: Cj 9144 replicate 1

description: Campylobacter jejuni,  strain 9144, genomic DNA

source_name: 9144 genomic DNA

tag: strain 9144


title: Cj MF20 replicate 1

description: Campylobacter jejuni,  strain MF20, genomic DNA

source_name: MF20 genomic DNA

tag: strain MF20


title: Cj GB05 replicate 1

description: Campylobacter jejuni,  strain GB05, genomic DNA

source_name: GB05 genomic DNA

tag: strain GB05


title: Cj GB01 replicate 1

description: Campylobacter jejuni,  strain GB01, genomic DNA

source_name: GB01 genomic DNA

tag: strain GB01


title: Cj 98652 replicate 1

description: Campylobacter jejuni,  strain 98652, genomic DNA

source_name: 98652 genomic DNA

tag: strain 98652


title: Cj GB16 replicate 1

description: Campylobacter jejuni,  strain GB16, genomic DNA

source_name: GB16 genomic DNA

tag: strain GB16


title: Cj CURA112 replicate 1

description: Campylobacter jejuni,  strain CURA112, genomic DNA

source_name: CURA112 genomic DNA

tag: strain CURA112


title: Cj CURA027 replicate 1

description: Campylobacter jejuni,  strain CURA027, genomic DNA

source_name: CURA027 genomic DNA

tag: strain CURA027


title: Cj CURA029 replicate 1

description: Campylobacter jejuni,  strain CURA029, genomic DNA

source_name: CURA029 genomic DNA

tag: strain CURA029


title: Cj 9138 replicate 1

description: Campylobacter jejuni,  strain 9138, genomic DNA

source_name: 9138 genomic DNA

tag: strain 9138


title: Cj GB21 replicate 1

description: Campylobacter jejuni,  strain GB21, genomic DNA

source_name: GB21 genomic DNA

tag: strain GB21


title: Cj MF06 replicate 1

description: Campylobacter jejuni,  strain MF06, genomic DNA

source_name: MF06 genomic DNA

tag: strain MF06

tag: strain NCTC11168 (control)


title: Cj 98623 replicate 1

description: Campylobacter jejuni,  strain 98623, genomic DNA

source_name: 98623 genomic DNA

tag: strain 98623


title: Cj GC191  replicate 1

description: Campylobacter jejuni,  strain GC191,  genomic DNA

source_name: GC191  genomic DNA

tag: strain GC191

source_name: NCTC11168 genomic DNA


title: Cj GC177  replicate 1

description: Campylobacter jejuni,  strain GC177,  genomic DNA

source_name: GC177  genomic DNA

tag: strain GC177


title: Cj GC176  replicate 1

description: Campylobacter jejuni,  strain GC176,  genomic DNA

source_name: GC176  genomic DNA

tag: strain GC176


title: Cj GB03 replicate 1

description: Campylobacter jejuni,  strain GB03, genomic DNA

source_name: GB03 genomic DNA

tag: strain GB03


title: Cj GC178  replicate 1

description: Campylobacter jejuni,  strain GC178,  genomic DNA

source_name: GC178  genomic DNA

tag: strain GC178


title: Cj GB28 replicate 1

description: Campylobacter jejuni,  strain GB28, genomic DNA

source_name: GB28 genomic DNA

tag: strain GB28


title: Cj CURA235 replicate 1

description: Campylobacter jejuni,  strain CURA235, genomic DNA

source_name: CURA235 genomic DNA

tag: strain CURA235


title: Cj GC170  replicate 1

description: Campylobacter jejuni,  strain GC170,  genomic DNA

source_name: GC170  genomic DNA

tag: strain GC170