title: H2A.Z Replicate 1 vs input | array 11_123


title: TNF treatment for 2hr triplicate 2

status: Public on Jul 31 2005

type: RNA

city: Atlanta

first: Hui

last: Zeng

state: GA

address: 1600 Clifton Rd. MS:G16

department: Influenza Branch

country: USA

institute: Centers for disease control

description: After scanning, the data analysis were proformed by Biodiscovery softwares and Cluster/TreeView.

hyb_protocol: The labelled cDNA were cleaned up, pooled, and hybridized to the array chips.

scan_protocol: Both channels were scanned separately and imput softwares GeneSight from Biodiscovery Inc.

data_processing: normalization, background substract, transformation, t-test

molecule: total RNA

organism: Homo sapiens

source_name: Reference total RNA

label_protocol: Reverse transcription labelling

tag: High quality RNA pool from ten human cell	lines.

source_name: Treated sample

label_protocol: Reverse Transcription

extract_protocol: TRizol

tag: T84 cells were treated with TNF for	4hr


title: TNF treatment for 2hr triplicate 3


title: TNF treatment for 3hr triplicate 1


title: TNF treatment for 2hr triplicate 1


title: TNF treatment for 1hr triplicate 3


title: Flagellin treatment for 6hr triplicate 3

tag: T84 cells were treated with flagellin for	4hr


title: TNF treatment for 1hr triplicate 1


title: TNF treatment for 1hr triplicate 2


title: Flagellin treatment for 3hr triplicate 2


title: Flagellin treatment for 3hr triplicate 1


title: Flagellin treatment for 1hr triplicate 3


title: Flagellin treatment for 2hr triplicate 3


title: Flagellin treatment for 5hr triplicate 1


title: Flagellin treatment for 4hr triplicate 1


title: Flagellin treatment for 5hr triplicate 3


title: Flagellin treatment for 5hr triplicate 2


title: Flagellin treatment for 4hr triplicate 3


title: Flagellin treatment for 3hr triplicate 3


title: Flagellin treatment for 2hr triplicate 2


title: Flagellin treatment for 1hr triplicate 2


title: Flagellin treatment for 4hr triplicate 2


title: Flagellin treatment for 6hr triplicate 2


title: Flagellin treatment for 1hr triplicate 1


title: Flagellin treatment for 2hr triplicate 1


title: Flagellin treatment for 6hr triplicate 1


title: EECs from stage II endometrioid carcinomas tamoxifen(TAM) rep 1

status: Public on Jul 29 2005

city: Beijing

first: Yongfeng

last: Shang

address: 38 Xue Yuan Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University

description: Data - Arrays were scanned with the GeneArray scanner, and raw data were collected and analyzed using Affymetrix MICROARRAY SUITE and DATA MINING TOOLS software. Mann-Whitney pairwise comparisons were performed to identify genes that were differentially expressed. Genes with concordance exceeding 80.6% in EECs from both stage I and stage II samples were considered statistically significant (P < 0.1).

label: biotin

source_name: Endometrial epithelial cells


title: EECs from stage I endometrioid carcinomas tamoxifen(TAM) rep 1

data_processing: Data - Arrays were scanned with the GeneArray scanner, and raw data were collected and analyzed using Affymetrix MICROARRAY SUITE and DATA MINING TOOLS software.


title: EECs from stage I endometrioid carcinomas oestrogen(E2) rep 1


title: EECs from stage II endometrioid carcinomas control rep 1

tag: EECs from stage II endometrioid carcinomas (control) rep 1


title: 029KAR tum

status: Public on Jul 28 2005

city: Redwood City

first: Jordan

last: Hiller

state: CA

address: 1400 Seaport Blvd.

institute: PDL BioPharma

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3764
age_at_surgery: 67
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 1 of 22
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 1.8
sex: F

source_name: breast


title: 055TAL tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3766
age_at_surgery: 48
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 5 of 13
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 3.5
sex: F


title: 013COO met1

description:
mastectomy,left breast, with axillary dissection
pdl_hyb_id: 3763
age_at_surgery: 39
histology: metastasis
Surgical_margins: positive
lymph_node_involvement: 20 of 35, with extranodal invasion
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: .
sex: F

source_name: lymph node, axillary


title: 184BEL tum

description:
wide local excision, with axillary dissection
pdl_hyb_id: 3691
age_at_surgery: 42
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 23
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 2.1
sex: F


title: 071WON tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3767
age_at_surgery: 54
histology: invasive medullary carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 35
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 2.8
sex: F


title: 198COC tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3701
age_at_surgery: 63
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 24
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 1.2
sex: F


title: 067WIS met

description:
left mastectomy,  lateral pectoralis major, and apical node
pdl_hyb_id: 3765
age_at_surgery: 68
histology: metastasis
Surgical_margins: positive
lymph_node_involvement: 8 of 22
grade: 1
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 1
tubule_formation: 2
tumor_size_cm: .
sex: F


title: 193NOR tum

description:
segmental mastectomy, left breast with axillary dissection
pdl_hyb_id: 3696
age_at_surgery: 45
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 2 of 12
grade: 1
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 2.2
sex: F


title: EECs from stage I endometrioid carcinomas control rep 1

description: Data - Arrays were scanned with the GeneArray scanner, and raw data were collected and analyzed using Affymetrix MICROARRAY SUITE and DATA MINING TOOLS software.  Mann-Whitney pairwise comparisons were performed to identify genes that were differentially expressed.  Genes with concordance exceeding 80.6% in EECs from both stage I and stage II samples were considered statistically significant (P < 0.1).


title: 201TIE tum

description:
mastectomy, right breast.
pdl_hyb_id: 3703
age_at_surgery: 53
histology: invasive ductal carcinoma
Surgical_margins: positive
lymph_node_involvement: not stated
grade: 2
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 6.5
sex: F


title: 187HAN tum

description:
mastectomy
pdl_hyb_id: 3693
age_at_surgery: 84
histology: invasive lobular carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 1 (sentinel)
grade: 1
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 1
tubule_formation: 3
tumor_size_cm: 1.3
sex: F


title: 213BAG tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3706
age_at_surgery: 66
histology: invasive lobular carcinoma
Surgical_margins: positive
lymph_node_involvement: 0 of 17
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 2.1
sex: F


title: 195LOW tum

description:
mastectomy, left breast, with  axillary clearance
pdl_hyb_id: 3698
age_at_surgery: 72
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 4 of 27 with extranodal spread
grade: 3
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 3
sex: male


title: 197KUS tum

description:
wide re-excision, left breast
pdl_hyb_id: 3700
age_at_surgery: 39
histology: DCIS
Surgical_margins: negative
lymph_node_involvement: not stated
grade: not stated
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 0.6
sex: F


title: 222WHI tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3707
age_at_surgery: 74
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 1
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 2
sex: male


title: 207ABD tum

description:
mastectomy, left breast, with axillary dissection, and muscle tissue
pdl_hyb_id: 3705
age_at_surgery: 73
histology: invasive lobular carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 28
grade: 3
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 2.5
sex: F


title: 189OBR tum

description:
mastectomy
pdl_hyb_id: 3695
age_at_surgery: 89
histology: DCIS
Surgical_margins: negative
lymph_node_involvement: not stated
grade: not stated
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 4
sex: F


title: 186PAL tum

description:
wide local excision, left breast, axillary dissection
pdl_hyb_id: 3692
age_at_surgery: 56
histology: invasive ductal carcinoma
Surgical_margins: not stated
lymph_node_involvement: 1 of 14
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 6
sex: F


title: 194FUL tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3697
age_at_surgery: 72
histology: invasive lobular carcinoma
Surgical_margins: negative
lymph_node_involvement: 13 of 19; extensive replacement
grade: 2
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 4.7
sex: F


title: 199FRE tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3702
age_at_surgery: 66
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 3 of 3
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 7
sex: F


title: 096MCC tum2

description:
mastectomy, right breast, with sentinel node biopsy
pdl_hyb_id: 3688
age_at_surgery: 53
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 1 of 1 (sentinel)
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 2.4
sex: F


title: 204PEP tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3704
age_at_surgery: 66
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 1 of 21
grade: 1
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 3
tubule_formation: 1
tumor_size_cm: 1.4
sex: F


title: 099DON tum

description:
mastectomy
pdl_hyb_id: 3690
age_at_surgery: 49
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 2 of 9
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 2.1
sex: F


title: 196KIR tum

description:
mastectomy, right breast, with axillary clearance
pdl_hyb_id: 3699
age_at_surgery: 45
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 17
grade: 2
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 1
tumor_size_cm: 1.2
sex: F


title: 188PAR tum

description:
double mastectomy. Tumors found in both breasts.
pdl_hyb_id: 3694
age_at_surgery: 75
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: Left 1 of 1; Right 0 of 1
grade: 1
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 2
tubule_formation: 2
tumor_size_cm: 4
sex: F


title: 098SHE tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3689
age_at_surgery: 63
histology: invasive lobular carcinoma
Surgical_margins: positive
lymph_node_involvement: 0 of 18
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 3
sex: F


title: 096MCC tum1

description:
mastectomy, right breast, with sentinel node biposy
pdl_hyb_id: 3687
age_at_surgery: 53
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 1 of 1 (sentinel)
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 2.4
sex: F


title: 087MAM tum

description:
segmental mastectomy, with axillary dissection
pdl_hyb_id: 3684
age_at_surgery: 71
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 13
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 2.5
sex: F


title: 094KAN tum

description:
segmental mastectomy, right breast, with sentinel node biopsy
pdl_hyb_id: 3686
age_at_surgery: 82
histology: invasive ductal carcinoma
Surgical_margins: positive
lymph_node_involvement: 0 of 2
grade: 1
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 1
tubule_formation: 3
tumor_size_cm: 1.5
sex: F


title: 088THO tum

description:
wide local excision, left breast, with axillary dissection
pdl_hyb_id: 3685
age_at_surgery: .
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 6 of 27
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 2
sex: F


title: 086WIL tum

description:
mastectomy, right breast, with axillary clearance
pdl_hyb_id: 3683
age_at_surgery: 45
histology: invasive mixed carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 17
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 4
sex: F


title: 084DAV met

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3679
age_at_surgery: 51
histology: metastasis
Surgical_margins: negative
lymph_node_involvement: 2 of 5 sentinel, 0 of 10 axillary
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: .
sex: F


title: 013COO met2

description:
mastectomy,left breast, with axillary dissection
pdl_hyb_id: 3667
age_at_surgery: 39
histology: metastasis
Surgical_margins: positive
lymph_node_involvement: 20 of 35, with extranodal invasion
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: .
sex: F


title: 057TAY met2

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3673
age_at_surgery: 45
histology: metastasis
Surgical_margins: negative
lymph_node_involvement: 3 of 14
grade: not stated
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: 085BEC tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3682
age_at_surgery: 61
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 3 of 7
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 2.5
sex: F


title: 084DAV tum2

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3681
age_at_surgery: 51
histology: invasive mixed carcinoma
Surgical_margins: negative
lymph_node_involvement: 2 of 5 sentinel, 0 of 10 axillary
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 0.7
sex: F


title: 041OHA met

description:
wide local excision, left breast, with axillary clearance
pdl_hyb_id: 3670
age_at_surgery: 70
histology: metastasis
Surgical_margins: negative
lymph_node_involvement: 15 of 15, extensive extranodal
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: .
sex: F


title: 074MCC tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3677
age_at_surgery: 74
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 1 of 16
grade: 1
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 2
tumor_size_cm: 6.4
sex: F


title: 011CLA tum

description:
mastectomy - left breast
pdl_hyb_id: 3666
age_at_surgery: 85
histology: invasive ductal carcinoma
Surgical_margins: not stated
lymph_node_involvement: 4 of 8, with extranodal extension
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 4.7
sex: F


title: 013COO tum

description:
mastectomy,left breast, with axillary dissection
pdl_hyb_id: 3668
age_at_surgery: 39
histology: invasive ductal carcinoma
Surgical_margins: positive
lymph_node_involvement: 20 of 35, with extranodal invasion
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 1.3
sex: F


title: 041OHA tum

description:
wide local excision, left breast, with axillary clearance
pdl_hyb_id: 3671
age_at_surgery: 70
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 15 of 15, extensive extranodal
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 1.8
sex: F


title: 070SIL tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3675
age_at_surgery: 62
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 1 of 12
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 2.8
sex: F


title: 082LEE tum

description:
wide local excision, with axillary dissection
pdl_hyb_id: 3678
age_at_surgery: 66
histology: invasive ductal carcinoma
Surgical_margins: positive
lymph_node_involvement: 4 of 15
grade: 3
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 3
tumor_size_cm: 2.5
sex: F


title: 084DAV tum1

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3680
age_at_surgery: 51
histology: invasive mixed carcinoma
Surgical_margins: negative
lymph_node_involvement: 2 of 5 sentinel, 0 of 10 axillary
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 4
sex: F


title: Breast 3

description:
cadaveric; death by trauma (no evidence of malignancy)
pdl_hyb_id: 2762
age_at_surgery: 52
histology: normal specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: male


title: 009BRA tum

description:
lumpectomy
pdl_hyb_id: 3665
age_at_surgery: 58
histology: invasive lobular carcinoma
Surgical_margins: negative
lymph_node_involvement: not stated
grade: not stated
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 0.9
sex: F


title: 019FOR met

description:
axillary dissection, left axilla
pdl_hyb_id: 3657
age_at_surgery: 68
histology: metastasis
Surgical_margins: not stated
lymph_node_involvement: 6 of 14
grade: not stated
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: 077HIC tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3663
age_at_surgery: 64
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 17 of 17
grade: 3
mitoses_per_10_hpf: 3
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 4.2
sex: F


title: 033MAM tum

description:
lumpectomy (frozen section), mastectomy, left breast with axillary dissection
pdl_hyb_id: 3659
age_at_surgery: .
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 12
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: 2
tumor_size_cm: 1.2
sex: F


title: 038NOR tum

description:
segmental mastectomy,with axillary dissection
pdl_hyb_id: 3669
age_at_surgery: 56
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 21
grade: 2
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 2
tubule_formation: 2
tumor_size_cm: 2.7
sex: F


title: 202DIC tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3664
age_at_surgery: 62
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 11
grade: 2
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 1
tumor_size_cm: 2.5
sex: F


title: 057TAY tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3674
age_at_surgery: 45
histology: DCIS
Surgical_margins: negative
lymph_node_involvement: 3 of 14
grade: not stated
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: 053SMY tum

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 3660
age_at_surgery: 81
histology: invasive ductal carcinoma
Surgical_margins: positive
lymph_node_involvement: 0 of 18
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 2
tubule_formation: 1
tumor_size_cm: 2.1
sex: F


title: 007BAS tum1

description:
wide local excision, right breast
pdl_hyb_id: 3654
age_at_surgery: 58
histology: invasive lobular carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 7
grade: 2
mitoses_per_10_hpf: 1
nuclear_pleiomorphisms: 2
tubule_formation: .
tumor_size_cm: 0.8
sex: F


title: 054STA tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3661
age_at_surgery: 26
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 0 of 15
grade: 3
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: 1.5
sex: F


title: 018FOG tum

description:
mastectomy, left breast, with axillary dissection
pdl_hyb_id: 3656
age_at_surgery: 86
histology: invasive ductal carcinoma
Surgical_margins: negative
lymph_node_involvement: 1 of 16
grade: 3
mitoses_per_10_hpf: 2
nuclear_pleiomorphisms: 3
tubule_formation: 3
tumor_size_cm: 2.6
sex: F


title: Breast 1

description:
cadaveric; death by trauma (no evidence of malignancy)
pdl_hyb_id: 2761
age_at_surgery: 50
histology: normal specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: Breast 033MAM

description:
lumpectomy (frozen section), mastectomy, left breast with axillary dissection
pdl_hyb_id: 2753
age_at_surgery: .
histology: normal adjacent specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex:


title: Breast 084DAV

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 2760
age_at_surgery: 51
histology: normal adjacent specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: Breast 024HIL

description:
mastectomy, right breast, with axillary dissection
pdl_hyb_id: 2752
age_at_surgery: 70
histology: normal adjacent specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: Breast 100DOY

description:
pdl_hyb_id: 2603
age_at_surgery: .
histology: normal adjacent specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex:


title: Breast 5

description:
cadaveric; death by trauma (no evidence of malignancy)
pdl_hyb_id: 2517
age_at_surgery: 40
histology: normal specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: Breast 4

description:
cadaveric; death by trauma (no evidence of malignancy)
pdl_hyb_id: 2514
age_at_surgery: 36
histology: normal specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: PA Obese M 7 subA

city: Phoenix

first: Saraswathy

last: Nair

state: AZ

address: 4212 N. 16th Street

department: Phoenix Epidemiology and Clinical Research Branch

institute: NIDDK, NIH

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese male (PA-OM7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue

source_name: Primary cultured  abdominal subcutaneous preadipocytes


title: PA Obese M 7 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese male (PA-OM7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: H4K16Ac_Grunstein Replicate 1 vs input | array 11_121

status: Public on Sep 01 2005

type: genomic

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: Nucleosomal DNA was isolated and amplified using TLAD, and labeled with Cy3 fluorescent dye (green).  DNA from a ChIP with 3 ul Grunstein rabbit anti-H4K16Ac was amplified using TLAD.  These two probes were mixed together and hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios were calculated to produce the values given in the data table.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: aRNA-amplifed MNase digested DNA

label_protocol: The cDNA were covalently coupled separately with either Cy5 or Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0. The Cy5 and Cy3 labelled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 50 µl of 3.4X SSC, 2 mg/ml of yeast tRNA, and 0.3% SDS for hybridization to the microarray.

tag: Strain

source_name: H4K16Ac Grunstein ChIP, 3 ul Ab, IVT #635


title: PA Obese M 3 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese male (PA-OM3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 6 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese male (PA-OM6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 6 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese female (PA-OF6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 3 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese male (PA-OM3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 6 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese male (PA-OM6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: Breast 2

description:
cadaveric; death by trauma (no evidence of malignancy)
pdl_hyb_id: 2531
age_at_surgery: 21
histology: normal specimen
Surgical_margins: n/a
lymph_node_involvement:
grade: n/a
mitoses_per_10_hpf: .
nuclear_pleiomorphisms: .
tubule_formation: .
tumor_size_cm: .
sex: F


title: PA Obese M 2 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese male (PA-OM2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 4 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese male (PA-OM4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 5 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese male (PA-OM5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 2 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese female (PA-OF2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 6 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese female (PA-OF6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 1 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese female (PA-OF1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 7 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese female (PA-OF7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 4 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese female (PA-OF4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 2 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese female (PA-OF2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 5 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese male (PA-OM5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 4 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese male (PA-OM4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 5 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese female (PA-OF5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 7 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese female (PA-OF7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 2 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese male (PA-OM2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 3 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese female (PA-OF3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 4 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese female (PA-OF4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 3 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese female (PA-OF3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 1 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese male (PA-OM1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 1 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese female (PA-OF1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese F 5 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Obese female (PA-OF5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Obese M 1 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Obese male (PA-OM1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 7 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type used: Affymetrix HG-U133B. Subject: Lean male (PA-LM7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 6 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type used: Affymetrix HG-U133B. Subject: Lean male (PA-LM6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 5 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type used: Affymetrix HG-U133B. Subject: Lean male (PA-LM5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 5 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean male (PA-LM5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 7 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean male (PA-LM7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 4 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean male (PA-LM4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 4 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type used: Affymetrix HG-U133B. Subject: Lean male (PA-LM4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 6 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean male (PA-LM6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 2 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean male (PA-LM2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 7 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean female (PA-LF7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 3 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type used: Affymetrix HG-U133B. Subject: Lean male (PA-LM3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 3 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean male (PA-LM3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 2 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean male (PA-LM2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 1 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean male (PA-LM1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 6 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean female (PA-LF6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 5 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean female (PA-LF5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 5 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean female (PA-LF5)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 6 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean female (PA-LF6)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean M 1 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean male (PA-LM1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 7 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean female (PA-LF7)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 2 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean female (PA-LF2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 3 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean female (PA-LF3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 2 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean female (PA-LF2)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 4 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean female (PA-LF4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 4 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean female (PA-LF4)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 3 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean female (PA-LF3)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 1 subA

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians. Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. The array type: Affymetrix HG-U133A. Subject: Lean female (PA-LF1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: PA Lean F 1 subB

description:
Source of cells: Subcutaneous abdominal fat needle biopsies were obtained from non-diabetic Pima  Indians . Preadipocytes (stromal vascular cells) were obtained from collagenase digested adipose tissue from the infranatant after fat cells (adipocytes) were allowed to float to the top. The stromal vascular cells were cultured until subconfluency and RNA extracted from the harvested cells. Array type: Affymetrix HG-U133B. Subject: Lean female (PA-LF1)
Keywords = Obesity
Keywords = inflammation
Keywords = microarray
Keywords = gene expression
Keywords = preadipocyte
Keywords = stromal-vascular cells
Keywords = adipose tissue


title: RWPE2 human prostate cancer cells treated with lunasin at 2 microM for 24 hr

status: Public on Jul 26 2005

city: Davis

first: Kevin

last: Dawson

address: 2795 Second Street, Suite 400

department: CCM

institute: UC Davis

data_processing: 2^(RMA-normalized data)

source_name: RWPE2 human prostate cancer cells

treatment_protocol: lunasin at 2 microM for 24 hr


title: Untreated RWPE1 non-tumorigenic prostate epithelial cells

description: RWPE1 control

tag: RWPE1, non-tumorigenic human prostate epithelial cells, cell culture


title: RWPE1 human non-tumorigenic prostate epihelial cells treated with lunasin

description: RWPE1 treated with lunasin at 2 microM for 24 hr


title: Slide 57; second technical replicate spots

status: Public on Jul 25 2005

city: Haren

first: Sacha

last: van Hijum

address: Kerklaan 30

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

hyb_protocol: See our previous publication: Van Hijum et al. 2005. A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics 6:77.

data_processing: MicroPreP (PMID: 15907200)

organism: Lactococcus lactis subsp. lactis Il1403

source_name: IL1403 wild-type

label_protocol: See manuscript: Den Hengst et al. 2005. The Lactococcus lactis CodY regulon: identification of a conserved cis-element

tag: IL1403 wild-type

source_name: IL1403 CodY knockout

tag: IL1403 CodY knockout


title: Slide 351; second technical replicate spots

scan_protocol: See our previous publication: Van Hijum et al. 2005. A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics 6:77.

growth_protocol: See manuscript: Den Hengst et al. 2005. The Lactococcus lactis CodY regulon: identification of a conserved cis-element


title: Slide 57; first technical replicate spots

extract_protocol: See manuscript: Den Hengst et al. 2005. The Lactococcus lactis CodY regulon: identification of a conserved cis-element


title: Slide 191; second technical replicate spots

treatment_protocol: See manuscript: Den Hengst et al. 2005. The Lactococcus lactis CodY regulon: identification of a conserved cis-element


title: RWPE2 untreated human prostate cancer cells


title: Slide 58; first technical replicate spots


title: Slide 191; first technical replicate spots


title: Slide 351; first technical replicate spots


title: Slide 58; second technical replicate spots


title: hat1hat2-1

status: Public on Jul 23 2005

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
Total RNA isolated from a exponentially growing culture of double mutant hat1hat2  yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP
Keywords = yeast
Keywords = HAT

source_name: exponential growing wild type yeast strain


title: hat1hat2-2


title: hat1hat2-3


title: hat2-3

description:
Total RNA isolated from a exponentially growing culture of hat2 mutant yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP
Keywords = yeast
Keywords = HAT


title: hat1-3

description:
Total RNA isolated from a exponentially growing culture of hat1 mutant yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP
Keywords = yeast
Keywords = HAT


title: hat1-2

description:
Total RNA isolated from exponentially growing culture of wild type yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP
Keywords = yeast
Keywords = HAT


title: wt3 filter2

description:
Total RNA isolated from a exponentially growing culture of wild type yeast cells. cDNA labelling using oligo(dT)15VN and 33P-dCTP
Keywords = yeast
Keywords = HAT


title: hat1-1


title: wt3 filter1


title: Wt2 filter1


title: Slide 352; first technical replicate spots


title: Slide 352; second technical replicate spots


title: hat2-1


title: hat2-2


title: wt2 filter2


title: wt1 filter2


title: N12 Codelink

status: Public on Jul 22 2005

city: Charlestown

first: Dimitri

last: Krainc

address: Building 114, 16th St.

department: Neurology

institute: MassGeneral Institute for Neurodegeneration

description: healthy control 12. Duplicate probes and probes with blank descriptions are removed.

source_name: human whole blood, PAXgene


title: N14 Codelink

description: healthy control 14. Duplicate probes and probes with blank descriptions are removed.


title: N13 Codelink

description: healthy control 13. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy3 Week18_Cy5

city: Dallas

first: Wendy

last: Pan

state: TX

address: 5323 HarryHines Blvd

institute: UT Southwestern

description: Value=normalized log ratio data of 18 weeks DOX treated sample(Cy5) vs control sample(Cy3)

data_processing: Channel 2/Channel 1

organism: Mus musculus

source_name: normal mouse heart

source_name: 18 weeks DOX treated mouse heart


title: N8 Codelink

description: healthy control 8. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy5 Week12_Cy3(reversed)

description: Value=normalized log ratio data of 12 weeks DOX treated sample(Cy3) vs control sample(Cy5)

data_processing: Channel 1/Channel 2

source_name: 12 weeks DOX treated mouse heart


title: N5 Codelink

description: healthy control 5. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: N7 Codelink

description: healthy control 7. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: N10 Codelink

description: healthy control 10. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy3 Week12_Cy5

description: Value=normalized log ratio data of 12 weeks DOX treated sample(Cy5) vs control sample(Cy3)


title: N9 Codelink

description: healthy control 9. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy5 Week18_Cy3(reversed)

description: Value=normalized log ratio data of 18 weeks DOX treated sample(Cy3) vs control sample(Cy5)


title: N4 Codelink

description: healthy control 4. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy3 Week1_Cy5

description: Value=normalized log ratio data of 1 week DOX treated sample(Cy5) vs control sample(Cy3)

source_name: 1 week DOX treated mouse heart


title: N3 Codelink

description: healthy control 3. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy5 Week1_Cy3(Reversed)

description: Value=normalized log ratio data of 1 week DOX treated sample(Cy3) vs control sample(Cy5)


title: N11 Codelink

description: healthy control 11. Duplicate probes and probes with blank descriptions are removed.


title: N6 Codelink

description: healthy control 6. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD11 Codelink

description: Huntington's disease patient 11, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy5 Day1_Cy3(reversed)

description: Value=normalized log ratio data of 1 day DOX treated sample(Cy3) vs control sample(Cy5)

source_name: 1 day DOX treated mouse heart


title: N2 Codelink

description: healthy control 2. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: N1 Codelink

description: healthy control 1. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: P2 Codelink

description: Huntington's disease patient 2, presymptomatic. Duplicate probes and probes with blank descriptions are removed.


title: P5 Codelink

description: Huntington's disease patient 5, presymptomatic. Duplicate probes and probes with blank descriptions are removed.


title: P3 Codelink

description: Huntington's disease patient 3, presymptomatic. Duplicate probes and probes with blank descriptions are removed.


title: P1 Codelink

description: Huntington's disease patient 1, presymptomatic. Duplicate probes and probes with blank descriptions are removed.


title: Control_Cy3 Day1_Cy5

description: Value=normalized log ratio data of 1 day DOX treated sample(Cy5) vs control sample(Cy3)


title: P4 Codelink

description: Huntington's disease patient 4, presymptomatic. Duplicate probes and probes with blank descriptions are removed.


title: HD12 Codelink

description: Huntington's disease patient 12, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD10 Codelink

description: Huntington's disease patient 10, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD9 Codelink

description: Huntington's disease patient 9, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD6 Codelink

description: Huntington's disease patient 6, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD8 Codelink

description: Huntington's disease patient 8, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: WT Vs Rv2869c mutant +Tw #2

city: New York

first: Michael

last: Glickman

state: NY

institute: Sloan Kettering Institute for Cancer Research

description: See replicate #1

data_processing: Intesnity Dependent Normalization

organism: Mycobacterium tuberculosis

source_name: Mtb Erdman RNA grown with Tween

tag: Mtb Erdman grown in log phase with Tween.

source_name: Mtb Rv2869c null mutant

tag: Mtb Rv2869c null mutant grown in log phase with Tween


title: HD5 Codelink

description: Huntington's disease patient 5, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD4 Codelink

description: Huntington's disease patient 4 symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD7 Codelink

description: Huntington's disease patient 7, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD2 Codelink

description: Huntington's disease patient 2, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: HD1 Codelink

description: Huntington's disease patient 1, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: WT Vs Rv2869c mutant +Tw

description: See other samples in this set

data_processing: Ratio is Cy5/Cy3. Intensity dependent normalization

tag: Mtb strain Erdman grown in +Tween media in logarithmic phase

tag: Mtb Rv2869c null mutant grown in +Tween media in logarithmic phase


title: T2Null_vs_MgCl2-T2_rep2 c

status: Public on Jul 21 2005

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

description: Replicate 2

hyb_protocol: Hegde P et al Biotechniques 2000 29:548-56

scan_protocol: scanner: Perkin-Elmer ScanArray Express Software: ScanArray Express v2.1

data_processing:
Spot raw data from GenePix4.0
glowess normalization using R/MAANOVA

organism: Glycine max

source_name: Pooled unifoliate leaves from 3-4 plants

label_protocol: Indirect incorporation using aa-dUTP

growth_protocol:
Growth Chamber (22C)
Light 100-120 umol photons/m2/sec
16 hour daylength

extract_protocol: Trizol Phase Lock Gel RNA Extraction

tag: Cultivar

value: Williams 82

tag: Age

value: approximately 14 days

treatment_protocol:
10mM MgCl2:vacuum infiltrated
2 hour post infiltration


title: S-T2_vs_S-T8_rep2 c

description: Replicate 2

treatment_protocol:
P. syringae avrB-
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
2 hour post inoculation

treatment_protocol:
P. syringae avrB-
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
8 hour post inoculation


title: HD3 Codelink

description: Huntington's disease patient 3, symptomatic. Data from Codelink Human Uniset I and II are combined. Duplicate probes and probes with blank descriptions are removed.


title: R-T24_vs_MgCl2-T24_rep2 c

description: Replicate 2

treatment_protocol:
P. syringae avrB+
OD600: 0.02 in 10mM MgCl2
Vacuum infiltrated
24 hour post inoculation

treatment_protocol:
10mM MgCl2
Vacuum infiltrated
24 hour post infiltration


title: R-T2_vs_R-T8_rep2 c

description: Replicate 2

treatment_protocol:
P. syringae avrB+
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
2 hour post inoculation

treatment_protocol:
P. syringae avrB+
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
8 hour post inoculation


title: MgCl2-T8_vs_S-T8_rep2 c

description: Replicate 2

treatment_protocol:
10mM MgCl2
Vacuum infiltrated
8 hour post infiltration


title: S-T8_vs_S-T24_rep2 c

description: Replicate 2

treatment_protocol:
P. syringae avrB-
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
24 hour post inoculation


title: S-T24_vs_R-T24_rep2 c

description: Replicate 2

treatment_protocol:
P. syringae avrB+
OD600:0.02 in 10mM MgCl2:vacuum infiltrated
24 hour post inoculation


title: MgCl2-T24_vs_S-T24_rep2 c

description: Replicate 2


title: R-T8_vs_R-T24_rep2

description: Replicate 2


title: MgCl2-T24_vs_S-T24_rep2

description: Replicate 2


title: R-T2_vs_R-T8_rep2

description: Replicate 2


title: S-T2_vs_S-T8_rep2

description: Replicate 2


title: S-T8_vs_R-T8_rep2 c

description: Replicate 2


title: MgCl2-T2_vs_S-T2_rep2 c

description: Replicate 2

treatment_protocol:
10mM MgCl2
Vacuum infiltrated
2 hour post infiltration


title: S-T24_vs_R-T24_rep2

description: Replicate 2


title: T2Null_vs_MgCl2-T2_rep2

description: Replicate 2


title: S-T8_vs_S-T24_rep2

description: Replicate 2


title: S-T2_vs_R-T2_rep2 c

description: Replicate 2


title: R-T2_vs_MgCl2-T2_rep2 c

description: Replicate 2

treatment_protocol:
P. syringae avrB+
OD600: 0.02 in 10mM MgCl2
Vacuum infiltrated
2 hour post inoculation


title: R-T24_vs_MgCl2-T24_rep2

description: Replicate 2


title: S-T8_vs_R-T8_rep2

description: Replicate 2


title: R-T8_vs_MgCl2-T8_rep2 c

description: Replicate 2

treatment_protocol:
P. syringae avrB+
OD600: 0.02 in 10mM MgCl2
Vacuum infiltrated
8 hour post inoculation


title: S-T24_vs_R-T24 c

description: Replicate 1


title: R-T8_vs_MgCl2-T8_rep2

description: Replicate 2


title: S-T2_vs_S-T8 c

description: Replicate 1


title: R-T8_vs_R-T24 c

description: Replicate 1


title: S-T8_vs_S-T24 c

description: Replicate 1


title: T2Null_vs_MgCl2-T2 c

description: Replicate 1


title: MgCl2-T8_vs_S-T8 c

description: Replicate 1


title: R-T2_vs_R-T8 c

description: Replicate 1


title: S-T2_vs_R-T2_rep2

description: Replicate 2


title: R-T8_vs_R-T24_rep2 c

description: Replicate 2


title: MgCl2-T2_vs_S-T2_rep2

description: Replicate 2


title: T2Null_vs_MgCl2-T2

description: Replicate 1


title: R-T24_vs_MgCl2-T24 c

description: Replicate 1


title: S-T8_vs_S-T24

description: Replicate 1


title: S-T8_vs_R-T8 c

description: Replicate 1


title: R-T8_vs_R-T24

description: Replicate 1


title: S-T2_vs_S-T8

description: Replicate 1


title: R-T2_vs_MgCl2-T2_rep2

description: Replicate 2


title: MgCl2-T24_vs_S-T24 c

description: Replicate 1


title: MgCl2-T2_vs_S-T2 c

description: Replicate 1


title: R-T24_vs_MgCl2-T24

description: Replicate 1


title: R-T2_vs_R-T8

description: Replicate 1


title: R-T8_vs_R-T24_rep2 b

description: Replicate 2


title: R-T8_vs_MgCl2-T8 c

description: Replicate 1


title: R-T2_vs_MgCl2-T2 c

description: Replicate 1


title: MgCl2-T8_vs_S-T8

description: Replicate 1


title: S-T2_vs_S-T8_rep2 b

description: Replicate 2


title: R-T2_vs_R-T8_rep2 b

description: Replicate 2


title: T2Null_vs_MgCl2-T2_rep2 b

description: Replicate 2


title: R-T8_vs_MgCl2-T8

description: Replicate 1


title: S-T24_vs_R-T24

description: Replicate 1


title: S-T2_vs_R-T2

description: Replicate 1


title: S-T2_vs_R-T2 c

description: Replicate 1


title: S-T2_vs_R-T2_rep2 b

description: Replicate 2


title: MgCl2-T24_vs_S-T24

description: Replicate 1


title: S-T8_vs_S-T24_rep2 b

description: Replicate 2


title: MgCl2-T8_vs_S-T8_rep2 b

description: Replicate 2


title: R-T8_vs_MgCl2-T8_rep2 b

description: Replicate 2


title: S-T8_vs_R-T8

description: Replicate 1


title: R-T8_vs_R-T24 b

description: Replicate 1


title: S-T8_vs_S-T24 b

description: Replicate 1


title: R-T2_vs_MgCl2-T2

description: Replicate 1


title: R-T2_vs_MgCl2-T2_rep2 b

description: Replicate 2


title: MgCl2-T24_vs_S-T24_rep2 b

description: Replicate 2


title: R-T24_vs_MgCl2-T24_rep2 b

description: Replicate 2


title: S-T24_vs_R-T24_rep2 b

description: Replicate 2


title: MgCl2-T2_vs_S-T2

description: Replicate 1


title: R-T2_vs_R-T8 b

description: Replicate 1


title: R-T24_vs_MgCl2-T24 b

description: Replicate 1


title: MgCl2-T24_vs_S-T24 b

description: Replicate 1


title: MgCl2-T8_vs_S-T8_rep2

description: Replicate 2


title: R-T2_vs_MgCl2-T2 b

description: Replicate 1


title: T2Null_vs_MgCl2-T2 b

description: Replicate 1


title: MgCl2-T2_vs_S-T2_rep2 b

description: Replicate 2


title: MgCl2-T2_vs_S-T2 b

description: Replicate 1


title: S-T2_vs_R-T2 b

description: Replicate 1


title: R-T8_vs_MgCl2-T8 b

description: Replicate 1


title: S-T8_vs_R-T8 b

description: Replicate 1


title: S-T24_vs_R-T24 b

description: Replicate 1


title: MgCl2-T8_vs_S-T8 b

description: Replicate 1


title: MM V IM 10.5dpc_mean transf.txt column 8

status: Public on Jul 20 2005

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description:
Sample; 2
File Name; MM V IM 10.5dpc_mean transf.txt
comparison; 1
Array Design; Mouse Compugen 22K Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Developmental Stage; embryonic
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp (Ambion)
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ, St Lucia, Australia
RNA type; aRNA
Sample Source; primary tissue
Sex; both
Age; 10.5
Sampling Method; dissection
Dye Swap; red/green; green/red
To account for dye swap, the signal channel and control channel measurements for sample(s) 3-4 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: 10.5dpc Metanephric Mesenchyme

source_name: 10.5dpc Intermediate Mesoderm


title: CGEN 10.5 Vs 13.5dpc.txt column 13

description:
Sample; 3
File Name; CGEN 10.5 Vs 13.5dpc.txt
Age; 10.5 V 13.5
Array Design; Mouse COmpugen 22K oligo
Author; Sean rimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R: Print tip Loess + between arrays (LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green; green/red
Experiment Type; Pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message AMp Ambion
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; Pool of both
Strain/Cell-line; CD1
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: 13.5 dpc Kidney

source_name: 10.5dpc Metanephric mesenchyme


title: CGEN 10.5 Vs 13.5dpc.txt column 8

description:
Sample; 2
File Name; CGEN 10.5 Vs 13.5dpc.txt
Age; 10.5 V 13.5
Array Design; Mouse COmpugen 22K oligo
Author; Sean rimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Data processing/normalization; R: Print tip Loess + between arrays (LIMAS+SMA)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green; green/red
Experiment Type; Pairwise comparison
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message AMp Ambion
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ
RNA type; aRNA
Sample Source; primary tissue
Sampling Method; microdissection
Sex; Pool of both
Strain/Cell-line; CD1
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.


title: temporal.txt e12.5 o-192055

description:
Individual ID; o-192055
Age; 12.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: Mouse Universal Reference RNA

source_name: e12.5 Kidney


title: MM V IM 10.5dpc_mean transf.txt column 13

description:
Sample; 3
File Name; MM V IM 10.5dpc_mean transf.txt
comparison; 1
Array Design; Mouse Compugen 22K Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Developmental Stage; embryonic
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp (Ambion)
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ, St Lucia, Australia
RNA type; aRNA
Sample Source; primary tissue
Sex; both
Age; 10.5
Sampling Method; dissection
Dye Swap; red/green; green/red
To account for dye swap, the signal channel and control channel measurements for sample(s) 3-4 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: 10.5dpc Intermediate Mesenchyme

source_name: 10.5dpc Metanephric mesoderm


title: MM V IM 10.5dpc_mean transf.txt column 3

description:
Sample; 1
File Name; MM V IM 10.5dpc_mean transf.txt
comparison; 1
Array Design; Mouse Compugen 22K Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); none
Concentration; 100
Developmental Stage; embryonic
Image Analysis Software; Imagene5.5
Labeling Protocol; Amino Allyl Message Amp (Ambion)
Organ/Organism part; kidney
Organism; Mus musculus
Organization; IMB, UQ, St Lucia, Australia
RNA type; aRNA
Sample Source; primary tissue
Sex; both
Age; 10.5
Sampling Method; dissection
Dye Swap; red/green; green/red
To account for dye swap, the signal channel and control channel measurements for sample(s) 3-4 were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.


title: temporal.txt e11.5 o-192060

description:
Individual ID; o-192060
Age; 11.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e11.5 Kidney


title: temporal.txt e16.5 o-192007

description:
Individual ID; o-192007
Age; 16.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e16.5 Kidney


title: temporal.txt e14.5 o-192038

description:
Individual ID; o-192038
Age; 14.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e14.5 Kidney


title: temporal.txt e10.5 o-192059

description:
Individual ID; o-192059
Age; 10.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e10.5 Kidney


title: temporal.txt e12.5 o-192033

description:
Individual ID; o-192033
Age; 12.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e10.5 o-192057

description:
Individual ID; o-192057
Age; 10.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.


title: temporal.txt e15.5 o-192083

description:
Individual ID; o-192083
Age; 15.5
Array Design; Mouse Compugen 22K Spotted Oligo
Author; Sean Grimmond
Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene)
Concentration; 100
Data processing/normalization; Lowess Normalisation GeneSpring)
Developmental Stage; embryonic
Diseased/Normal; normal
Dye Swap; red/green
Experiment Type; time course
Genetic Characteristic; Wild type
Image Analysis Software; Imagene5.5 (Biodiscovery)
Labeling Protocol; Amino Allyl Message Amp- Ambion
Organ/Organism part; kidney
Organism; Mus Musculus
RNA type; aRNA Message Amp-ambion
Tissue Type; Pool of whole organs
Organization; IMB, Uni of QLD, Brisbane Australia
Sample Source; primary tissue
Sampling Method; Dissection of whole organ
Sex; Pool of both sexes
Strain/Cell-line; CD1
To account for dye swap, the signal channel and control channel measurements for each sample were reversed.  A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Specific samples were normalized to one another:  sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: e15.5 Kidney