title: Filling panicle AP2


title: Heading panicle AP3

status: Public on May 24 2005

type: RNA

city: NEW HAVEN

first: Ligeng

last: Ma

state: CT

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

country: USA

institute: Yale University

description:
Panicle vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_transformation: raw data

molecule: total RNA

organism: Oryza sativa Indica Group

source_name: Panicle(or root or panicle etc)

source_name: cultured cell (for all samples)


title: Heading panicle BP2

description:
Panicle vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_title_ch[1]: panicle(or root or panicle etc)
Sample_title_ch[2]: cultured cell (for all samples)
Sample_transformation: raw data

source_name: total RNA


title: Filling panicle BP3


title: Root BP3

description:
Root vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_title_ch[1]: Root(or root or panicle etc)
Sample_title_ch[2]: cultured cell (for all samples)
Sample_transformation: raw data


title: Heading panicle BP3


title: GC (HKG24N)

status: Public on May 25 2005

city: San Francisco

first: Xin

last: Chen

state: CA

institute: UCSF

description:
Simple annotation: Non-tumor tissue, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16254.gif; format: GIF

organism: Homo sapiens

source_name: channel 1: Cy3 - CRG, common reference

source_name: channel 2: Cy5 - gastric tissue


title: GC (HKG93T)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-08/19638.gif; format: GIF


title: GC (HKG91T)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-10/21035.gif; format: GIF


title: Filling panicle BP2


title: Heading panicle AP1


title: GC (HKG47L)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-08/19482.gif; format: GIF


title: GC (HKG89T_1)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-08/19637.gif; format: GIF


title: GC (HKG6T)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14540.gif; format: GIF


title: Root AP1

description:
Root vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_transformation: raw data

source_name: Root(or root or panicle etc)


title: GC (HKG2N)

description:
Simple annotation: Non-tumor tissue, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-06/17266.gif; format: GIF


title: Root BP2


title: Filling panicle BP1


title: Heading panicle AP2


title: Root AP2


title: Root AP3


title: Heading panicle BP1


title: GC (HKG24L)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/16252.gif; format: GIF


title: GC (HKG62T)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-05/16712.gif; format: GIF


title: GC (HKG1T)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-03/14715.gif; format: GIF


title: Yeast histone H4 WT 3

city: Columbus

first: Mark

last: Parthun

state: OH

address: 1645 Neil Ave.

department: Molecular and Cellular Biochemistry

institute: Ohio State University

description: Expression in a yeast histone H4 WT strain.  Cells grown in YPD and harvested in mid-log phase.  Replicate 3.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae


title: GC (HKG92T)

description:
Simple annotation: Primary tumor, Stomach cancer
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-09/20204.gif; format: GIF


title: Yeast histone H4 K91A 3


title: Shoot AP3

description:
Shoot vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_transformation: raw data

source_name: Shoot (or root or panicle etc)


title: Root BP1


title: Yeast histone H4 WT 1

description: Expression in a yeast histone H4 WT strain.  Cells grown in YPD and harvested in mid-log phase.  Replicate 1.


title: Yeast histone H4 K91A 2

description: Expression in a yeast histone H4 K91A allele.  Cells grown in YPD and harvested in mid-log phase.  Replicate 2.


title: Shoot AP1


title: Yeast histone H4 K91A 1

description: Expression in a yeast histone H4 K91A allele.  Cells grown in YPD and harvested in mid-log phase.  Replicate 1.


title: Shoot BP1

description:
Shoot vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_title_ch[1]: Shoot(or root or panicle etc)
Sample_title_ch[2]: cultured cell (for all samples)
Sample_transformation: raw data


title: Shoot BP3


title: Shoot BP2


title: Shoot AP2


title: Seedling BP3

description:
Seedling vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_title_ch[1]: Seedling (or root or panicle etc)
Sample_title_ch[2]: cultured cell (for all samples)
Sample_transformation: raw data


title: t21

status: Public on May 22 2005

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

country: Japan

institute: The University of Tokyo

description:
Sample_ID:t21 // Patient:J-275 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t21, surgically resected from patient of gastric cancer.


title: ACTH-secreting pituitary adenoma

status: Public on May 23 2005

city: London

first: Damian

last: Morris

department: Endocrinology

country: United Kingdom

institute: St. Bartholomew’s and the Royal London School of Medicine and Dentistry

description:
RNA from 5 ACTH-secreting pituitary adenomas obtained at transphenoidal surgery was extracted using a Promega SV kit. Targets were produced using standard Affymetrix procedures from 15ug of pooled total RNA.
This sample is also known as pACTH.
Keywords = Homo sapiens, ACTH-secreting pituitary adenoma

source_name: pooled ACTH-secreting pituitary adenoma


title: PRL-secreting pituitary adenoma

description:
RNA from 5 prolactin(PRL)-secreting pituitary adenomas obtained at transphenoidal surgery was extracted using a Promega SV kit. Targets were produced using standard Affymetrix procedures from 15ug of pooled total RNA.
This sample is also known as pPRL.
Keywords = Homo sapiens, PRL-secreting pituitary adenoma

source_name: pooled PRL-secreting pituitary adenoma


title: non-functioning pituitary adenoma

description:
RNA from 5 non-functioning pituitary adenomas obtained at transphenoidal surgery was extracted using a Promega SV kit. Targets were produced using standard Affymetrix procedures from 15ug of pooled total RNA.
This sample is also known as pNFPA.
Keywords = Homo sapiens, non-functioning pituitary adenoma

source_name: pooled non-functioning pituitary adenoma


title: GH-secreting pituitary adenoma

description:
RNA from 5 GH-secreting pituitary adenomas obtained at transphenoidal surgery was extracted using a Promega SV kit. Targets were produced using standard Affymetrix procedures from 15ug of pooled total RNA.
This sample is also known as pGH.
Keywords = Homo sapiens, GH-secreting pituitary adenoma

source_name: pooled GH-secreting pituitary adenoma


title: normal pituitary

description:
RNA from 5 post-mortem pituitary glands obtained within 12 hours of death was extracted using a Promega SV kit. Targets were produced using standard Affymetrix procedures from 15ug of pooled total RNA.
This sample is also known as pNP.
Keywords = Homo sapiens, normal pituitary

source_name: pooled post-mortem normal pituitary


title: t22

description:
Sample_ID:t22 // Patient:J-287 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t22, surgically resected from patient of gastric cancer.


title: Yeast histone H4 WT 2

description: Expression in a yeast histone H4 WT strain.  Cells grown in YPD and harvested in mid-log phase.  Replicate 2.


title: seedling AP1

description:
seedling vs cultured cell
Sample_extract_protocol_ch[1]: Trizol/RNeasy
Sample_extract_protocol_ch[2]: Trizol/RNeasy
Sample_hyb_protocol: 42C 50% formamide
Sample_label_ch[1]: cy5
Sample_label_ch[2]: cy3
Sample_label_protocol_ch[1]: amino-allyl and monofunctional dye
Sample_label_protocol_ch[2]: amino-allyl and monofunctional dye
Sample_molecule_ch[1]: total RNA
Sample_molecule_ch[2]: total RNA
Sample_organism_ch[1]: Oryza sativa (indica cultivar-group)
Sample_organism_ch[2]: Oryza sativa (indica cultivar-group)
Sample_scan_protocol: Axon GenePix 4000B
Sample_specimen_provider_ch[1]: Deng
Sample_specimen_provider_ch[2]: Deng
Sample_transformation: raw data

source_name: seedling (or root or panicle etc)


title: seedling AP2


title: t15

description:
Sample_ID:t15 // Patient:J-264 // Histology:Intestinal // Metastasis:- // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:++
Keywords = Gastric cancer

source_name: t15, surgically resected from patient of gastric cancer.


title: t16

description:
Sample_ID:t16 // Patient:J-277 // Histology:Intestinal // Metastasis:- // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:++
Keywords = Gastric cancer

source_name: t16, surgically resected from patient of gastric cancer.


title: Seedling BP1


title: t14

description:
Sample_ID:t14 // Patient:J-256 // Histology:Intestinal // Metastasis:- // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t14, surgically resected from patient of gastric cancer.


title: t17

description:
Sample_ID:t17 // Patient:J-166 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:+
Keywords = Gastric cancer

source_name: t17, surgically resected from patient of gastric cancer.


title: Seedling BP2

source_name: total RNA


title: seedling AP3

source_name: cultured cell (for all samples)


title: t18

description:
Sample_ID:t18 // Patient:J-209 // Histology:Intestinal // Metastasis:- // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:+
Keywords = Gastric cancer

source_name: t18, surgically resected from patient of gastric cancer.


title: t19

description:
Sample_ID:t19 // Patient:J-222 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t19, surgically resected from patient of gastric cancer.


title: t08

description:
Sample_ID:t08 // Patient:J-125 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:++
Keywords = Gastric cancer

source_name: t08, surgically resected from patient of gastric cancer.


title: t13

description:
Sample_ID:t13 // Patient:J-194 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t13, surgically resected from patient of gastric cancer.


title: t01

description:
Sample_ID:t01 // Patient:J-159 // Histology:Diffuse // Metastasis:- // p53_mut:- // E-cadherin_mut:- // beta-Catenin_mut:+
Keywords = Gastric cancer

source_name: t01, surgically resected from patient of gastric cancer.


title: t07

description:
Sample_ID:t07 // Patient:J-199 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t07, surgically resected from patient of gastric cancer.


title: t12

description:
Sample_ID:t12 // Patient:J-191 // Histology:Intestinal // Metastasis:- // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t12, surgically resected from patient of gastric cancer.


title: n24

description:
Sample_ID:n24 // Patient:J-n24 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n24, surgically resected from patient of gastric cancer.


title: t04

description:
Sample_ID:t04 // Patient:J-133 // Histology:Diffuse // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t04, surgically resected from patient of gastric cancer.


title: n23

description:
Sample_ID:n23 // Patient:J-n23 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n23, surgically resected from patient of gastric cancer.


title: t05

description:
Sample_ID:t05 // Patient:J-108 // Histology:Diffuse // Metastasis:+ // p53_mut:- // E-cadherin_mut:- // beta-Catenin_mut:+
Keywords = Gastric cancer

source_name: t05, surgically resected from patient of gastric cancer.


title: t11

description:
Sample_ID:t11 // Patient:J-175 // Histology:Intestinal // Metastasis:+ // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t11, surgically resected from patient of gastric cancer.


title: t06

description:
Sample_ID:t06 // Patient:J-111 // Histology:Intestinal // Metastasis:+ // p53_mut:++ // E-cadherin_mut:+ // beta-Catenin_mut:++
Keywords = Gastric cancer

source_name: t06, surgically resected from patient of gastric cancer.


title: t10

description:
Sample_ID:t10 // Patient:J-163 // Histology:Intestinal // Metastasis:+ // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t10, surgically resected from patient of gastric cancer.


title: t02

description:
Sample_ID:t02 // Patient:J-258 // Histology:Diffuse // Metastasis:+ // p53_mut:++ // E-cadherin_mut:- // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t02, surgically resected from patient of gastric cancer.


title: n09

description:
Sample_ID:n09 // Patient:J-128 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n09, surgically resected from patient of gastric cancer.


title: t09

description:
Sample_ID:t09 // Patient:J-128 // Histology:Intestinal // Metastasis:- // p53_mut:+ // E-cadherin_mut:+ // beta-Catenin_mut:+
Keywords = Gastric cancer

source_name: t09, surgically resected from patient of gastric cancer.


title: n04

description:
Sample_ID:n04 // Patient:J-133 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n04, surgically resected from patient of gastric cancer.


title: n12

description:
Sample_ID:n12 // Patient:J-191 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n12, surgically resected from patient of gastric cancer.


title: n16

description:
Sample_ID:n16 // Patient:J-277 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n16, surgically resected from patient of gastric cancer.


title: t03

description:
Sample_ID:t03 // Patient:J-290 // Histology:Diffuse // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t03, surgically resected from patient of gastric cancer.


title: n22

description:
Sample_ID:n22 // Patient:J-287 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n22, surgically resected from patient of gastric cancer.


title: Sham 50d replicate 2

status: Public on May 21 2005

first: Jakir

last: Ullah

institute: Novartis

description: DRG collected from ipsilateral limb after 50 days from sham operated animals

organism: Rattus norvegicus

source_name: Rat Dorsal Root Ganglia


title: Sham 50d replicate 1


title: t20

description:
Sample_ID:t20 // Patient:J-274 // Histology:Intestinal // Metastasis:+ // p53_mut:- // E-cadherin_mut:+ // beta-Catenin_mut:-
Keywords = Gastric cancer

source_name: t20, surgically resected from patient of gastric cancer.


title: n03

description:
Sample_ID:n03 // Patient:J-290 // Histology:Normal // Metastasis:NA // p53_mut:NA // E-cadherin_mut:NA // beta-Catenin_mut:NA
Keywords = Gastric cancer

source_name: n03, surgically resected from patient of gastric cancer.


title: Sham 21 replicate 3

description: DRG collected from ipsilateral limb after 21 days from sham operated animals


title: Sham 21 replicate 2


title: Seltzer 50d replicate 2

description: DRG collected from ipsilateral limb 50d days after sciatic nerve transection surgery


title: Seltzer 50d replicate 1


title: Sham 14 replicate 2

description: DRG collected from ipsilateral limb after 14 days from sham operated animals


title: Sham 21 replicate 1


title: Sham 14 replicate 1


title: Seltzer 21d replicate 3

description: DRG collected from ipsilateral limb 21d days after sciatic nerve transection surgery


title: CC1 21d replicate 3

description: DRG collected from ipsilateral limb 21 days after chronic constriction injury


title: Seltzer 14d replicate 1

description: DRG collected from ipsilateral limb 14d days after sciatic nerve transection surgery


title: Seltzer 21d replicate 1


title: Seltzer 14d replicate 2


title: Seltzer 21d replicate 2


title: CC1 21d replicate 1

description:
DRG collected from ipsilateral limb 21 days after chronic constriction injury
Lot batch = Replicate 1


title: CCI 14d replicate 3

description:
DRG collected from ipsilateral limb 14 days after chronic constriction injury
Lot batch = Replicate 3


title: CC1 21d replicate 2


title: CCI 14d replicate 1

description: DRG collected from ipsilateral limb 14 days after chronic constriction injury


title: WT_vs_SIPK-Ri_8h_xox_3

status: Public on May 19 2005

city: Rockville

first: Li

last: Zheng

state: MD

address: 9712 Medical Center Dr.

institute: The Institute for Genomic Research

description:
Wildtype and SIPK -silenced (RNAi) tobacco cell suspension cultures were grown in MS medium at 25 C in the dark. Cell suspension cultures were transferred to fresh growth medium 3 days prior to pooling each genotype and dividing the pool into 3 x 10ml volumes per genotype. A 30 minute pre-incubation was used with xanthine (for abiotic controls and treatments), but no pre-treatment was used for the biotic stressors. For each treatment and abiotic/biotic controls, the cells were harvested by vacuum filtration at the appropriate time points (controls sampled at 0 hrs) and frozen in N2(l) for RNA extraction. In order to discern the effect of silencing SIPK on the transciptome in defence response, biological replicates of WT and SIPK-Ri were randomly paired on 3 slides per treatment or control group.
Keywords = Nicotiana tabacum, Cell suspension culture, Biotic stress

organism: Nicotiana tabacum

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Xanthine:xanthine oxidase, 8 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Xanthine:xanthine oxidase, 8 h; CH1: Cy5


title: WT_vs_WT_4h_harp_FD

source_name: Query sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Harpin (P.syringae) 4 hr; CH1: Cy5

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: None: biotic control 0 hr; CH2: Cy3


title: CCI 14d replicate 2

description:
DRG collected from ipsilateral limb 14 days after chronic constriction injury
Lot batch = Replicate 2


title: WT_vs_SIPK-Ri_4h_xox_3

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Xanthine:xanthine oxidase, 4 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Xanthine:xanthine oxidase, 4 h; CH1: Cy5


title: WT_vs_WT_4h_harp_3

source_name: Query sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Harpin (P.syringae) 4 hr; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: None: biotic control 0 hr; CH1: Cy5


title: WT_vs_SIPK-Ri_4h_xox_2


title: WT_vs_SIPK-Ri_8h_xox_1


title: WT_vs_WT_4h_harp_2


title: WT_vs_SIPK-Ri_4h_xox_1


title: WT_vs_WT_4h_mega_2

source_name: Query sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Megaspermin (P.syringae) 4 hr; CH2: Cy3


title: WT_vs_WT_4h_harp_1


title: WT_vs_SIPK-Ri_ab_cont_FD

source_name: Query sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Abiotic biological control, 0 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Abiotic biol. control, 0 h; CH1: Cy5


title: WT_vs_WT_4h_mega_3


title: WT_vs_SIPK-Ri_8h_xox_2


title: WT_vs_SIPK-Ri_ab_cont_3

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Abiotic biological control, 0 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Abiotic biological control, 0 h; CH1: Cy5


title: WT_vs_WT_4h_mega_1


title: WT_vs_SIPK-Ri_ab_cont_2


title: WT_vs_SIPK-Ri_8h_mega_2

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Megaspermin (P.megasperma), 8 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Megaspermin (P.megasperma), 8 h; CH1: Cy5


title: WT_vs_SIPK-Ri_8h_mega_3


title: WT_vs_SIPK-Ri_8h_harp_3

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Harpin (P.syringae), 8 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Harpin (P.syringae), 8 h; CH1: Cy5


title: WT_vs_SIPK-Ri_8h_mega_1


title: WT_vs_SIPK-Ri_8h_harp_2


title: WT_vs_SIPK-Ri_4h_mega_1

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Megaspermin (P.megasperma), 4 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Megaspermin (P.megasperma), 4 h; CH1: Cy5


title: WT_vs_SIPK-Ri_4h_mega_3


title: Total RNA from Human NB4 Cells treated with TPA Bioligical Sample 2

city: New Haven

first: Joel

last: Rozowsky

address: 266 Whitney Ave, Bass 437

department: Molecular Biophysics & Biochemistry

description:
NB4 cells were grown and maintained in RPMI-1640 medium (GIBCO, Grand Island, NY) supplemented with 10% heat-inactivated fetal calf serum, 2 mmol/L L-glutamine, 100 pg/mL penicillin and 100 U/mL of streptomycin. The cells were incubated at 37C in a humidified air atmosphere supplemented with 5% CO2.
For the monocytes differentiation, NB4 cells were grown to a concentration of 1 X 10e5/mL and pre-treated with 200-nM 1,25(OH)2D3 for 8 h, then with 200-nM TPA for a total treatment time of 72 h.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).
Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays

source_name: Human NB4 Cells treated with TPA


title: Total RNA from untreated Human NB4 Cells Bioligical Sample 4

description:
NB4 cells were grown and maintained in RPMI-1640 medium (GIBCO, Grand Island, NY) supplemented with 10% heat-inactivated fetal calf serum, 2 mmol/L L-glutamine, 100 pg/mL penicillin and 100 U/mL of streptomycin. The cells were incubated at 37C in a humidified air atmosphere supplemented with 5% CO2.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).
Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays

source_name: Human NB4 Cells (untreated)


title: WT_vs_SIPK-Ri_8h_harp_1


title: WT_vs_SIPK-Ri_4h_mega_2


title: WT_vs_SIPK-Ri_4h_harp_3

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Harpin (P.syringae), 4 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Harpin (P.syringae), 4 h; CH1: Cy5


title: Total RNA from untreated Human NB4 Cells Bioligical Sample 1


title: WT_vs_SIPK-Ri_4h_harp_2


title: WT_vs_SIPK-Ri_4h_harp_1


title: WT_vs_SIPK-Ri_b_cont_2

source_name: Query sample; Genotype: Xanthi SIPK-Ri; Tissue: Cell suspension culture; Treatment: Biotic control, 0 h; CH2: Cy3

source_name: Reference sample; Genotype: Xanthi; Tissue: Cell suspension culture; Treatment: Biotic control, 0 h; CH1: Cy5


title: Total RNA from Human NB4 Cells treated with RA Bioligical Sample 3

description:
NB4 cells were grown and maintained in RPMI-1640 medium (GIBCO, Grand Island, NY) supplemented with 10% heat-inactivated fetal calf serum, 2 mmol/L L-glutamine, 100 pg/mL penicillin and 100 U/mL of streptomycin. The cells were incubated at 37C in a humidified air atmosphere supplemented with 5% CO2.
Cells were grown to a concentration of 1 X 10e5/mL under the conditions described above and induced with 5 pmol/L ATRA (Sigma, St Louis, MO)for 4 days which leading the cells to differentiate to neutrophils.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).
Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays

source_name: Human NB4 Cells treated with Retanoic Acid (RA)


title: WT_vs_SIPK-Ri_ab_cont_1


title: Total RNA from Human NB4 Cells treated with RA Bioligical Sample 2


title: Total RNA from Human NB4 Cells treated with TPA Bioligical Sample 4


title: 35S::GLB1(HE7L) Shoots, aiw100026.gpr

status: Public on May 18 2005

city: Canberra

first: Andrew

last: Spriggs

state: ACT

address: GPO Box 1600

department: Bioinformatics Group

country: Australia

institute: CSIRO Plant Industry

description:
35S::GLB1(HE7L) compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress

organism: Arabidopsis thaliana

source_name: Over-expression of wild type GLB1

source_name: Empty vector (pBI101.1) control


title: Total RNA from Human NB4 Cells treated with RA Bioligical Sample 1


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 9

description:
Human Neutrophils were isolated from venous blood (freshly drawn at 8 to 9 AM) of healthy volunteers, using dextran sedimentation and centrifugation through Ficoll-Paque Plus (Pharmacia, Uppsala, Sweden), as described previously [Subrahmanyam, Y. V., Yamaga, S., Prashar, Y., Lee, H. H., Hoe, N. P., Kluger, Y., Gerstein, M., Goguen, J. D., Newburger, P. E., Weissman, S. M. (2001) RNA expression patterns change dramatically in human neutrophils exposed to bacteria Blood 97,2457-2468[Abstract/Free Full Text]  ].
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).
Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays

source_name: Human Neutrophil (PMN)


title: Total RNA from untreated Human NB4 Cells Bioligical Sample 2


title: WT_vs_SIPK-Ri_b_cont_3


title: Total RNA from Human NB4 Cells treated with TPA Bioligical Sample 3


title: 35S::GLB1(HE7L) Shoots, aiw100025.gpr

description:
35S::GLB1(HE7L) compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: WT_vs_SIPK-Ri_b_cont_1


title: 35S::GLB1(HE7L) Shoots, aiw100023.gpr

description:
35S::GLB1(HE7L) compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 1, Technical Replicate: 0, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1(HE7L) Shoots, aiw100024.gpr

description:
35S::GLB1(HE7L) compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1(HE7L) Hypoxic Shoots, aiw100034.gpr

description:
35S::GLB1(HE7L) compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 8


title: Total RNA from untreated Human NB4 Cells Bioligical Sample 3


title: 35S::GLB1 Hypoxic Shoots, aiw100031.gpr

description:
35S::GLB1 compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1 Shoots, aiw100029.gpr

description:
35S::GLB1 compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 4, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1(HE7L) Hypoxic Shoots, aiw100033.gpr

description:
35S::GLB1(HE7L) compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1(HE7L) Hypoxic Shoots, aiw100035.gpr

description:
35S::GLB1(HE7L) compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 6


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 5


title: 35S::GLB1 Hypoxic Shoots, aiw100032.gpr

description:
35S::GLB1 compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1 Shoots, aiw100028.gpr

description:
35S::GLB1 compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: liver replicate 5

city: Sydney

first: Peter

last: Little

institute: School of Biotechnology and Biomolecular Sciences, The University of New South Wales

description:
Samples labelled with Alexa Fluors 647 and 555, resp. Values were extracted with Spot, and print-tip lowess normalised with the R limma library from the BioConductor project.

Sample data table files are generated by SPOT (http://experimental.act.cmis.csiro.au/Spot/index.php)

organism: Mus musculus

source_name: DBA2/J whole liver RNA (pool of 9)

source_name: C57Bl/6J whole liver RNA (pool of 9)


title: 35S::GLB1 Shoots, aiw100022.gpr

description:
35S::GLB1 compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1 Hypoxic Shoots, aiw100030.gpr

description:
35S::GLB1 compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: liver replicate 3


title: liver replicate 1


title: liver replicate 6


title: 35S::GLB1(HE7L) Roots, aiw100041.gpr


title: liver replicate 2


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 4


title: Total RNA from Human NB4 Cells treated with RA Bioligical Sample 4


title: 35S::GLB1(HE7L) Roots, aiw100040.gpr


title: 35S::GLB1 Shoots, aiw100027.gpr

description:
35S::GLB1 compared to transgenic controls (empty vector pBI101.1, lines 3&5).
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 1


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 7


title: kidney replicate 2

source_name: DBA2/J whole kidney RNA (pool of 10)

source_name: C57Bl/6J whole kidney RNA (pool of 10)


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 2


title: 35S::GLB1 Roots, aiw100042.gpr


title: 35S::GLB1 Roots, aiw100044.gpr


title: Human Neutrolphil (PMN) Total RNA Bioligical Sample 3


title: kidney replicate 6


title: liver replicate 4


title: kidney replicate 5


title: 35S::GLB1 Roots, aiw100043.gpr


title: 35S::GLB1(HE7L) Hypoxic Roots, aiw100047.gpr

description:
35S::GLB1(HE7L) plants compared to empty vector control plants
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 2, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: brain replicate 6

source_name: DBA2/J whole brain RNA (pool of 10)

source_name: C57Bl/6J whole brain RNA (pool of 10)


title: kidney replicate 4


title: 35S::GLB1(HE7L) Hypoxic Roots, aiw100021.gpr

description:
35S::GLB1(HE7L) plants compared to empty vector control plants
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 1, Technical Replicate: 1, Dye Swapped: false
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: 35S::GLB1 Hypoxic Roots, aiw100050.gpr


title: kidney replicate 3


title: brain replicate 5


title: 35S::GLB1 Hypoxic Roots, aiw10045.gpr


title: brain replicate 2


title: kidney replicate 1


title: 35S::GLB1 Hypoxic Roots, aiw100046.gpr


title: Differential gene expression between wildtype and ft[fd] larvae in Drosophila- Array II

status: Public on May 17 2005

city: Hyderabad

first: L S

last: Shashidhara

state: AP

address: Uppal Road

country: India

institute: Centre for Cellular and Molecular Biology

description: RNA was isolated from wildtype (Canton-S) 3rd instar larvae and from ft[fd] larvae. RNA from wildtype larvae was labeled with Cy3 and that of ft[fd] larvae with Cy5 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

organism: Drosophila melanogaster

source_name: Wildtype larvae

source_name: ft[fd] larvae


title: 35S::GLB1(HE7L) Hypoxic Roots, aiw100049.gpr

description:
35S::GLB1(HE7L) plants compared to empty vector control plants
Publication Title: GLB1, a class 1 haemoglobin gene from Arabidopsis thaliana (GLB1) is essential for plant survival following hypoxic stress
Biological Replicate: 3, Technical Replicate: 1, Dye Swapped: true
Normalization Method: Spatial Normalization. Ref: Wilson DL, Buckley MJ, Helliwell CA, Wilson IW (2003) New normalization methods for cDNA microarray data. Bioinformatics 19, 1325-32.
Keywords = haemoglobin, hypoxic stress, stress


title: Cacahuacintle leaves under solar UV-B-3

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: Idem GSM 31150

organism: Zea mays

source_name: leaves under solar UV-B

source_name: leaves under no UV-B


title: Differential gene expression between ft[fd] and wildtype larvae in Drosophila- Array II

description: RNA was isolated from wildtype (Canton-S) 3rd instar larvae and from ft[fd] larvae. RNA from wildtype larvae was labeled with Cy5 and that of ft[fd] larvae with Cy3 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

source_name: wild type larvae


title: Differential gene expression between wildtype wing and haltere imaginal discs in Drosophila - Array II

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wing and haltere imaginal discs from wildtype (Canton-S) 3rd instar larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wing discs was labeled with Cy3 and that of halter discs with Cy5 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

source_name: Wildtype wing discs

source_name: Wildtype haltere discs


title: Differential gene expression between ft[fd] and wildtype larvae in Drosophila - Array I

source_name: wildtype larvae


title: brain replicate 4


title: SS0/SS60 RAP primer28 slide4

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

description: Serum starvation - refeeding experiment. Time 0 and time 60min. slide 1 and slide 2 are technical duplicate. slide 3 and slide 4 are biological duplicate.

source_name: fibroblast RAP, SS0

source_name: fibroblast RAP, SS60


title: Differential gene expression between wildtype and ft[fd] larvae in Drosophila - Array I


title: Differential gene expression between vg-GAL4/UAS-Ubx and wildtype wing imaginal discs in Drosophila - Array I

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wildtype wing imaginal discs from wildtype (Canton-S) 3rd instar larvae and vg-GAL4/UAS-Ubx wing imaginal discs from larvae of that cross. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy5 and that of vg-GAL4/UAS-Ubx wing discs with Cy3 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

source_name: vg-GAL4/UAS-Ubx wing discs

source_name: Wildtype Wing discs


title: Differential gene expression between vg-GAL4/UAS-Ubx and wildtype wing imaginal discs in Drosophila- Array II

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wing and haltere imaginal discs from wildtype (Canton-S) 3rd instar larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy5 and that of vg-GAL4/UAS-Ubx wing discs with Cy3 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.


title: Differential gene expression between wildtype and Cbx wing imaginal discs in Drosophila - Array I

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wildtype wing imaginal discs from wildtype (Canton-S) 3rd instar larvae and Cbx wing imaginal discs from Cbx[Hm] larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy3 and that of Cbx wing discs with Cy5 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

source_name: Cbx wing discs


title: brain replicate 3


title: Differential gene expression between wildtype and vg-GAL4/UAS-Ubx wing imaginal discs in Drosophila - Array I

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wildtype wing imaginal discs from wildtype (Canton-S) 3rd instar larvae and vg-GAL4/UAS-Ubx wing imaginal discs from 3rd larvae of that cross. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy3 and that of vg-GAL4/UAS-Ubx wing discs with Cy5 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.


title: SS0/SS60 RAP primer28 slide3


title: SS0/SS60 RAP primer28 slide1


title: OCI/AML2 ATRA + VPA

city: Toronto

last: Minden

country: Canada

institute: Princess Margaret Hospital

description:
Acute myeloid leukemia cell line, OCI/AML2 treated with Valproic Acid, 0.6mM for 24hr and ATRA 10E-6M for 24hrs.
Keywords = Leukemia
Keywords = Myeloid


title: SS0/SS60 RAP primer28 slide2


title: Differential gene expression between Cbx and wildtype wing imaginal discs in Drosophila - Array I

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wildtype wing imaginal discs from wildtype (Canton-S) 3rd instar larvae and Cbx wing imaginal discs from Cbx[Hm] larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy5 and that of Cbx wing discs with Cy3 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

source_name: Cbx wing imaginal discs

source_name: Wildtype wing imaginal discs


title: Human Placenta Poly(A)+ RNA Bioligical Sample 1

description:
Triple selected polyA RNA for placenta was obtained from Ambion (Austin, TX). All RNA samples had an agilent ratio greate than 1 indicating that degradation had not occurred. All RNA samples were prepared from a pool of several different individuals.
First-strand cDNA synthesis was achieved using SuperScript II reverse transcriptase (Invitrogen) in the reaction volume of 105 ul for 15 of starting RNA material or scaled accordingly using the following protocol. RNA was mixed with random hexamers (83.3 ng/ g of mRNA; Invitrogen) and the bacterial control transcripts (see below) and subjected to the following cycling conditions in PE GeneAmp9600 PCR System: 70?C- 10 min and 20min ramp to 15C after which the 5x Superscript II First Strand buffer (Life Technologies), DTT and four dNTPs were added to the following final concentrations of 1x, 10mM and 0.5mM, respectively, followed by a 30 min incubation at 15C. At this point, Superscript II RTase was added (200Units/ g of mRNA; Life Technologies) followed by a 20 min ramp to 42C and 60 min incubation at 42C. At this point the SuperScript II was inactivated by 15 min incubation at 75C.
The first strand cDNA synthesis reaction was used for the second-strand cDNA synthesis in the presence of 50U of E. coli DNA Ligase, 200U of E. coli DNA polymerase I, and 10U of E. coli RNAse H supplemented with 0.2mM dNTPs in the final volume of 750 ul at 16oC (all reagents were from Invitrogen) based on 15ug of starting RNA or scaled appropriately. Upon treatment with RNAse H (Epicentre) and RNAse A/T1 (Ambion), double-stranded cDNA was extracted using QIAquick PCR purification kit (Qiagen) and subjected to further fragmentation to 50-100 bp by DNAse I (1U/ul; Epicentre) treatment in 1X One-Phor-All buffer (Pharmacia).
Following DNAse I inactivation at 99C for 10 min, the size ditsribution of fragmented DNA was verified on a 1% agarose gel. The fragmented cDNA was then end-labeled with 70nM of bio-ddATP (Perkin Elmer) using 6-10U of terminal transferase (TdT, Roche) per 1ug of fragmented DNA in 1X TdT buffer (Roche) and 5mM CoCl2 (Roche) for 2 hours at 37C. The labeled DNA material was subsequently hybridized to the chips (previously prehybridized for 1 hour in 1X MES-triton at 45C) for 18 hours at 45C in a 3 M TMAC/1X MES-based solution.
Keywords = Transcript Mapping, Human, Affymetrix, Genome Tiling Arrays

source_name: Human Placenta


title: Human Placenta Poly(A)+ RNA Bioligical Sample 3


title: SS0/SS60 RAP primer22 slide4


title: SS0/SS60 RAP primer22 slide1


title: Human Placenta Poly(A)+ RNA Bioligical Sample 2


title: OCI/AML2 ATRA

description:
Acute myeloid leukemia cell line, OCI/AML2 treated with ATRA, 10E-6M for 24hr.
Keywords = Leukemia
Keywords = Myeloid


title: SS0/SS60 RAP primer19 slide1


title: OCI/AML2 VPA

description:
Acute myeloid leukemia cell line, OCI/AML2 treated with Valproic Acid, 0.6mM for 24hr.
Keywords = Leukemia
Keywords = Myeloid


title: SS0/SS60 RAP primer19 slide3


title: SS0/SS60 RNA slide3

source_name: fibroblast RNA, SS0

source_name: fibroblast RNA, SS60


title: brain replicate 1

description:
Samples labelled with Alexa Fluors 647 and 555, resp. Values were extracted with Spot, and print-tip lowess normalised with the R limma library from the BioConductor project.

Sample data table files are generated by SPOT (http://experimental.act.cmis.csiro.au/Spot/index.php)

source_name: DBA2/J whole brain RNA (pool of 10)

source_name: C57Bl/6J whole brain RNA (pool of 10)


title: Differential gene expression between wildtype and vg-GAL4/UAS-Ubx wing imaginal discs in Drosophila- Array II

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wing imaginal discs from wildtype (Canton-S) and vg- GAL4/UAS-Ubx 3rd instar larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy3 and that of vg-GAL4/UAS-Ubx wing discs with Cy5 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.


title: SS0/SS60 RNA slide2


title: OCI/AML2 control

description:
Acute myeloid leukemia cell line, OCI/AML2
Keywords = Leukemia
Keywords = Myeloid


title: Differential gene expression between wildtype and Cbx wing imaginal discs in Drosophila - Array II

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wing imaginal discs from wildtype (Canton-S) and Cbx [Hm] 3rd instar larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy3 and that of Cbx wing discs with Cy5 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.


title: Differential gene expression between wildtype haltere and wing imaginal discs in Drosophila - Array II

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wing and haltere imaginal discs from wildtype (Canton-S) 3rd instar larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wing discs was labeled with Cy5 and that of halter discs with Cy3 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

source_name: Wildtype haltere Discs


title: SS0/SS60 RNA slide4


title: Differential gene expression between Cbx and wildtype wing imaginal discs in Drosophila- Array II

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wing imaginal discs from wildtype (Canton-S) and Cbx [Hm] 3rd instar larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wildtype wing discs was labeled with Cy5 and that of Cbx wing discs with Cy3 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.


title: SS0/SS60 RAP primer19 slide4


title: SS0/SS60 RAP primer22 slide3


title: Differential gene expression between wildtype wing and haltere imaginal discs in Drosophila - Array I

description:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity.

This is a part of series of experiments carried out to determine targets of homeotic gene function. We isolated wing and haltere imaginal discs from wildtype (Canton-S) 3rd instar larvae. RNA was isolated from these discs using Triazol (Gibco-BRL, USA). RNA samples were further amplified using Eberwine method (using Ambion RNA-amplification kit). The amplified RNA from wing discs was labeled with Cy3 and that of halter discs with Cy5 and hybridized to the arrays. Specific activity was determined on a spectrophotometer and equal activity of Cy3 and Cy5-labeled targets were added on a slide for two-color hybridization. Hybridized slides were scanned using the Molecular Dynamics Gen III scanner. Image analysis was done using Amersham Array Vision software.

source_name: Wildtype Haltere discs


title: treatment=uninf time=9 (hrs) uninf3-9hr

status: Public on May 15 2005

city: Hamilton

first: Frank

middle: R.

last: DeLeo

state: MT

address: 903 South 4th Street

department: Laboratory of Human Bacterial Pathogenesis

institute: National Institute of Allergy and Infectious Diseases

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM

source_name: Human polymorphonuclear (PMN) leukocytes


title: treatment=uninf time=24 (hrs) uninf4-24hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 24
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: SS0/SS60 RAP primer22 slide2

description: Serum starvation - refeeding experiment. Time 0 and time 60min. slide 1 and slide 2 are technical duplicate. slide 3 and slide 4 are biological duplicate.


title: SS0/SS60 RNA slide1


title: treatment=uninf time=9 (hrs) uninf4-9hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=uninf time=9 (hrs) uninf6-9hr


title: treatment=uninf time=24 (hrs) uninf5-24hr


title: treatment=uninf time=24 (hrs) uninf6-24hr


title: SS0/SS60 RAP primer19 slide2


title: treatment=uninf time=9 (hrs) uninf5-9hr


title: treatment=uninf time=6 (hrs) uninf2-6hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 6
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=uninf time=24 (hrs) uninf3-24hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 24
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=uninf time=9 (hrs) uninf2-9hr


title: treatment=uninf time=3 (hrs) uninf2-3hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 3
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=uninf time=24 (hrs) uninf1-24hr


title: Differential gene expression between wildtype haltere and wing imaginal discs in Drosophila - Array I


title: treatment=uninf time=1.5 (hrs) uninf2-1.5hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 1.5
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=uninf time=3 (hrs) uninf1-3hr


title: treatment=uninf time=3 (hrs) uninf3-3hr


title: treatment=uninf time=9 (hrs) uninf1-9hr


title: treatment=uninf time=12 (hrs) uninf2-12hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 12
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=uninf time=1.5 (hrs) uninf3-1.5hr


title: treatment=uninf time=6 (hrs) uninf1-6hr


title: treatment=uninf time=0 (hrs) uninf2-0hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = uninf
Sample_descripton: Sample_time = 0
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=hklys time=9 (hrs) hklys1-9hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = hklys
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=hklys time=9 (hrs) hklys2-9hr


title: treatment=uninf time=1.5 (hrs) uninf1-1.5hr


title: treatment=uninf time=24 (hrs) uninf2-24hr


title: treatment=uninf time=0 (hrs) uninf1-0hr


title: treatment=hklys time=24 (hrs) hklys2-24hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = hklys
Sample_descripton: Sample_time = 24
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=uninf time=12 (hrs) uninf1-12hr


title: treatment=hklys time=24 (hrs) hklys1-24hr


title: treatment=hkAP time=9 (hrs) hkAP3-9hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = hkAP
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=hklys time=24 (hrs) hklys3-24hr


title: treatment=hkAP time=9 (hrs) hkAP2-9hr


title: treatment=hkAP time=24 (hrs) hkAP2-24hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = hkAP
Sample_descripton: Sample_time = 24
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=hkAP time=9 (hrs) hkAP1-9hr


title: treatment=hkAP time=24 (hrs) hkAP3-24hr


title: treatment=hkAP time=24 (hrs) hkAP1-24hr


title: treatment=ctrl time=9 (hrs) ctrl3-9hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = ctrl
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=ctrl time=9 (hrs) ctrl2-9hr


title: treatment=AP time=9 (hrs) AP4-9hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=SA time=9 (hrs) SA3-9hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = SA
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=SA time=9 (hrs) SA2-9hr


title: treatment=AP time=24 (hrs) AP5-24hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 24
Sample_descripton: Affymetrix MAS version = GCOS1.2
Sample_descripton: GeneSpring (version 7.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=SA time=9 (hrs) SA1-9hr


title: treatment=AP time=9 (hrs) AP5-9hr


title: treatment=ctrl time=9 (hrs) ctrl1-9hr


title: treatment=AP time=9 (hrs) AP6-9hr


title: treatment=AP time=3 (hrs) AP3-3hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 3
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=AP time=24 (hrs) AP4-24hr


title: treatment=AP time=24 (hrs) AP6-24hr


title: treatment=AP time=0 (hrs) AP3-0hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 0
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=AP time=9 (hrs) AP2-9hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 9
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=AP time=1.5 (hrs) AP3-1.5hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 1.5
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=AP time=9 (hrs) AP3-9hr


title: treatment=AP time=24 (hrs) AP3-24hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 24
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=AP time=3 (hrs) AP2-3hr


title: treatment=AP time=24 (hrs) AP1-24hr


title: treatment=AP time=1.5 (hrs) AP2-1.5hr


title: treatment=AP time=12 (hrs) AP2-12hr

description:
Polymorphonuclear (PMN) leukocytes were obtained from healthy individuals.  "time" indicates time at which transcript levels were analyzed (hours). "treatment" indicates whether the polymorphonuclear leukocytes were untreated (ctrl) or treated with Anaplasma phagocytophilum (AP), Staphylococcus aureus (SA), HL60 cell lysate (uninf), heat-killed Anaplasma phagocytophilum (hkAP), or heat-killed HL60 cell lysate (hklys).
Sample_descripton: Sample_PMN_treatment = AP
Sample_descripton: Sample_time = 12
Sample_descripton: Affymetrix MAS version = MAS5
Sample_descripton: GeneSpring (version 6.0)normalization protocol:
Sample_descripton: 1.  Data Transformation:  Set measurements less than 0.0 to 0.0
Sample_descripton: 2.  Per Chip:  Normalize to a constant value of 150.0 (MAS scaling factor)
Sample_descripton: 3.  Per Gene:  Normalize to median
Keywords = NEUTROPHIL RESPONSE TO ANAPLASMA PHAGOCYTOPHILUM


title: treatment=AP time=9 (hrs) AP1-9hr