title: Bladder_T3vsC0_Dye

description:
Tissue RNA degradation state 3.
filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0


title: Liver_Control _Rep4

status: Public on Aug 24 2005

type: RNA

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

country: USA

institute: University of Viginia

description: No

hyb_protocol: Affymetrix Standard Protocol

scan_protocol: Affymetrix Standard Protocol

data_processing: Normalized with MAS5 across the 8 samples in this project; All probe sets included; No log transformation

label: Affymetrix Standard Protocl

molecule: total RNA

organism: Rattus norvegicus

source_name: Control rat liver, snap frozen

label_protocol: Affymetrix Standard Protocol

growth_protocol: Rat AIN 76A chow (Harlan Teklad, WI)

extract_protocol: Total RNA extraction kit: Stat-60 (Tel-Test Inc, TX)

treatment_protocol: gavage with 0.2 ml vehicle (saturated sucrose); 1st, 3rd and 5th day, once per day

tag: Strain

value: Fischer 344

tag: Gender

value: Male

tag: Age

tag: Tissue

value: Liver of vehicle treated rat


title: Liver_D3T _Rep1

description: No

source_name: D3T treated rat liver, snap frozen

treatment_protocol: gavage with D3T (3H-1, 2-dithiole-3-thione) for 0.3 mmol/kg body weight, disolved in vehicle (saturated sucrose); 1st, 3rd and 5th day, once per day

value: Liver of D3T treated rat


title: Liver_Control _Rep3

description: No


title: Liver_Control _Rep2

description: No

treatment_protocol: gavage with 0.2 ml vehicle (saturated sucrose);


title: 430MM

status: Public on Aug 25 2005

city: San Diego

first: Tim

last: Jatkoe

state: CA

institute: Veridex

description: Normal skin

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

organism: Homo sapiens

source_name: skin

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA was isolated from skin, nevus and melanoma samples according to Standard Trizol protocol or Qiagen RNeasy Mini Kit protocol.

tag: Normal


title: HWS23

status: Public on Aug 23 2005

city: Sacramento

first: Chris

middle: J

last: Sullivan

address: 6000 J Street

department: Biological Sciences

institute: California State University, Sacramento

description:
10 week Diabetic cavernosal tissue sample, streptozotocin induced
Keywords = penis
Keywords = cavernosum
Keywords = diabetes
Keywords = erectile dysfunction

source_name: Diabetic F344 RAT penis


title: HWS26


title: HWS18

description:
10 week Diabetic cavernosal tissue sample, streptozotocin induced
Keywords = penis cavernosum diabetes


title: HWS22


title: 435MM

description: Normal skin


title: Bladder_T1vsC0

city: Barcelona

first: Moises

middle: Burset

last: Albareda

state: Barcelona

address: Cartagena, 340-350

department: Molecular biology

country: Spain

institute: Fundacio Puigvert

description: Tissue RNA degradation state 1

data_processing: log2((Rmedian-morphR)/(Gmedian-morphG)) adjusting previously mean intensity to 400 for all arrays and channels

tag: Normal urothelium pool (4 males)

tag: Individual tumoral urothelium (pT2 G3)


title: Morex stress and unstress replicate 3

city: Riverside

first: xinping

last: cui

address: Department of Statistics, University of California, Riverside

department: Statistics

institute: University of California,Riverside

description: drought stress and unstressed

data_processing: GCOS 1.2

organism: Hordeum vulgare

source_name: whole seedling

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

extract_protocol: Five seedlings were used for RNA extraction

tag: cv. Morex

tag: drought stress and unstressed


title: Bladder_T1vsC0_Dye

description:
Tissue RNA degradation state 1

filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0


title: Bladder_T0vsC0_Dye

description:
Tissue intact RNA

filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0


title: HWS17

description:
10 week Diabetic cavernosal tissue sample
Streptozotocin induced
Keywords = penis cavernosum diabetes


title: 480MM

description: Melanoma

tag: Melanoma


title: HWC7

description:
Control cavernosal tissue sample
Keywords = penis cavernosum

source_name: Control F344 RAT penis


title: Barke stress and unstress replicate 3

description: drought stress and unstressed

tag: cv. Barke


title: HWC14


title: HWC16


title: NF2 MRC5

status: Public on Aug 20 2005

city: Epalinges

first: Eugenia

last: Migliavacca

state: Vaud

address: Ch des Boveresses 155

country: Switzerland

institute: ISREC

description: nodular fasciitis from neck

data_processing: print tip normalization without background substruction

source_name: cy3 MRC5

tag: primary fetal lung fibroblasts (MRC-5)

source_name: cy5 NF2

tag: nodular fasciitis


title: HWC13


title: HWC17


title: Bladder_T0vsC0


title: NF3 MRC5

description: nodular fasciitis from forearm

source_name: cy5 NF3


title: DT3 MRC5

description: desmoid tumor from thoracic wall

source_name: cy5 DT3

tag: desmoid tumor


title: DT10 MRC5

description: desmoid tumor from axilla

source_name: cy5 DT10


title: DT9 MRC5

description: desmoid tumor from buttock

source_name: cy5 DT9


title: NF4 MRC5

description: nodular fasciitis from arm

source_name: cy5 NF4


title: TPK versus tpk1-3 deletion MDN (2)

status: Public on Aug 19 2005

city: Davis

first: Ted

last: Powers

address: One Shields Ave

department: Molecular and Cellular Biology

institute: UC Davis

description: TPK versus tpk1-3 deletion grown in MDN (2)

data_processing: AMAD

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: TPK MDN

tag: TPK grown in MDN

source_name: tpk1-3 deletion MDN

tag: tpk1-3 deletion grown in MDN


title: DT4 MRC5

description: desmoid tumor from buttock

source_name: cy5 DT4


title: DT2 MRC5

description: desmoid tumor from abdomen

source_name: cy3 DT2

source_name: cy5  MRC5


title: DT12 MRC5

description: desmoid tumor from lower back

source_name: cy5 DT12


title: DT5 MRC5

description: desmoid tumor from abdomen

source_name: cy5 DT5


title: DT6 MRC5

description: desmoid tumor from abdomen

source_name: cy3 DT6


title: DT1 dye-swap MRC5

description: desmoid tumor from abdomen, patient with Gardner syndrome

source_name: cy3 DT1


title: DT11 MRC5

description: desmoid tumor from neck

source_name: cy5 DT11


title: DT1 MRC5

description: desmoid tumor from the abdomen, patient with Gardner syndrome

data_processing: print tip normalization

source_name: cy3 MRC5

source_name: cy5 DT1


title: TPK MDN -/+ Rapamycin (2)

description: TPK grown in MDN -/+ Rapamycin (2)

source_name: TPK MDN + Rapamycin

tag: TPK grown in MDN + Rapamycin


title: NF6 MRC5

description: nodular fasciitis from knee

source_name: cy5 NF6


title: NF5 MRC5

description: nodular fasciitis from elbow

source_name: cy5 NF5


title: DT7 MRC5

description: desmoid tumor from the retroperitoneum

source_name: cy5 DT7


title: cyclical mechanical strain experiment (24 hours, 1 Hz , 15%)

status: Public on Aug 22 2005

city: Dublin

first: Ruaidhri

middle: Patrick

last: Kirwan

state: Leinster

address: Belfield

department: Conway Institute of Biomolecular and Biomedical Research & School of Medicine and Medical Science

country: Ireland

institute: University College Dublin

description: experimental array data exposing LC cells to 24 hours of 15% 1 Hz cyclical mechanical strain.

data_processing: Robust multichip average (RMA)

source_name: human optic nerve head lamina cribrosa

tag: GFAP-negative LC cells

tag: human

tag: optic nerve head tissue

tag: lamina cribrosa layer

tag: primary cultures


title: BCY1 MDN -/+ Rapamycin (2)

description: BCY1 grown in MDN -/+ Rapamycin (2)

source_name: BCY1 MDN

tag: BCY1 grown in MDN

source_name: BCY1 MDN + Rapamycin

tag: BCY1 grown in MDN + Rapamycin


title: BCY1 versus bcy1 deletion MDN (2)

description: BCY1 versus bcy1 deletion grown in MDN (2)

source_name: bcy1 deletion MDN

tag: bcy1 deletion grown in MDN


title: TPK verus tpk1-3 deletion MDN -/+ Rapamycin

description: TPK versus tpk1-3 deletion grown in MDN + Rapamycin

source_name: tpk1-3 deletion MDN + Rapamycin


title: Strain S288c YPD -/+ Rapamycin

description: WT grown in YPD -/+ Rapamycin

source_name: YPD

tag: WT grown in YPD

source_name: YPD + Rapamycin

tag: WT grown in YPD + Rapamycin


title: BCY1 versus bcy1 deletion MDN

description: BCY1 versus bcy1 deletion grown in MDN


title: TPK versus tpk1-3 deletion MDN

description: TPK versus tpk1-3 deletion grown in MDN

source_name: TPK MDN

source_name: tpk1-3 deletion MDN


title: Strain S288c MDN -/+ Rapamycin

description: WT grown in MDN -/+ Rapamycin

source_name: MDN

tag: WT grown in MDN

source_name: MDN + Rapamycin

tag: WT grown in MDN + Rapamycin


title: BCY1 + Rapamycin MDN versus bcy1 deletion + Rapamycin MDN

description: BCY1 + rapamycin versus bcy1 deletion + rapamycin, both grown in MDN

source_name: BCY1 + Rapamycin MDN

source_name: bcy1 deletion + Rapamycin MDN

tag: bcy1 deletion grown in MDN + Rapamycin


title: bcy1 deletion MDN -/+ Rapamycin

description: bcy1 deletion grown in MDN -/+ Rapamycin

source_name: bcy1 deletion MDN + Rapamycin


title: Strain S288c grown in YPD versus MDN

description: WT grown in YPD versus MDN


title: TPK MDN -/+ Rapamycin

description: TPK grown in MDN -/+ Rapamycin

source_name: TPK MDN + Rapamycin


title: tpk1-3 deletion MDN -/+ Rapamycin

description: tpk1-3 deletion grown in MDN -/+ Rapamycin

tag: tpk1-3 grown in MDN + Rapamycin


title: Strain S288c grown in SCD versus MDN

description: WT grown in SCD versus MDN

source_name: SCD

tag: WT grown in SCD


title: BCY1 MDN -/+ Rapamycin

description: BCY1 grown in MDN -/+ Rapamycin


title: Strain S288c YPD -/+ Rapamycin (2)

description: WT grown in YPD -/+ Rapamycin (2)


title: Strain S288c MDN -/+ Rapamycin (2)

description: WT grown in MDN -/+ Rapamycin


title: BMM_C57BL6_time21h

first: Timothy

last: Ravasi

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California-San Diego

description: Total RNA was extracted using Qiagen RNeasy midi-kit from bone marrow macrophages in-vitro differentiated using human colony stimulator factor-1 (CSF-1) or from C57BL6/J 17.5 whole embryo.

data_processing: Genespring Lowess Normalisation

organism: Mus musculus

source_name: Total RNA from bone marrow derived macrophage from C57BL6 mice

source_name: Total RNA from C57BL6/J 17.5 days whole embryo


title: BMM_C57BL6_time0.5h

description:
Total RNA was extracted using Qiagen RNeasy midi-kit from bone marrow macrophages in-vitro differentiated using human colony stimulator factor-1 (CSF-1) or from C57BL6/J 17.5 whole embryo.
The cDNA derived from the total RNA was labeled using the amino-alyll indirect labeling with Cy3 mono-reactive dye.
Keywords = macrophages

tag: Total RNA from bone marrow derived macrophage from C57BL6 mice

tag: Total RNA from C57BL6/J 17.5 days whole embryo


title: BMM_C57BL6_time0h


title: BMM_C57BL6_time2h

source_name: Total RNA from bone marrow derived macrophage from C57/BL6 mice


title: Ames 4 month Wild Type Liver JP170

status: Public on Aug 18 2005

city: Galveston

first: James

middle: H

last: DeFord

state: TX

address: 301 University Blvd.

department: Human Biological Chemistry and Genetics

institute: University of Texas at Galveston

description: Wild type third instar larvae imaginal wing discs

source_name: liver

label_protocol: Approximately 20 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 10 mg of snap frozen liver was used to extract >25 ug of total RNA using Ambion's RNAqueous-4PCR RNA extraction kit.

tag: Wild type control for the Prop-1 mutant (Ames) resulting in long lived dwarf pheontype


title: BMM_C57/BL6_time7h


title: Bladder_T2vsC0

description:
Tissue RNA degradation state 2

filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0

tag: Normal urothelium pool (4 males)

tag: Individual tumoral urothelium (pT2 G3)


title: Ames 4 month Wild Type Liver JP183


title: Ames 4 month Wild Type Liver JP159


title: Ames 4 month Wild Type Liver JP161


title: Ames 4 month Wild Type Liver JP177

extract_protocol: Approximately 10 mg of snap frozen liver was used to extract >25 ug of total RNA using Ambion's RNAqueous-4PCR RNA exstraction kit.


title: DT8 MRC5

description: desmoid tumor from the thoracic wall

source_name: cy3 MRC5

tag: primary fetal lung fibroblasts (MRC-5)

source_name: cy5 DT8

tag: desmoid tumor


title: Ames 4 month Dwarf Liver Df188

tag: Prop-1 mutant (Ames) resulting in long lived dwarf pheontype


title: Ames 4 month Dwarf Liver Df168


title: Ames 10 month Dwarf Liver JDF63


title: Ames 10 month Dwarf Liver Df152


title: Ames 10 month Dwarf Liver Df151


title: Ames 4 month Dwarf Liver Df186


title: Ames 10 month Wild Type Liver JP133


title: Ames 10 month Wild Type Liver 03C15


title: Ames 10 month Dwarf Liver JDF56


title: Ames 10 month Wild Type Liver 03C13


title: Ames 22 month Wild Type LiverJP39


title: Ames 22 month Wild Type Liver JP73


title: Primary mouse keratinocytes_GST_6h_replicate 2

last: Dotto

state: VD

address: 153 Chemin de Bovaress

department: Biochemistry

institute: Lausanne University

description: Total RNA was purified from primary mouse keratinocytes treated with the only GST protein for 6 hours. PolyA+ RNA was reverse trnscribed and used for biotin-labeled cRNA probe prepatation and hybridization to Affymetrix U74Av2 gene chips according to manufacturer's instruction. cRNA probes from this condition were tested in duplicate.

label: Biotin-labeled

source_name: Primary mouse keratinocytes, GST, 6h, replicate 2

tag: Primary mouse keratinocytes


title: Primary mouse keratinocytes_GST_6h_replicate 1

source_name: Primary mouse keratinocytes, GST, 6h, replicate 1


title: Ames 4 month Dwarf Liver Df179


title: Primary mouse keratinocytes_CRIK-SK_48h_replicate 1

description: Total RNA was purified from primary mouse keratinocytes infected with adeno-CRIK-SK for 48 hours. PolyA+ RNA was reverse trnscribed and used for biotin-labeled cRNA probe prepatation and hybridization to Affymetrix U74Av2 gene chips according to manufacturer's instruction. cRNA probes from this condition were tested in duplicate.

source_name: Primary mouse keratinocytes, CRIK-SK, 48h, replicate 1


title: Primary mouse keratinocytes_Rho_48h_replicate 1

description: Total RNA was purified from primary mouse keratinocytes infected with adeno-Rho for 48 hours. PolyA+ RNA was reverse transcribed and used for biotin-labeled cRNA probe preparation and hybridization to Affymetrix U74Av2 gene chips according to manufacturer's instruction. cRNA probes from this condition were tested in duplicate.

source_name: Primary mouse keratinocytes, Rho, 48h, replicate 1


title: Primary mouse keratinocytes_CRIK-SK_48h_replicate 2

description: Total RNA was purified from primary mouse keratinocytes infected with adeno-CRIK-SKfor 48 hours. PolyA+ RNA was reverse trnscribed and used for biotin-labeled cRNA probe prepatation and hybridization to Affymetrix U74Av2 gene chips according to manufacturer's instruction. cRNA probes from this condition were tested in duplicate.

source_name: Primary mouse keratinocyte, CRIK-SK, 48h, replicate 2


title: Primary mouse keratinocytes_Rho_48h_replicate 2

source_name: Primary mouse keratinocytes, Rho, 48h, replicate 2


title: Ames 22 month Wild Type Liver SN3


title: Ames 10 month Wild Type Liver JP154


title: Ames 10 month Wild Type Liver JP149


title: Ames 22 month Dwarf Liver JDF213

extract_protocol: Approximately 10 mg of snap frozen liver was used to extract >25 ug of total RNA was extracted using Ambion's RNAqueous-4PCR.


title: Ames 4 month Dwarf Liver Df167


title: Ames 22 month Wild Type Liver JP9


title: Ames 22 month Dwarf Liver 03Df26

extract_protocol: Approximately 10 mg of snap frozen liver was used to extract >25 ug of total RNA using Ambion's RNAqueous-4PCR.


title: Primary mouse keratinocytes_GFP_48h_replicate 2

description: Total RNA was purified from primary mouse keratinocytes infected with adeno-GFP for 48 hours. PolyA+ RNA was reverse trnscribed and used for biotin-labeled cRNA probe prepatation and hybridization to Affymetrix U74Av2 gene chips according to manufacturer's instruction. cRNA probes from this condition were tested in duplicate.

source_name: Primary mouse keratinocytes, GFP, 48h, replicate 2


title: Primary mouse keratinocytes_C3_6h_replicate 1

description: Total RNA was purified from primary mouse keratinocytes treated with C3 for 6 hours, a toxin produced by C. botulinum that selectively inhibits RhoA, B and C. PolyA+ RNA was reverse trnscribed and used for biotin-labeled cRNA probe prepatation and hybridization to Affymetrix U74Av2 gene chips according to manufacturer's instruction. cRNA probes from this condition were tested in duplicate.

source_name: Primary mouse keratinocyte, C3, 6h, replicate 1


title: Primary mouse keratinocytes_C3_6h_replicate2

description: Total RNA was purified from primary mouse keratinocytes treated with C3, a toxin produced by C. botulinum that selectively inhibits RhoA, B and C. PolyA+ RNA was reverse trnscribed and used for biotin-labeled cRNA probe prepatation and hybridization to Affymetrix U74Av2 gene chips according to manufacturer's instruction. cRNA probes from this condition were tested in duplicate.

source_name: Primary mouse keratinocytes, C3 treatment, 6h, replicate 2


title: Ames 22 month Wild Type Liver df41


title: Ames 22 month Dwarf Liver DF3


title: Ames 22 month Wild Type Liver JP75


title: Ames 22 month Dwarf Liver Df1


title: Snell 6 month Dwarf Liver 87dw

status: Public on Aug 16 2005

description: Pit-1 mutant (Snell) resulting in long lived dwarf pheontype


title: Snell 6 month Dwarf Liver 89dw

tag: Pit-1 mutant (Snell) resulting in long lived dwarf pheontype


title: Primary mouse keratinocytes_GFP_48h_replicate 1

source_name: Primary mouse keratinocytes, GFP, 48h, replicate 1


title: Ames 10 month Dwarf Liver JDF57


title: NF1 MRC5

description: nodular fasciitis from buttock

source_name: cy5 NF1

tag: nodular fasciitis


title: Snell 6 month Dwarf Liver 85dw


title: Snell 6 month Wild Type Liver 88c

description: Wild Type Control for Pit-1 mutant (Snell) resulting in long lived dwarf pheontype


title: Snell 6 month Dwarf Liver 83dw


title: Snell 22 month Wild Type Liver 2c

tag: Wild Type Control for Pit-1 mutant (Snell) resulting in long lived dwarf pheontype


title: Snell 22 month Dwarf Liver 4dw


title: Pseudomonas aeruginosa_hydrogen peroxide_ 20min_replicate3

status: Public on Aug 15 2005

city: Singapore

first: Matthew

middle: Wook

last: Chang

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: Hydrogen peroxide treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 150)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

label: Biotin

organism: Pseudomonas aeruginosa PAO1

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated P. aeruginosa cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.  Then, we added 1mM hydrogen peroxide immediately after OD600 reached 0.8.

extract_protocol: Total RNA was isolated after 20 min incubation with hydrogen peroxide using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol.

treatment_protocol: Hydrogen peroxide (1mM)

tag: Wild type


title: Snell 6 month Wild Type Liver 86c


title: Snell 22 month Dwarf Liver 8dw


title: Snell 22 month Wild Type Liver 24c


title: Snell 22 month Dwarf Liver 3dw


title: Pseudomonas aeruginosa_hydrogen peroxide_ 20min_replicate2

description: Hydrogen peroxide treatment


title: Pseudomonas aeruginosa_hydrogen peroxide_ 20min_replicate5

description: Hydrogen peroxide treatment


title: Snell 22 month Wild Type Liver 1c


title: Pseudomonas aeruginosa_hydrogen peroxide_ 20min_replicate4

description: Hydrogen peroxide treatment


title: Pseudomonas aeruginosa_hydrogen peroxide_ 20min_replicate1

description: Hydrogen peroxide treatment


title: Snell 6 month Wild Type Liver 82c


title: Ames 22 month Dwarf Liver JDF215


title: Snell 6 month Wild Type Liver 84c


title: 6 hr KLF4 Time Course Control

status: Public on Aug 13 2005

city: Atlanta

first: Vincent

middle: W.

last: Yang

state: GA

address: 201 Whitehead Research Building 615 Michael Street

department: Digestive Diseases Division

institute: Emory University

description: KLF4 over-eexpressed Ponesterone-treated samples and untreated controls

source_name: RKO colon cancer cells

label_protocol: RNA was processed to produce biotinylated 15 mg cRNA targets.

extract_protocol: Total RNA was extracted from the cell lysate using an RNeasy kit (Qiagen).

tag: untreated or induced


title: 12 hr KLF4 Time Course Control


title: 4 hr KLF4 Time Course Induced


title: 2 hr KLF4 Time Course Control


title: 6 hr KLF4 Time Course Induced


title: 8 hr KLF4 Time Course Control


title: 4 hr KLF4 Time Course Control


title: 1 hr KLF4 Time Course Control


title: Expression hos2 (F010D #14)

status: Public on Aug 11 2005

type: genomic

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: We carried out expression profiling experiments in which gene expression in logarithmically growing cultures of HDAC mutant cells was compared to that in wt controls. Wt, hos2D, clr6-1, clr3D and sir2D cells were grown to midlogarithmic phase (5*10power6 cells/ml) in rich medium, and RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004).

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: hos2 mut.

tag: hos2 mut. sample

source_name: WT

tag: WT sample


title: 8 hr KLF4 Time Course Induced


title: 0 hr KLF4 Time Course


title: 2 hr KLF4 Time Course Induced


title: 12 hr KLF4 Time Course Induced


title: 24 hr KLF4 Time Course Induced


title: 24 hr KLF4 Time Course Control


title: 1 hr KLF4 Time Course Induced


title: Expression clr6 (D080C #10)

source_name: clr6 mut.

tag: clr6 mut. sample


title: Digit, Tongue, Trachea

city: Toronto

first: Mark

last: Robinson

country: Canada

institute: University of Toronto

description: Custom 22K 60-mer ink-jet arrays designed by Naveed Mohammad (Tim Hughes lab, University of Toronto) and manufactured by Agilent technologies

data_processing: SVM

label: Cy3 or Cy5

source_name: Pool 8: Digit (1.3 ug), Tongue (0.6 ug), Trachea (0.15 ug)

tag: Pool 8


title: Expression clr6 (D080C #12)


title: Expression in TSA (D080C #6)

description: We carried out expression profiling experiments in which gene expression in logarithmically growing cultures of HDAC mutant cells was compared to that in wt controls. Wt, hos2D, clr6-1, clr3D and sir2D cells were grown to midlogarithmic phase (5*10power6 cells/ml) in rich medium, and RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004). It was previously shown that the Clr6 enzyme is sensitive to the HDAC inhibitor Trichostatin A (TSA) in vitro(Nakayama et al, 2003); hence, for comparison, we also determined the expression profile of wt cells after a 15-min exposure to TSA.

source_name: WT after a 15-min exposure to TSA

tag: WT after a 15-min exposure to TSA


title: Expression in TSA (D080C #17)


title: Expression in TSA (D080C #19)


title: Expression clr6 (D080C #11)


title: Expression in TSA (D080C #7)


title: Expression clr6 (D080C #8)


title: Expression hos2 (K130C #1)


title: Expression sir2 (K130C #16)

source_name: sir2 mut.

tag: sir2 mut. sample


title: Expression sir2 (K130C #14)


title: Expression in TSA (D080C #16)


title: Expression in TSA (D080C #18)


title: C2C12 myotubes 1000uM H2O2 rep 4

city: Lexington

first: Colleen

middle: A

last: McMullen

state: KY

address: 800 Rose St MS508

department: Physiology

institute: University of Kentucky

description: C2C12 transcriptome changes in response to hydrogen peroxide

label: Cy3, Cy5

source_name: C2C12 myotubes

tag: 1000uM H2O2 rep 4


title: Expression sir2 (K130C #15)


title: Femur, Knee, Teeth

source_name: Pool 6: Femur (0.9 ug), Knee (0.4 ug), Calvaria (0.06 ug), Teeth+mandible (1.3 ug), Teeth (0.4 ug)

tag: Pool 6


title: Testis, Epididymis

source_name: Pool 5: Testis (3 ug), Epididymis (0.4 ug)

tag: Pool 5

value: Testis (3 ug), Epididymis (0.4 ug)


title: Expression clr6 (D080C #9)


title: Salivary, Lymph

source_name: Pool 10: Salivary gland (1.26 ug), Lymph node (0.74 ug)

tag: Pool 10


title: C2C12 myotubes 1000uM H2O2 rep3

tag: 1000uM H2O2 rep3


title: Pancreas, Glands

source_name: Pool 9: Pancreas (1 ug), Mammary gland (0.9 ug), Adrenal gland (0.25 ug), Prostate gland (0.25 ug)

tag: Pool 9


title: Expression clr3 (K130C #9)

source_name: clr3 mut.

tag: clr3 mut. sample


title: Embryo, ES

source_name: Pool 7: 15 day Embryo (1.3 ug), 12.5 day Embryo (12.5 ug), 9.5 day Embryo (0.31 ug), 14.5 day Embryo head (0.25 ug), ES cells (0.24 ug)

tag: Pool 7


title: Colon, Intestine

source_name: Pool 4: Colon (0.96 ug), Intestine (1.04 ug)

tag: Pool 4

value: Colon (0.96 ug), Intestine (1.04 ug)


title: Expression clr3 (K130C #7)


title: Lung, Kidney

source_name: Pool 12: Lung (1 ug), Kidney (1 ug), Adipose (1 ug), Bladder (0.05 ug)

tag: Pool 12


title: C2C12 myotubes 100uM H2O2 rep 4

tag: 100uM H2O2 rep 4


title: C2C12 myotubes 1uM H2O2 rep 4

tag: 1uM H2O2 rep 4


title: C2C12 myotubes 100uM H2O2 rep 2

tag: 100uM H2O2 rep 2


title: Whole brain, Cerebellum, Olfactory bulb

source_name: Pool 3: Whole brain (1.5 ug), Cerebellum (0.48 ug), Olfactory bulb (0.15 ug)

tag: Pool 3


title: C2C12 myotubes 10uM H2O2 rep 4

tag: 10uM H2O2 rep 4


title: Heart, Muscle

source_name: Heart, Muscle

tag: Pool 1

value: Heart (2 ug), Skeletal muscle (2 ug)


title: C2C12 myotubes 1uM H2O2 rep 3

tag: 1uM H2O2 rep 3


title: C2C12 myotubes 1000uM H2O2 rep 2

tag: 1000uM H2O2 rep 2


title: Expression clr3 (J160B #25)

tag: WT sample


title: Placenta, 3 days

source_name: Pool 11: 12.5 day Placenta (1.15 ug), 9.5 day Placenta (0.5 ug), 15 day Placenta (0.35 ug)

tag: Pool 11


title: C2C12 myotubes 100uM H2O2 rep 3

tag: 100uM H2O2 rep 3


title: C2C12 myotubes 1uM H2O2 rep2

tag: 1uM H2O2 rep2


title: C2C12 myotubes 1000uM H2O2 rep1


title: ORF K080D clr6-1 H3 cter (#14)

description: we used an antibody against histone H3 C-terminal region (H3 cter) to control for nucleosome occupancy.

source_name: CHIP IP clr6-1 H3 cter

tag: clr6-1 sample where H3 cter antibody was used

source_name: CHIP Input

tag: CHIP input clr6-1 H3 cter


title: C2C12 myotubes 0uM H2O2 rep4

tag: control rep 4


title: ORF K080D hos2D H3 cter (#6)

source_name: CHIP IP hos2D H3 cter

tag: hos2D sample where H3 cter antibody was used

tag: CHIP input hos2D H3 cter


title: ORF K080D clr6-1 H3 cter (#13)


title: C2C12 myotubes 0uM H2O2 rep 3

tag: control rep 3


title: ORF K080D clr3D H3 cter (#9)

source_name: CHIP IP clr3D H3 cter

tag: clr3D sample where H3 cter antibody was used

tag: CHIP input clr3D H3 cter


title: C2C12 myotubes 10uM H2O2

tag: 10uM H2O2


title: ORF K080D hos2D H3 cter (#7)


title: C2C12 myotubes 100uM H2O2 rep 1


title: ORF K080D clr3D H3 cter (#15)


title: IGR J230C clr3 H3K14Ac

description: A set of five highly specific antibodies for H3K9Ac, H3K14Ac, H4K5Ac, H4K12Ac and H4K16Ac developed and titrated for ChIP (Suka et al., 2001) were used for ChIP of chromatin extracts from wt, hos2-D, clr6-1, clr3-D and sir2-D cells. The mutant alleles were first backcrossed with the standard laboratory strain (972 h-) to ensure isogenic strain backgrounds . Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was labeled with Cy5. The wt control ChIP DNA was labeled with Cy3 and simultaneously hybridized with the Cy5 labeled DNA to the IGR+ORF microarrays to produce genome wide mutant versus wt histone acetylation maps.

source_name: CHIP IP clr3-D H3K14Ac

tag: clr3-D sample where H3K14Ac antibody was used

source_name: CHIP IP clr3-D Wt

tag: Wt sample of clr3-D


title: IGR K080D hos2D H3 cter (#6)


title: ORF I240c clr3 H4K16Ac

source_name: CHIP IP clr3-D H4K16Ac

tag: clr3-D sample where H4K16Ac antibody was used


title: C2C12 myotubes 0uM H202 rep1

source_name: C2C12 myotubes

tag: Control


title: IGR I240C clr3 H3K14Ac


title: C2C12 myotubes 1ulMH202 rep 1

tag: 1uM H2O2


title: IGR I240c sir2 K3K9Ac

source_name: CHIP IP sir2-D K3K9Ac

tag: sir2-D sample where K3K9Ac antibody was used

source_name: CHIP IP sir2-D Wt

tag: Wt sample of sir2-D


title: C2C12 myotubes 10uM H2O2 rep 3

tag: 10uM H2O2 rep 3


title: IGR I240c clr3 H4K16Ac


title: ORF I240c clr3 H3K14Ac


title: Liver (Mouse Exons)

description:
Custom 22K 60-mer ink-jet arrays designed by Naveed
Mohammad (Tim Hughes lab, University of Toronto) and manufactured by
Agilent technologies

source_name: Pool 2: Liver (2 ug)

tag: Pool 2

value: Liver (2 ug)


title: IGR J230C clr3 H3K9Ac

source_name: CHIP IP clr3-D H3K9Ac

tag: clr3-D sample where H3K9Ac antibody was used


title: IGR K080D hos2D H3 cter (#7)


title: IGR K080D clr6-1 H3 cter (#14)

tag: clr6-1 sample where H3 cter antibody was used

tag: CHIP input clr6-1 H3 cter


title: ORF I240C hos2-D H3K14Ac

description: A set of five highly specific antibodies for H3K9Ac, H3K14Ac, H4K5Ac, H4K12Ac and H4K16Ac developed and titrated for ChIP (Suka et al., 2001) were used for ChIP of chromatin extracts from wt, hos2?, clr6-1, clr3? and sir2? cells. The mutant alleles were first backcrossed with the standard laboratory strain (972 h-) to ensure isogenic strain backgrounds . Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was labeled with Cy5. The wt control ChIP DNA was labeled with Cy3 and simultaneously hybridized with the Cy5 labeled DNA to the IGR+ORF microarrays to produce genome wide mutant versus wt histone acetylation maps.

source_name: CHIP IP hos2-D H3K14Ac

tag: hos2-D sample where H3K14Ac antibody was used

source_name: CHIP IP hos2-D

tag: hos2-D sample


title: C2C12 myotubes 10uM H2O2 rep 2

tag: 10uM H2O2 rep 2


title: IGR K080D clr6-1 H3 cter (#13)


title: IGR K080D clr3-D H3 cter (#9)

source_name: CHIP IP clr3-D H3 cter

tag: CHIP IP clr3-D H3 cter

source_name: CHIP Input clr3-D H3 cter

tag: CHIP input clr3-D


title: ORF I240C hos2-D H4K12Ac

source_name: CHIP IP hos2-D H4K12Ac

tag: hos2-D sample where H4K12Ac antibody was used


title: ORF I240C hos2-D H3K9Ac

source_name: CHIP IP hos2-D H3K9Ac

tag: hos2-D sample where H3K9Ac antibody was used


title: Expression clr3 (J160B #23)

source_name: clr3 mut.

tag: clr3 mut. sample

source_name: WT

tag: WT sample


title: IGR K080D clr3-D H3 cter (#15)

tag: CHIP input clr3-D H3 cter


title: IGR I240C hos2-D H3K14Ac


title: IGR I240C hos2-D H4K12Ac


title: ORF I240C hos2-D H4K5Ac

source_name: CHIP IP hos2-D H4K5Ac

tag: hos2-D sample where H4K5Ac antibody was used


title: IGR I240C hos2-D H3K9Ac


title: IGR J230C clr6 H3K14Ac

source_name: CHIP IP clr6-D H3K14Ac

tag: clr6-D sample where H3K14Ac antibody was used

source_name: CHIP IP clr6-D Wt

tag: Wt sample of clr6-D


title: IGR J230C clr3 H4K12Ac

source_name: CHIP IP clr3-D H4K12Ac

tag: clr3-D sample where H4K12Ac antibody was used

source_name: CHIP IP clr3-D Wt

tag: Wt sample of clr3-D


title: IGR J230C clr6 H3K9Ac

source_name: CHIP IP clr6-D H3K9Ac

tag: clr6-D sample where H3K9Ac antibody was used


title: ORF I240C clr6-1 H3K9Ac

source_name: CHIP IP clr6-1 H3K9Ac

tag: clr6-1 sample where H3K9Ac antibody was used

source_name: CHIP IP clr6-1

tag: clr6-1 sample


title: IGR I240C hos2-D H4K5Ac

tag: hos2-D sample


title: ORF I240C hos2-D H4K16Ac

source_name: CHIP IP hos2-D H4K16Ac

tag: hos2-D sample where H4K16Ac antibody was used


title: IGR J230C clr6 H4K12Ac

source_name: CHIP IP clr6-D H4K12Ac

tag: clr6-D sample where H4K12Ac antibody was used


title: IGR J230C clr3 H4K16Ac

source_name: CHIP IP clr3-D H4K16Ac

tag: clr3-D sample where H4K16Ac antibody was used


title: ORF I240C clr6-1 H4K12Ac

source_name: CHIP IP clr6-1 H4K12Ac

tag: clr6-1 sample where H4K12Ac antibody was used


title: IGR I240C hos2-D H4K16Ac

source_name: CHIP IP hos2-D


title: IGR J230C clr6 H4K16Ac

source_name: CHIP IP clr6-D H4K16Ac

tag: clr6-D sample where H4K16Ac antibody was used


title: ORF I240C clr6-1 H4K5Ac

source_name: CHIP IP clr6-1 H4K5Ac

tag: clr6-1 sample where H4K5Ac antibody was used


title: ORF I240C clr6-1 H4K16Ac

source_name: CHIP IP clr6-1 H4K16Ac

tag: clr6-1 sample where H4K16Ac antibody was used


title: ORF I240C clr6-1 H3K14Ac

source_name: CHIP IP clr6-1 H3K14Ac

tag: clr6-1 sample where H3K14Ac antibody was used


title: C2C12 myotubes 0uM H2O2 rep 2

source_name: C2C12 myotubes

tag: Control rep 2


title: IGR J230C clr3 H4K5Ac

source_name: CHIP IP clr3-D H4K5Ac

tag: clr3-D sample where H4K5Ac antibody was used


title: IGR I240C clr6-1 H3K9Ac


title: IGR J230C clr6 H4K5Ac

source_name: CHIP IP clr6-D H4K5Ac

tag: clr6-D sample where H4K5Ac antibody was used

source_name: CHIP IP clr6-D Wt

tag: Wt sample of clr6-D


title: IGR I240C clr6-1 H3K14Ac


title: ORF I240C wt H3K14Ac

source_name: CHIP IP wt H3K14Ac

tag: wt sample where H3K14Ac antibody was used

source_name: CHIP IP  Wt

tag: Wt sample


title: Phage DT1-1st exp-22min

city: Québec

first: Sylvain

last: Moineau

state: Québec

department: Biochemistry and microbiology

institute: Université Laval

description: Custom microarray developed to study the gene expression of two S. thermophilus phages (DT1 and 2972) during infection. Gene expression was measured at nine time intervals (0, 2, 7, 12, 17, 22, 27, 32, 37 minutes) during phage infection. Non infected sample were compared to the infected sample at a specific time point.

data_processing: Log2 transformed normalized CH2/CH1 ratio

organism: Moineauvirus DT1

source_name: Streptococcus thermophilus non-infected cell sample

tag: non-infected cell sample

source_name: Streptococcus thermophilus infected cell sample at 22 min post infection


title: Phage DT1-1st exp-37min

source_name: Streptococcus thermophilus infected cell sample at 37 min post infection


title: ORF I240C wt H4K5Ac

source_name: CHIP IP wt H4K5Ac

tag: wt sample where H4K5Ac antibody was used


title: ORF I240C wt H4K12Ac

source_name: CHIP IP wt H4K12Ac

tag: wt sample where H4K12Ac antibody was used


title: IGR I240C wt H3K14Ac


title: ORF I240C wt H4K16Ac

source_name: CHIP IP wt H4K16Ac

tag: wt sample where H4K16Ac antibody was used


title: Expression pSwi6 (J060C #19)

description: We carried out expression profiling experiments in which gene expression in logarithmically growing cultures of HDAC mutant cells was compared to that in wt controls. Wt, hos2D, clr6-1, clr3D and sir2D cells were grown to midlogarithmic phase (5*10power6 cells/ml) in rich medium, and RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004).To investigate the roles of HDACs at heterochromatic genes we also analyzed Swi6, the fission yeast heterochromatin protein 1 (HP1) homolog, by expression profiling of swi6D and Swi6 over expression (pSwi6) strains.

source_name: pSwi6 mut.

tag: pSwi6 mut. sample

source_name: WT

tag: WT sample


title: Phage DT1-1st exp-17min

source_name: Streptococcus thermophilus infected cell sample at 17 min post infection


title: IGR I240C wt H3K9Ac

source_name: CHIP IP wt H3K9Ac

tag: wt sample where H3K9Ac antibody was used


title: IGR I240C wt H4K12Ac


title: Phage DT1-1st exp-32min

source_name: Streptococcus thermophilus infected cell sample at 32 min post infection


title: Phage DT1-1st exp-27min

source_name: Streptococcus thermophilus infected cell sample at 27 min post infection


title: Phage DT1-1st exp-12min

source_name: Streptococcus thermophilus infected cell sample at 12 min post infection


title: IGR I240C wt H4K16Ac


title: IGR I240C clr6-1 H4K5Ac

source_name: CHIP IP clr6-1 H4K5Ac

source_name: CHIP IP clr6-1

tag: clr6-1 sample


title: Phage DT1-1st exp-7min

source_name: Streptococcus thermophilus Streptococcus thermophilus non-infected cell sample

source_name: Streptococcus thermophilus infected cell sample at 7 min post infection


title: ORF I240C wt H3K9Ac

source_name: CHIP IP  Wt


title: IGR I240C wt H4K5Ac


title: Expression pSwi6 (J060C #17)


title: IGR J130C hos2 H4K16Ac

source_name: CHIP IP hos2-D H4K16Ac

tag: hos2-D sample where H4K16Ac antybody was used

source_name: CHIP IP hos2-D Wt

tag: Wt sample od hos2-D


title: IGR J130C hos2 H4K12Ac

source_name: CHIP IP hos2-D H4K12Ac

tag: hos2-D sample where H4K12Ac antybody was used


title: Expression swi6 (J060C #16)

source_name: swi6 mut.

tag: swi6 mut. sample


title: Expression swi6 (J060C #20)


title: IGR J130C clr6 H4K16Ac

source_name: CHIP IP clr6-D H4K16Ac

tag: clr6-D sample where H4K16Ac antybody was used

source_name: CHIP IP clr6-D Wt

tag: Wt sample od clr6-D


title: Phage DT1-1st exp-2min

source_name: Streptococcus thermophilus non-infected cell sample

source_name: Streptococcus thermophilus infected cell sample at 2 min post infection


title: Phage DT1-1st exp-0min

source_name: Streptococcus thermophilus infected cell sample at 0 min post infection


title: Phage DT1-2nd exp-17min

source_name: Streptococcus thermophilus infected cell sample at 17 min post infection


title: Phage DT1-2nd exp-22min

source_name: Streptococcus thermophilus infected cell sample at 22 min post infection


title: Phage 2972-1st exp-32min

organism: Brussowvirus bv2972

source_name: Streptococcus thermophilus infected cell sample at 32 min post infection


title: Phage DT1-2nd exp-37min

source_name: Streptococcus thermophilus infected cell sample at 37 min post infection


title: Phage DT1-2nd exp-32min

tag: infected cell sample at 32 min post infection


title: Phage 2972-1st exp-37min

tag: infected cell sample at 37 min post infection


title: Phage 2972-1st exp-27min

source_name: Streptococcus thermophilus infected cell sample at 27 min post infection


title: IGR J130C clr6 H4K12Ac

source_name: CHIP IP clr6-D H4K12Ac

tag: clr6-D sample where H4K12Ac antybody was used


title: Phage DT1-2nd exp-27min

tag: non-infected cell sample

tag: infected cell sample at 27 min post infection


title: Phage 2972-1st exp-17min

tag: infected cell sample at 17 min post infection


title: Phage DT1-2nd exp-7min

source_name: Streptococcus thermophilus infected cell sample at 7 min post infection


title: Phage 2972-1st exp-0min

tag: Infected cell sample at 0 min post infection


title: Phage 2972-1st exp-7min

tag: infected cell sample at 7 min post infection


title: Phage 2972-2nd exp-32 min

status: Public on Aug 10 2005


title: IGR J130C clr6 H3K9Ac

source_name: CHIP IP clr6-D H3K9Ac

tag: clr6-D sample where H3K9Ac antybody was used


title: Phage 2972-1st exp-2min

tag: infected cell sample at 2 min post infection


title: Phage DT1-2nd exp-2min


title: Phage DT1-2nd exp-12min

source_name: Streptococcus thermophilus infected cell sample at 12 min post infection


title: Phage DT1-2nd exp-0min

tag: infected cell sample at 0 min post infection


title: Phage 2972-1st exp-22min

tag: infected cell sample at 22 min post infection


title: Phage 2972-1st exp-12min

tag: infected cell sample at 12 min post infection


title: Phage 2972-2nd exp-37 min


title: Phage 2972-2nd exp-27 min


title: IGR I240C clr6-1 H4K16Ac

source_name: CHIP IP clr6-1 H4K16Ac

tag: clr6-1 sample where H4K16Ac antibody was used

source_name: CHIP IP clr6-1

tag: clr6-1 sample


title: Phage 2972-2nd exp-22 min


title: Phage DT1-3rd exp-17 min


title: Phage DT1-3rd exp-22 min


title: Phage DT1-3rd exp-12 min


title: Phage 2972-2nd exp-0 min


title: Phage 2972-2nd exp-17 min


title: Phage 2972-2nd exp-2 min


title: Phage 2972-2nd exp-12 min


title: Phage DT1-3rd exp-32 min


title: Phage DT1-3rd exp-7 min


title: Phage 2972-2nd exp-7 min


title: Phage DT1-3rd exp-27 min


title: Phage DT1-3rd exp-2 min


title: Phage DT1-3rd exp-0min


title: Phage DT1-3rd exp-37 min


title: DCV_24h_rep_c

status: Public on Aug 08 2005

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

description: Analytic steps were performed using the programs within Affymetrix Microarray Suite 5.0 (Affymetrix) or Excel (Microsoft, Redmond, WA) with a combination of built in functions and custom formulae. The raw data were sorted using the Absent/Marginal/Present flags generated by the Microarray Suite functions. Whilst an Absent might indicate that there was no mRNA of particular type present in a sample, Marginal and Absent flags may indicate problems with the hybridisation, therefore only data points marked as present were retained.

data_processing: The remaining data mass for each microarray was then normalised to itself, making the median of all the present measurements one. The subsequent analysis of results was carried out on the genes present in all three replicates of a sample type.

organism: Drosophila melanogaster

source_name: entire body

label_protocol: For each experimental type, three biologically independent samples were used. Biotinylated RNA was produced and hybridized to Affymetrix Drosophila GeneChip microarrays (Part Number 510548; Affymetrix, Santa Clara, USA) according to the method published in Irving et al, 2001.

extract_protocol: Samples of 45 flies were ground to a fine powder were ground to a fine powder using matched glass pestle and grinder, followed by the immediate addition of 600 µl of RNeasy lysis buffer (QIAGEN, Courtaboeuf, France). After initial tissue disruption, total RNA was extracted using the RNeasy system, following the manufacturer’s instructions.

tag: Strain

value: Oregon R


title: Tris_48h_rep_c


title: DCV_48h_rep_a


title: DCV_48h_rep_c


title: Tris_24h_rep_c


title: DCV_24h_rep_a


title: DCV_48h_rep_b


title: DCV_24h_rep_b


title: Tris_48h_rep_b


title: Tris_24h_rep_b


title: Tris_24h_rep_a


title: B12 DEFICIENT PATIENT

status: Public on Aug 05 2005

city: Oxford

first: Alexander

last: Sternberg

state: Oxon

address: Headley Way

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

description: BM blasts <1%

data_processing: MAS 5.0

label: BIOTIN

source_name: B12 DEFICIENT BM CD34 CELLS

tag: 87 y/o male 46,XY


title: Tris_48h_rep_a


title: MDS12

description: BM blasts 2%

source_name: MDS BM CD34 CELLS

tag: 59 y/o male 46,XY


title: MDS14

description: BM blasts <1%

tag: 81 y/o female 46,XX


title: MDS10

description: BM blasts 2%

tag: 77 y/o female 46,XX


title: RHA3

description: BM blasts <1%

source_name: BM CD34 CELLS FROM PATIENT WITH RHEUMATOID ARTHRITIS ON METHOTREXATE

tag: 51 y/o female 46,XX. On oral methotrexate for RhA


title: RHA2

description: BM blasts <1%

source_name: BM CD34 CELLS FROM PATIENT WITH RHEUMATOID ARTHRITIS ON METHROTREXATE

tag: 82 y/o female 46,XX On oral methotrexate for RhA


title: FOLATE DEFICIENT PATIENT

description: BM blasts <1%

source_name: BM CD34 CELLS

tag: 84 y/o female 46,XY


title: MDS13

description: BM blasts <1%

tag: 89 y/o male 46,XY


title: MDS7

description: BM blasts 1%

tag: 63 y/o female 46,XX


title: Grape (Vitis riparia) buds long day (paradormant) verses short day (endodormancy induced) on Arabidopsis 12K (A)

city: Brookings

first: Anne

middle: Y

last: Fennell

state: SD

address: 201 N. Campus Dr

department: Plant Science

institute: South Dakota State University

description: This experiment compares the differences in expression of grape buds following 6 weeks growth under long photoperiods (LD-14h paradormancy maintenance) followed by either 2 weeks LD or 2 weeks SD (8h - endodormancy induction).

hyb_protocol: Schaffer R., J. Landgraf, M. Accerbi, V. V. Simon, M. Larson and El Wisman. 2001.  Microarray analysis of diurnal and circadian regulated genes in Arabidopsis.  Plant Cell 13:113-123.

scan_protocol: Hybridization was visualized using an Affy428scanner.  Spots were identified and signal intensities calculated using Jaguar software provided with the scanner.

data_processing: average signal intensities were nearly identical between Cy 5 and Cy3, thus they were not subjected to normalization. The VALUE given is the log base 2 of the ratio of long day over short day

organism: Vitis riparia

source_name: Short day axillary buds

growth_protocol: Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies.  In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite.  Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed .  Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night  temperatures (D/N) with  600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings,  S. Dak. (42oN).   High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was  below 600 µmol·m-2·s-1.  All plants were watered daily and fertilized weekly with a complete nutrient solution.  After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June.  White covered black cloth was used daily to impose SD starting at 1700 h.   Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments.  Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions.   For this study, buds were harvested between 8:00 and 12:00 AM after 2 weeks of SD, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

extract_protocol: Total RNA was isolated from ground axillary buds using the Pine tree extraction method (Chang et al. 1993).

treatment_protocol: Axillary buds were collected from intact plants after 6 weeks of LD + 2 weeks of SD.  Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

tag: Axillary buds harvested from shoot basal nodes 2 to 12.  Buds were harvested from plants that were grown for 6 weeks under long photoperiods (LD-14h) and then 2 weeks under short photoperiod (SD-8h).

source_name: Long day axillary buds

growth_protocol: Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies.  In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite.  Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed .  Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night  temperatures (D/N) with  600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings,  S. Dak. (42oN).   High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was  below 600 µmol·m-2·s-1.  All plants were watered daily and fertilized weekly with a complete nutrient solution.  After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June.  White covered black cloth was used daily to impose SD starting at 1700 h.   Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments.  Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions.   For this study, buds were harvested between 8:00 and 12:00 AM after 8 weeks of LD, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

treatment_protocol: Axillary buds were collected from intact plants after 8 weeks of LD.  Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

tag: Axillary buds harvested from shoot basal nodes 2 to 12.  Buds were harvested from plants that were grown for 8 weeks under long photoperiods (LD-14h).


title: IGR I240C clr6-1 H4K12Ac

source_name: CHIP IP clr6-1 H4K12Ac

tag: clr6-1 sample where H4K12Ac antibody was used


title: MDS8

description: BM blasts 3%

tag: 82 y/o female 46,XX


title: MDS9

description: BM blasts<1%

tag: 82 y/o female


title: MDS4

description: BM blasts <1%

tag: 79 y/o male 46,XY


title: RHA1

description: BM blasts <1%

source_name: BM CD34 CELLS FROM PATIENT WITH RHEUMATOID ARTHRITIS

tag: 69 y/o female 46,XX. Not receiving any treatment for RhA at time of marrow


title: MDS11

description: BM blasts 3%

tag: 90 y/o male 46,XY


title: MDS3

description: BM blasts 2%

tag: 83 y/o male 46,XY


title: MDS5

description: BM blasts <1%

tag: 81 y/o male 46,XY


title: MDS1

description: BM blasts 2%

tag: 65 y/o male 46,XY


title: MDS2

description: BM blasts <1%

tag: 89 y/o female. 46,XX


title: N8

description: BM blasts<1%

source_name: NORMAL BM CD34 CELLS

tag: 64 y/o female


title: N6

description: BM blasts<1%

tag: 41 y/o male


title: MDS6

description: BM blasts <1%

tag: 42 y/o male 46, XY


title: N7

description: BM blasts<1%

tag: 78 y/o female


title: N1

description: BM blasts<1%

tag: 67 y/o female


title: N5

description: BM blasts<1%

tag: 70 y/o female


title: N4

description: BM blasts<1%

tag: 58 y/o male


title: TGFb1 treated experiment A (10ng/ml 24 hours)

description: Human GFAP-negative lamina cribrosa cells were treated for 24 hours with 10ng/ml TGFB1.  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).

source_name: GFAP-negative lamina cribrosa cells


title: fls04052004dgv2_11-p_act-f

city: Basel

first: Edward

last: Oakeley

address: Maulbeerstrasse 66

institute: FMI

description: Total RNA from male 3rd instar larvae

data_processing: Bioconductor RMA

source_name: larvae

tag: Gender

value: female

tag: strain

tag: Genotype


title: vehicle treated experiment A (4mM HCL/1% BSA) 24 hours

description: Human GFAP-negative lamina cribrosa cells were generated from optic nerve head tissue. They were treated for 24 hours with 4mM HCL/ 1% BSA (vehicle).  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).


title: N3

description: BM blasts<1%

source_name: Normal BM CD34 cells

tag: 56 y/o male


title: fls04052004dgv2_08-+_p-f

description: Total RNA from male 3rd instar larvae


title: fls04052004dgv2_07-+_p-f

description: Total RNA from male 3rd instar larvae


title: vehicle treated experiment B (4mM HCL/1% BSA) 24 hours

description: Human GFAP-negative lamina cribrosa cells were generated from optic nerve head tissue. They were treated for 24 hours with vehicle (4mM HCl/1% BSA).  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).


title: TGFb1 treated experiment B (10ng/ml 24 hours)

description: Human GFAP-negative lamina cribrosa cells were generated from optic nerve head tissue. They were treated for 24 hours with TGFB1 (10ng/ml).  RNA extraced using Qiagen RNeasy mini collumns. *.Cel file normalised using Robust multichip average (RMA). Cell cultures from human donor A. Experiment conducted in duplicate (separate passages).


title: N9

description: BM blasts<1%

tag: 60 y/o female


title: fls04052004dgv2_06-+_p-m

description: Total RNA from male 3rd instar larvae

value: male


title: fls04052004dgv2_05-+_p-m

description: Total RNA from male 3rd instar larvae


title: fls04052004dgv2_09-p_act-m

description: Total RNA from male 3rd instar larvae


title: N2

description: BM blasts<1%

tag: 62 y/o male


title: fls04052004dgv2_01-+_act-m

description: Total RNA from male 3rd instar larvae

source_name: Larvae


title: fls04052004dgv2_03-+_act-f

description: Total RNA from male 3rd instar larvae


title: fls04052004dgv2_02-+_act-m

description: Total RNA from male 3rd instar larvae


title: Mixed gastric epithelial cell suspension RNA

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

institute: UCLA

description: Agilent oligonucleotide expression microarray (G4130A), hybridized with cRNA derived from mixed gastric epithelial cell suspensions after digest of rat gastric mucosa.

label: Cy5 or Cy3

source_name: Rat stomach mixed epithelial cells


title: fls04052004dgv2_04-+_act-f

description: Total RNA from male 3rd instar larvae


title: 80% Parietal cell suspension RNA from Rat Stomach

description: Agilent oligonucleotide expression microarray (G4130A), hybridized with cRNA derived from a 80% pure parietal cell suspension after digest of rat gastric mucosa.

source_name: Purified Rat Stomach Parietal cells


title: 99% Parietal cell suspension RNA from Rat Stomach

description: Agilent oligonucleotide expression microarray (G4130A), hybridized with cRNA derived from a 99% pure parietal cell suspension after digest of rat gastric mucosa.


title: IR29 salt stressed replicate 3

status: Public on Aug 04 2005

first: HARKAMAL

last: WALIA

address: Department of Botany & Plant Sciecnes

institute: University of California

description: IR29 salt stressed

organism: Oryza sativa Indica Group

source_name: crown and growing point

extract_protocol: Approximately 12 plants were dissected to obtain the crown and growing point tissue

tag: salt-tolerant salt stressed


title: Grape (Vitis riparia) buds long day (paradormant) verses short day (endodormancy induced) on Arabidopsis 9.2K (B)

hyb_protocol: Schaffer R., J. Landgraf, M. Accerbi, V. V. Simon, M. Larson and El Wisman. 2001. Microarray analysis of diurnal and circadian regulated genes in Arabidopsis. Plant Cell 13:113-123.

scan_protocol: Hybridization was visualized using an Affy428scanner. Spots were identified and signal intensities calculated using Jaguar software provided with the scanner.

data_processing: The N_LOG_VALUE is the log base 2 of the ratio of long day over short day spot intensities following removal of poorly hybridizing or high background (>1.5X CH/CH_BG) in both channels followed by log normalization.

growth_protocol: Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies. In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite. Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed . Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night temperatures (D/N) with 600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings, S. Dak. (42oN). High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was below 600 µmol·m-2·s-1. All plants were watered daily and fertilized weekly with a complete nutrient solution. After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June. White covered black cloth was used daily to impose SD starting at 1700 h. Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments. Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions. For this study, buds were harvested between 8:00 and 12:00 AM after 8 weeks of LD , frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

treatment_protocol: Axillary buds were collected from intact plants after 8 weeks of LD. Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were preformed.

tag: Axillary buds harvested from shoot basal nodes 2 to 12. Buds were harvested from plants that were grown for 8 weeks under long photoperiods (LD-14h).

growth_protocol: Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies. In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite. Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed . Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night temperatures (D/N) with 600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings, S. Dak. (42oN). High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was below 600 µmol·m-2·s-1. All plants were watered daily and fertilized weekly with a complete nutrient solution. After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June. White covered black cloth was used daily to impose SD starting at 1700 h. Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments. Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions. For this study, buds were harvested between 8:00 and 12:00 AM after 6 weeks of LD + 2 weeks of SD treatment, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

treatment_protocol: Axillary buds were collected from intact plants after 6 weeks of LD + 2 weeks of SD. Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

tag: Axillary buds harvested from shoot basal nodes 2 to 12. Buds were harvested from plants that were grown for 6 weeks under long photoperiods (LD-14h) and then 2 weeks under short photoperiod (SD-8h).


title: Grape (Vitis riparia) buds long day (paradormant) verses short day (endodormancy induced) on Arabidopsis 9.2K (A)

hyb_protocol: Schaffer R., J. Landgraf, M. Accerbi, V. V. Simon, M. Larson, and E. Wisman. 2001. Microarray Analysis of Diurnal and Circadian Regulated Genes in Arabidopsis. Plant Cell 13:113-123

scan_protocol: Hybridization was visualized using an Affy428 scanner. Spots were identified and signal intensities calculated using Jaguar software provided with the scanner.

data_processing: The N_LOG_VALUE is the log base 2 of the ratio of long day over short day spot intensities following removal of poorly hybridizing or high background (>1.5X CH/CH_BG in both channels) followed by log normalization.

growth_protocol: Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies. In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite. Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed . Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night temperatures (D/N) with 600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings, S. Dak. (42oN). High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was below 600 µmol·m-2·s-1. All plants were watered daily and fertilized weekly with a complete nutrient solution. After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June. White covered black cloth was used daily to impose SD starting at 1700 h. Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments. Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions. For this study, buds were harvested between 8:00 and 12:00 AM after 6 weeks of LD + 2 weeks of SD, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

source_name: Long day buds

growth_protocol: Five to seven-year-old clonally propagated Vitis riparia vines were used for these studies. In mid-March, two hundred forty ecodormant spur pruned vines with three or four spurs were placed in 15-L containers with media consisting of a 1:2:2 (v/v) mixture of soil, peat, and perlite. Three or four shoots (one on each spur) were trained vertically on each plant and all flower clusters were removed . Plants were grown under a long photoperiod (LD, 14 h) at 25/20 + 3 oC day/night temperatures (D/N) with 600 to 1400 µmol·m-2·s-1 photosynthetic photon flux (PPF) in a climate-controlled unshaded glass greenhouse (En Tech Control Systems Inc., Montrose, Minn.) from March through May in Brookings, S. Dak. (42oN). High pressure sodium lamps (400 W) were used to extend daylength to 15 h (March through May) and to increase PPF when the natural PPF was below 600 µmol·m-2·s-1. All plants were watered daily and fertilized weekly with a complete nutrient solution. After 6 weeks of growth two hundred uniform plants (having 3 shoots with 12 or more nodes) were selected and randomly assigned to the long photoperiod (endodormancy inhibiting) or short photoperiod (endodormancy inducing) during May and June. White covered black cloth was used daily to impose SD starting at 1700 h. Temperatures were maintained at 25/20 + 3 oC D/N in both photoperiod treatments. Thirty plants were randomly assigned to each of the 2, 4, and 6 treatment weeks in the LD and SD conditions. For this study, buds were harvested between 8:00 and 12:00 AM after 8 weeks of LD, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.

treatment_protocol: Axillary buds were collected from intact plants after 8 weeks of LD. Buds were excised, frozen in liquid nitrogen, and stored at -80C until RNA extractions were performed.


title: FL478 salt stressed replicate 2

description: FL478 salt stressed


title: IR29 salt stressed replicate 2

description: IR29 salt stressed


title: FL478 salt stressed replicate 1

description: FL478 salt stressed


title: FL478 control replicate 2

description: FL478 control

tag: salt-tolerant control


title: FL478 control replicate 1

description: FL478 control


title: FL478 control replicate 3

description: FL478 control


title: FL478 salt stressed replicate 3

description: FL478 salt stressed


title: IR29 control replicate 2

description: IR29 control


title: IR29 salt stressed replicate 1

description: IR29 salt stressed


title: IR29 control replicate 1

description: IR29 control


title: fls04052004dgv2_10-p_act-m

description: Total RNA from male 3rd instar larvae


title: 1251614

status: Public on Oct 29 2004

city: Rockville

first: David

last: Rasko

state: MD

address: 9712 Medical Center Drive

department: Microbial Genomics

institute: The Institute for Genomic Research

description:
Potential coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
Genomic DNA was labeled with Cy3 and Cy5 according to J. DeRisi (http://www.microarrays.org/Pdfs/GenomicDNALabel_B.pdf), except that genomic DNA was not digested or sheared before labeling.
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive using probes derived from B. anthracis Ames (reference) and a B. cereus group (query) strain. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).
Data representing weak signal were removed. The ratios from a maximum of six data points (duplicate spots, hybridizations performed in triplicate) were placed in three bins (<0.1) gene is absent in query strain, (0.1-0.3) present but diverged in query strain, and (>0.3) gene is present in the query strain. A majority rule was applied to the data for binning such that more than 50% of ratios were in agreement as to assignment and that at least two data points were used (exceeded in 99% of the cases). In cases where less than two data points existed, the gene was treated as data missing.
The criteria for the numerical ranges of our bins were established in two ways. First, we determined the presence or absence of sequences homologous to 3601 B. anthracis genes in the sequence of B. cereus ATCC 14579 (Integrated Genomics, Inc; http://www.integratedgenomics.com/) using BLASTN and compared that to the assignments inferred from hybridization ratios. A threshold of 0.1 was found to be suitable for classifying a gene as absent (i.e., agreement between sequence and CGH data in 99% of the cases), while a cutoff value of 0.3 was conservative for gene presence (agreement in 92% of the cases). Second, we used a set of 65 genes conserved in 26 bacterial genomes, NCBI COG database (http://www.ncbi.nlm.nih.gov/COG/). Genes judged as present in query strains using our selected cut-offs correctly binned data in 1225 out of 1235 total calls. There was a tendency for underprediction of plasmid homologs by CGH, when compared to results from the sequence analysis. Two possible explanations for this are variability in plasmid copy number in B. cereus strains relative to B. anthracis and/or that the average divergence of plasmid genes is greater than chromosomal genes and that at least two data points were used (exceeded in 99% of the cases).
Keywords = Comparative Genomic Hybridization

organism: Bacillus cereus

source_name: Bacillus cereus strain 31673

organism: Bacillus anthracis str. Ames

source_name: Bacillus anthracis Ames


title: TREF667

status: Public on Mar 27 2004

city: Bethesda

first: Rafael

middle: Dan

last: Camerini-Otero

address: 5 Memorial Dr. Rm.205

department: GBB

institute: NIDDK

description: Comparison of mouse testes and reference RNA

source_name: Universal mouse refence RNA (Stratagene)

source_name: Wild type whole testis


title: YA761

description: Comparison of 15 day and adult wild-type mouse testes.

source_name: Adult wild type whole testis

source_name: 15 day wild type whole testis


title: 12514683

description:
Potential coding regions predicted by Glimmer 30 were arrayed onto glass microscope slides (Telechem, Inc).
Genomic DNA was labeled with Cy3 and Cy5 according to J. DeRisi (http://www.microarrays.org/Pdfs/GenomicDNALabel_B.pdf), except that genomic DNA was not digested or sheared before labeling.
Arrays were scanned with a GenePix 4000B scanner (Axon Inc.).
Hybridization signals were quantitated using TIGR SPOTFINDER (software available at http://www.tigr.org/softlab).
Hybridization experiments were competitive using probes derived from B. anthracis Ames (reference) and a B. cereus group (query) strain. Normalized signal intensities were used to generate relative hybridization ratios (query/reference).
Data representing weak signal were removed. The ratios from a maximum of six data points (duplicate spots, hybridizations performed in triplicate) were placed in three bins (<0.1) gene is absent in query strain, (0.1-0.3) present but diverged in query strain, and (>0.3) gene is present in the query strain. A majority rule was applied to the data for binning such that more than 50% of ratios were in agreement as to assignment and that at least two data points were used (exceeded in 99% of the cases). In cases where less than two data points existed, the gene was treated as data missing.
The criteria for the numerical ranges of our bins were established in two ways. First, we determined the presence or absence of sequences homologous to 3601 B. anthracis genes in the sequence of B. cereus ATCC 14579 (Integrated Genomics, Inc; http://www.integratedgenomics.com/) using BLASTN and compared that to the assignments inferred from hybridization ratios. A threshold of 0.1 was found to be suitable for classifying a gene as absent (i.e., agreement between sequence and CGH data in 99% of the cases), while a cutoff value of 0.3 was conservative for gene presence (agreement in 92% of the cases). Second, we used a set of 65 genes conserved in 26 bacterial genomes, NCBI COG database (http://www.ncbi.nlm.nih.gov/COG/). Genes judged as present in query strains using our selected cut-offs correctly binned data in 1225 out of 1235 total calls. There was a tendency for underprediction of plasmid homologs by CGH, when compared to results from the sequence analysis. Two possible explanations for this are variability in plasmid copy number in B. cereus strains relative to B. anthracis and/or that the average divergence of plasmid genes is greater than chromosomal genes, and that at least two data points were used (exceeded in 99% of the cases).
Keywords = Comparative Genomic Hybridization


title: OREF758

description: Comparison of mouse ovaries and reference RNA

source_name: Wild type whole ovary


title: OT734

description: Comparison of ovaries and testes


title: YA760


title: 12516416


title: OT759

description: Comparison of ovaries and testes


title: OREF757


title: OT668

description: Comparison of ovaries and testes


title: TREF666


title: OREF733


title: OT731

description: Comparison of ovaries and testes


title: TREF735


title: SPO542

description: Comparison of Spo11 knockout mouse testes and wild-type mouse testes.

source_name: Spo11 knockout whole testis


title: SPO547


title: SPO543


title: OREF664


title: TREF756


title: RNA polymerase II in uninduced HeLa cells - rep2 of 3 with nimblegen ENCODE HG17

status: Public on Jun 15 2005

city: San Diego

first: Chunxu

last: Qu

department: Gene Regulation

institute: Ludwig Institute for Cancer Research

description:
Human cervix epithelial adenocarcinoma, HeLa cells Array ID is 45651_h. Replicate 2 of 3.
Genome-wide location analysis of RNA polymerase II binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45651_h. Replicate 2 of 3.

data_processing: The two channels in each array are loess-normalized using R.  The replicate arrays are then intensity-quantile normalized.  The log2 ratio are then derived from the normalized intensities.

source_name: Chromatin immunoprecipiated DNA using RNA polymerase II antibody, HeLa cells

tag: Human cervix epithelial adenocarcinoma cells, HeLa cells, RNA polymerase II antibody

source_name: Input DNA from HeLa cells


title: SPO546


title: YA568


title: trimethyl-K4 histone H3 in uninduced HeLa cells - rep2 of 3 with nimblegen ENCODE HG17

description: Genome-wide location analysis of trimethyl-K4 histone H3 binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45655_h. Replicate 2 of 3.

source_name: Chromatin immunoprecipiated DNA using trimethyl-K4 histone H3 antibody, HeLa cells

tag: Human cervix epithelial adenocarcinoma cells, HeLa cells, tmH3K4 antibody


title: trimethyl-K4 histone H3 in 30 minutes IFg-treated HeLa cells - rep3 of 3 with nimblegen ENCODE HG17

description: Genome-wide location analysis of trimethyl-K4 histone H3 binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) treated with interferon gamma for 30 minutes using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45654_h. Replicate 3 of 3.

source_name: Chromatin immunoprecipiated DNA using trimethyl-K4 histone H3 antibody, HeLa cells with IFg treated for 30 minutes

tag: Human cervix epithelial adenocarcinoma cells, HeLa cells, tmH3K4 antibody, IFg-treatment for 30 minutes

source_name: Input DNA from HeLa cells with IFg treated for 30 minutes

tag: Human cervix epithelial adenocarcinoma cells, HeLa cells, IFg-treatment for 30 minutes


title: RNA polymerase II in 30 minutes IFg-treated HeLa cells - rep3 of 3 with nimblegen ENCODE HG17

description:
Human cervix epithelial adenocarcinoma, HeLa cells, IFg-treatment for 30 minutes Array ID is 45656_h. Replicate 3 of 3.
Genome-wide location analysis of RNA polymerase II binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) treated with interferon gamma for 30 minutes using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45656_h. Replicate 3 of 3.

source_name: Chromatin immunoprecipiated DNA using RNA polymerase II antibody, HeLa cells with IFg treated for 30 minutes

tag: Human cervix epithelial adenocarcinoma cells, HeLa cells, RNA polymerase II antibody, IFg-treatment for 30 minutes


title: YA569


title: RNA polymerase II in uninduced HeLa cells - rep1 of 3 with nimblegen ENCODE HG17

description:
Human cervix epithelial adenocarcinoma, HeLa cells Array ID is 45649_h. Replicate 1 of 3.
Genome-wide location analysis of RNA polymerase II binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45649_h. Replicate 1 of 3.

tag: Human cervix epithelial adenocarcinoma cells, HeLa cells


title: trimethyl-K4 histone H3 in uninduced HeLa cells - rep1 of 3 with nimblegen ENCODE HG17

description: Genome-wide location analysis of trimethyl-K4 histone H3 binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 42312. Replicate 1 of 3.


title: trimethyl-K4 histone H3 in uninduced HeLa cells - rep3 of 3 with nimblegen ENCODE HG17

description: Genome-wide location analysis of trimethyl-K4 histone H3 binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 42317_3h. Replicate 3 of 3.


title: RNA polymerase II in uninduced HeLa cells - rep3 of 3 with nimblegen ENCODE HG17

description:
Human cervix epithelial adenocarcinoma, HeLa cells Array ID is 45657. Replicate 3 of 3.
Genome-wide location analysis of RNA polymerase II binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45657. Replicate 3 of 3.


title: trimethyl-K4 histone H3 in 30 minutes IFg-treated HeLa cells - rep2 of 3 with nimblegen ENCODE HG17

description: Genome-wide location analysis of trimethyl-K4 histone H3 binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) treated with interferon gamma for 30 minutes using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 42321_3h. Replicate 2 of 3.


title: trimethyl-K4 histone H3 in 30 minutes IFg-treated HeLa cells - rep1 of 3 with nimblegen ENCODE HG17

description: Genome-wide location analysis of trimethyl-K4 histone H3 binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) treated with interferon gamma for 30 minutes using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 42302. Replicate 1 of 3.


title: RNA polymerase II in 30 minutes IFg-treated HeLa cells - rep1 of 3 with nimblegen ENCODE HG17

description:
Human cervix epithelial adenocarcinoma, HeLa cells, IFg-treatment for 30 minutes Array ID is 45650_h. Replicate 1 of 3.
Genome-wide location analysis of RNA polymerase II binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) treated with interferon gamma for 30 minutes using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45650_h. Replicate 1 of 3.


title: RNA polymerase II in 30 minutes IFg-treated HeLa cells - rep2 of 3 with nimblegen ENCODE HG17

description:
Human cervix epithelial adenocarcinoma, HeLa cells, IFg-treatment for 30 minutes Array ID is 45652_h. Replicate 2 of 3.
Genome-wide location analysis of RNA polymerase II binding in Human cervix epithelial adenocarcinoma cells (HeLa cells) treated with interferon gamma for 30 minutes using nimblegen ENCODE HG17 tiling array with 50mer probe at 38bp interval. Array ID is 45652_h. Replicate 2 of 3.


title: OREF665


title: day11 slide8

status: Public on Dec 05 2005

city: Lelystad

first: Saskia

middle: van

last: Hemert

address: PO box 65

country: Netherlands

institute: Animal Sciences Group

description: comparison 2 chicken lines

data_processing: genepix pro

organism: Gallus gallus

source_name: jejunum slow salmonella d11

tag: tissue

value: jejunum

tag: infection

value: salmonella

source_name: jejunum fast salmonella d11


title: Mouse_C57_E11.5_necortex_rostral_vs_caudal_r1

status: Public on Aug 26 2005

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

description:
Sample details: rostral or caudal thirds of E11.5 C57 neocortex where pooled from three embryos.

RNA was extracted by the Invitrogen Trizol Protocol, Ref: Chomczynski, P. and Sacchi, N. (1987) Analytical Biochemistry 162, 156. "Single Step Method of RNA Isolation by Acid Guanidinium Thiocyanate-Phenol-Chloroform Extraction."

Amplification and probe labelling were carried out as detailed in this paper: Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10

hyb_protocol: See Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M. and Cepko, C. L. (2000). Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol 10, 301-10

scan_protocol: Hybridised microarrays were scanned on a GenePix 4000B microarray scanner and the resulting images were analysed with GenePix 5 array analysis software.

data_processing: log ratios were lowess normalised, and filted to exclude (1) spots flagged as bad and (2) spots where 55% of the foreground pixels in either channel where less intense than the (background intensity  + 1SD)

tag: See description


title: IGR J130C clr6 H4K5Ac

description: A set of five highly specific antibodies for H3K9Ac, H3K14Ac, H4K5Ac, H4K12Ac and H4K16Ac developed and titrated for ChIP (Suka et al., 2001) were used for ChIP of chromatin extracts from wt, hos2?, clr6-1, clr3? and sir2? cells. The mutant alleles were first backcrossed with the standard laboratory strain (972 h-) to ensure isogenic strain backgrounds . Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was labeled with Cy5. The wt control ChIP DNA was labeled with Cy3 and simultaneously hybridized with the Cy5 labeled DNA to the IGR+ORF microarrays to produce genome wide mutant versus wt histone acetylation maps.

source_name: CHIP IP clr6-D H4K5Ac

tag: clr6-D sample where H4K5Ac antybody was used

source_name: CHIP IP clr6-D Wt

tag: Wt sample od clr6-D


title: Grape (Vitis riparia) buds long day (paradormant) verses short day (endodormancy induced) on Arabidopsis 12K(B)

description: This experiment compares the differences in expression of grape buds following 6 weeks growth under long photoperiods (LD-14h paradormancy maintenance) followed by either 2 weeks LD or 2 weeks SD (8h - endodormancy induction).

source_name: Long day axillary buds

label_protocol: Schaffer R., J. Landgraf, M. Accerbi, V. V. Simon, M. Larson and El Wisman. 2001. Microarray analysis of diurnal and circadian regulated genes in Arabidopsis. Plant Cell 13:113-123.

source_name: Short day buds