title: Halobacterium NRC-1 grown in to an OD600 0.430, Array 9920

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-88


title: Halobacterium NRC-1 grown in to an OD600 0.195, Array 9915

status: Public on Feb 23 2007

type: RNA

city: Seattle

first: Marc

last: Facciotti

state: WA

address: 1441 North 34th Street

country: USA

institute: Institute for Systems Biology

description: Halobacterium NRC-1 grown in standard growth media to an OD600 &RIGHT(C2,5)

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

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

data_processing: AnalyzerDG software for spotfinding.  see the ISB Microarray Pipeline webpage for more details

label: Alexa 547

molecule: total RNA

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC1, wild-type

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-83

growth_protocol: Halobacterium NRC-1 grown in standard growth media to an OD600 0.195

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

label: Alexa 647

source_name: Halobacterium NRC1, reference

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


title: Knockout of transcription factor ura3grown to OD600 0.842 in standard growth media, Array 9911

description: knockout of transcription factor ura3grown to OD600 0.842 in standard growth media

source_name: Halobacterium NRC1, ura3 knockout strain

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-79

tag: knockout of transcription factor ura3 grown in standard growth media

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

tag: Halobacterium NRC-1 grown in standard growth media


title: Knockout of transcription factor ura3grown to OD600 0.828 in standard growth media, Array 9914

description: knockout of transcription factor ura3grown to OD600 0.828 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-82


title: Knockout of transcription factor ura3grown to OD600 0.376 in standard growth media, Array 9910

description: knockout of transcription factor ura3grown to OD600 0.376 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-78


title: Halobacterium NRC-1 grown in to an OD600 0.195, Array 9916

description: Halobacterium NRC-1 grown in standard growth media to an OD600 &RIGHT(E2,5)

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-84


title: Knockout of transcription factor ura3grown to OD600 0.828 in standard growth media, Array 9913

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-81

growth_protocol: knockout of transcription factor ura3grown to OD600 0.828 in standard growth media


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.835 with mevinolin, Array 10044

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.835 in standard growth media with 20microgram/ml mevinolin versus standard reference

source_name: Halobacterium NRC1, tfbE expression from plasmid pMTFcmyc

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-67

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor tfbE grown in standard growth media with mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.877 with mevinolin, Array 10047

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.877 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-70


title: Knockout of transcription factor ura3grown to OD600 0.376 in standard growth media, Array 9909

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-77

growth_protocol: knockout of transcription factor ura3grown to OD600 0.376 in standard growth media


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.439 with mevinolin, Array 10042

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.439 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-65


title: Knockout of transcription factor ura3grown to OD600 0.405 in standard growth media, Array 9908

description: knockout of transcription factor ura3grown to OD600 0.405 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-76


title: Knockout of transcription factor ura3grown to OD600 0.405 in standard growth media, Array 9907

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-75

growth_protocol: knockout of transcription factor ura3grown to OD600 0.405 in standard growth media


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.835 with mevinolin, Array 10045

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-68

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.835 in standard growth media with 20microgram/ml mevinolin


title: Knockout of transcription factor ura3grown to OD600 0.189 in standard growth media, Array 9899

description: knockout of transcription factor ura3grown to OD600 0.189 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-73


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.877 with mevinolin, Array 10046

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-69

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.877 in standard growth media with 20microgram/ml mevinolin


title: Knockout of transcription factor ura3grown to OD600 0.189 in standard growth media, Array 9906

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-74

growth_protocol: knockout of transcription factor ura3grown to OD600 0.189 in standard growth media


title: Knockout of transcription factor ura3grown to OD600 0.178 in standard growth media, Array 9897

description: knockout of transcription factor ura3grown to OD600 0.178 in standard growth media

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-71


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.439 with mevinolin, Array 10043

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-66

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.439 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.416 with mevinolin, Array 10041

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.416 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-64

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


title: Knockout of transcription factor ura3grown to OD600 0.178 in standard growth media, Array 9898

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-72

growth_protocol: knockout of transcription factor ura3grown to OD600 0.178 in standard growth media


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.416 with mevinolin, Array 10040

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-63

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.416 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.169 with mevinolin, Array 10039

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.169 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-62


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.169 with mevinolin, Array 10038

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-61

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.169 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.170 with mevinolin, Array 10036

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.170 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-59


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.851 with mevinolin, Array 10035

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.851 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-58

source_name: Halobacterium NRC1, tfbD expression from plasmid pMTFcmyc

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor tfbD grown in standard growth media with mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.899 with mevinolin, Array 10033

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.899 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-56


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.416 with mevinolin, Array 10031

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.416 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.851 with mevinolin, Array 10034

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-57

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.851 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.899 with mevinolin, Array 10032

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-55

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.899 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.416 with mevinolin, Array 10019

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-53

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.416 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.417 with mevinolin, Array 10018

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.417 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-52


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbE grown to OD600 0.170 with mevinolin, Array 10037

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-60

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbE grown to OD600 0.170 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.417 with mevinolin, Array 10017

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-51

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.417 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.835 with mevinolin, Array 10009

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.835 in standard growth media with 20microgram/ml mevinolin versus standard reference

source_name: Halobacterium NRC1, Cmyc expression from plasmid pMTFcmyc

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-43

tag: plasmid (pMTFcmyc) based expression of cmyc tagged transcription factor Cmyc grown in standard growth media with mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.833 with mevinolin, Array 10012

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.833 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-46


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.176 with mevinolin, Array 10015

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.176 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-49

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


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.417 with mevinolin, Array 10005

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.417 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.835 with mevinolin, Array 10010

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.835 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.399 with mevinolin, Array 10007

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.399 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-41

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


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.399 with mevinolin, Array 10008

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-42

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.399 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.417 with mevinolin, Array 10006

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.417 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.185 with mevinolin, Array 10013

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.185 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-47


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.833 with mevinolin, Array 10011

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-45

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.833 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.176 with mevinolin, Array 10016

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-50

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.176 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing tfbD grown to OD600 0.185 with mevinolin, Array 10014

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-48

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing tfbD grown to OD600 0.185 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.179 with mevinolin, Array 9989

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.179 in standard growth media with 20microgram/ml mevinolin versus standard reference

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38


title: NST library

type: MPSS

city: Davis

first: Blake

middle: C.

last: Meyers

state: CA

address: 451 Health Sciences Dr.

department: UC Davis Genome Center

institute: University of California - Davis

description: MPSS data were obtained from Nipponbare rice 60 days Stem.

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

organism: Oryza sativa

source_name: 60 days - Stem

extract_protocol: Total RNA was isolated using TRIzol reagent.

tag: Cultivar

value: Nipponbare

tag: 60 days - Stem


title: SNU library

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

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

source_name: Germinating seedlings

tag: Germinating seedlings


title: NYR library

description: MPSS data were obtained from Nipponbare rice 14 days root leaves.

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

source_name: 14 days - Young Roots

tag: 14 days - Young Roots


title: STM library

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

source_name: Stem

tag: Stem


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.175 with mevinolin, Array 9986

description: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.175 in standard growth media with 20microgram/ml mevinolin versus standard reference


title: Thymus, technical replicate 2 at Yerkes National Primate Research Center

city: Providence

first: Fenghai

last: Duan

state: RI

address: 121 S. Main Street

department: Biostatistics

institute: Brown University

description: Gene expression data from thymus

hyb_protocol: Following fragmentation, the biotinylated cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus Macaque Array

scan_protocol: GeneChips were scanned on Affymetrix scanner 3000

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) using MAS background correction and quantile normalization within the center.

label: biotin

organism: Macaca mulatta

source_name: rhesus macaques thymus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

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

tag: Tissue

value: thymus


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.179 with mevinolin, Array 9988

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.179 in standard growth media with 20microgram/ml mevinolin


title: Halobacterium NRC-1 with pMTFcmyc expressing Cmyc grown to OD600 0.175 with mevinolin, Array 9987

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing Cmyc grown to OD600 0.175 in standard growth media with 20microgram/ml mevinolin


title: Thymus, technical replicate 1 at Yerkes National Primate Research Center

description: Gene expression data from thymus


title: NYL library

description: MPSS data were obtained from Nipponbare rice 14 days young leaves.

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

source_name: 14 days - Young leaves

tag: 14 days - Young leaves


title: Fibroblasts, technical replicate 1 at Yerkes National Primate Research Center

description: Gene expression data from fibroblasts

source_name: rhesus macaques fibroblasts

tag: Cell Line

value: immortalized fibroblasts


title: NPO library

description: MPSS data were obtained from Nipponbare rice mature pollen.

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

source_name: Mature Pollen

tag: Mature Pollen


title: FLR library

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

source_name: Nipponbare Immature panicles- 90 days old plants


title: NSR library

description: MPSS data were obtained from Nipponbare rice 14 days - Young roots stressed in 250 mM NaCl for 24h.

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


title: NSO library

description: MPSS data were obtained from Nipponbare rice ovary and mature stigma.

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

source_name: Ovary and mature stigma

tag: Ovary and mature stigma


title: NR2 library

description: MPSS data were obtained from Nipponbare rice mature roots.  Combination of 2 root libraries (biological replicates).

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the NR2 library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/rice.

source_name: 60 days Mature Root - Combination of Replicates


title: Testis, technical replicate 1 at Yerkes National Primate Research Center

description: Gene expression data from testis

source_name: rhesus macaques testis

value: testis


title: NSL library

description: MPSS data were obtained from Nipponbare rice 14 days - Young leaves stressed in 250 mM NaCl for 24h.

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


title: NME library

description: MPSS data were obtained from Nipponbare rice 60 days crown vegetative meristematic tissue.

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

source_name: 60 days - Crown vegetative meristematic tissue


title: Pancreas, technical replicate 2 at Yerkes National Primate Research Center

description: Gene expression data from pancreas

source_name: rhesus macaques pancreas

value: pancreas


title: NL4 library

description: MPSS data were obtained from Nipponbare rice 60 days Mature Leaves. This library is the combinded set of 4 biological replicates.

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the NL4 library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/rice.

source_name: Mature Leaf - Combination of Replicates

tag: 60 days Mature Leaf - Combination of Replicates


title: Pancreas, technical replicate 1 at Yerkes National Primate Research Center

description: Gene expression data from pancreas


title: Cerebral cortex, technical replicate 2 at Yerkes National Primate Research Center

description: Gene expression data from cerebral cortex

source_name: rhesus macaques cerebral cortex

value: cerebral cortex


title: Testis, technical replicate 2 at Yerkes National Primate Research Center

description: Gene expression data from testis


title: Fibroblasts, technical replicate 2 at Yerkes National Primate Research Center

description: Gene expression data from fibroblasts


title: NGD library

description: MPSS data were obtained from 10 days rice germinating seedlings grown in dark.

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

source_name: 10 days - germinting rice seedlings grown in dark

tag: 10 days - Germinating seedlings grown in dark


title: NIP library

description: MPSS data were obtained from rice 90 days Immature panicle.

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

source_name: 90 days - Immature panicle

tag: 90 days - Immature panicle


title: Cerebral cortex, technical replicate 1 at Yerkes National Primate Research Center


title: Thymus, technical replicate 1 at University of Nebraska Medical Center

description: Gene expression data from thymus


title: NDR library

description: MPSS data were obtained from rice young roots stressed in drought for 5days.

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

source_name: 14 days rice young root stressed in drought for 5days

tag: 14 days - Young roots stressed in drought for 5 days


title: NCR library

description: MPSS data were obtained from rice young roots stressed in 4C cold for 24 hrs.

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

source_name: 14 days rice young root stressed in 4C cold for 24 hrs

tag: 14 days - Young roots stressed in 4C cold for 24h


title: NDL library

description: MPSS data were obtained from rice young leaves stressed in drought for 5days.

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

source_name: 14 days rice young leaf stressed in drought for 5days

tag: 14 days - Young leaves stressed in drought for 5 days


title: Testis, technical replicate 1 at University of Nebraska Medical Center

description: Gene expression data from testis


title: NGS library

description: MPSS data were obtained from 3 days rice germinating seed.

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

source_name: 3 days - rice germinating seed

tag: 3 days - Germinating seed


title: NCL library

description: MPSS data were obtained from rice young leaves stressed in 4C cold for 24 hrs.

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

source_name: 14 days rice young leaf stressed in 4C cold for 24 hrs

tag: Cultivar

tag: 14 days - Young leaves stressed in 4C cold for 24h


title: Thymus, technical replicate 2 at University of Nebraska Medical Center

description: Gene expression data from thymus

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) using MAS background correction and quantile normalization within the center.

source_name: rhesus macaques thymus


title: Testis, technical replicate 2 at University of Nebraska Medical Center

description: Gene expression data from testis


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBe, Halobacterium  GTF growth curve experiment, Array 7285

type: genomic

description: IP sample of Cmyc tagged TFBe expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBe grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36

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

data_processing: AnalyzerDG software for spotfinding. see the ISB Microarray Pipeline webpage for more details.

molecule: genomic DNA

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBe

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-57

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBe grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

extract_protocol: Cells were cross-linked with 1.2% formaldehyde and subsequently lysed via sonication.  DNA was sheared via sonication.  A small fraction of total DNA was kept for a whole cell extract (wce) background while the rest of the DNA was immunoprecipitated with antibody against the epitope tag in question.  Each DNA sample was treated with protease and RNAase and amplified by PCR utilizing ligated universal linkers as templates for amplification.  The resulting DNA was cleaned and quantified.

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBe grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

label: Alexa 532

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBe

tag: whole cell extract of CCmyc tagged transcription factor TFBe grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: NCA library

description: MPSS data were obtained from 35 days old rice callus.

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

source_name: 35 days old rice callus

tag: 35 days - Callus


title: Pancreas, technical replicate 2 at University of Nebraska Medical Center

description: Gene expression data from pancreas

tag: Tissue


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBe, Halobacterium  GTF growth curve experiment, Array 7284

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-56


title: Thymus, technical replicate 2 at Oregon National Primate Research Center

description: Gene expression data from thymus


title: Cerebral cortex, technical replicate 1 at University of Nebraska Medical Center


title: Fibroblasts, technical replicate 1 at University of Nebraska Medical Center

description: Gene expression data from fibroblasts

source_name: rhesus macaques fibroblasts


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBe, Halobacterium  GTF growth curve experiment, Array 7283

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-55


title: Pancreas, technical replicate 1 at University of Nebraska Medical Center

description: Gene expression data from pancreas


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7281

description: IP sample of Cmyc tagged TFBc expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBc grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBc

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBc grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBc grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBc

tag: whole cell extract of CCmyc tagged transcription factor TFBc grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: Fibroblasts, technical replicate 2 at University of Nebraska Medical Center

description: Gene expression data from fibroblasts

tag: Cell Line


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 7511

description: IP sample of Cmyc tagged TFBf expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBf

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-60

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBf grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBf

tag: whole cell extract of CCmyc tagged transcription factor TFBf grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: Thymus, technical replicate 1 at Oregon National Primate Research Center

description: Gene expression data from thymus


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 7512

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-61


title: Pancreas, technical replicate 2 at Oregon National Primate Research Center

description: Gene expression data from pancreas

source_name: rhesus macaques pancreas


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7279

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-52


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7280

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-53

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7272

description: IP sample of Cmyc tagged TFBa expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBa grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBa

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-49

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBa grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBa grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBa

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

tag: whole cell extract of CCmyc tagged transcription factor TFBa grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: Testis, technical replicate 1 at Oregon National Primate Research Center

description: Gene expression data from testis

source_name: rhesus macaques testis


title: Testis, technical replicate 2 at Oregon National Primate Research Center

description: Gene expression data from testis


title: Cerebral cortex, technical replicate 2 at University of Nebraska Medical Center

source_name: rhesus macaques cerebral cortex


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 7510

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-59


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7271

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-48

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40


title: Yeast Replicate #7

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

description: Transcriptional comparison of WT and ACE2 knockout strains grown in the yeast form

hyb_protocol: Before hybridization, one of the labeled cDNA samples was resuspended in 45 µl of hybridization buffer (1x Dig Ease buffer [Roche] containing 0.5 mg ml–1 baker's tRNA and 0.5 mg ml–1 salmon sperm DNA) and then added to the second labeled cDNA. The mixture was heat denatured at 95°C for 2 min, quickly cooled on ice, applied to the DNA microarray, and covered with a 24-mm by 60-mm coverslip. Slides were placed in a hybridization chamber (Corning, Palo Alto, CA) with 9 µl of 3x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) in each of the wells and incubated at 37°C for 16 h by immersion in a water bath. Following hybridization, the slides were immersed in 1x SSC at 50°C until the coverslip fell off, washed twice for 15 min each in 1x SSC-0.1% sodium dodecyl sulfate (SDS) at 50°C and once in 0.1x SSC-0.1% SDS for 20 min at 50°C, and rinsed three times in 1x SSC at 50°C and, finally, once in 0.2x SSC at room temperature. The slides were dried by centrifugation at 900 rpm for 5 min. Seven independent comparisons (incorporating three dye swaps) were performed for yeast growth conditions, and five independent comparisons (with two dye swaps) were performed for growth under hypha-inducing conditions.

scan_protocol: The microarrays were scanned using an Axon 4000B scanner at a 10-µm resolution

data_processing: Low-quality spots were automatically flagged by Genepix Pro 5.0.  Lowess normalization was carried out in GeneSpring.

organism: Candida albicans

source_name: ACE2 knockout strain (MK106)

label_protocol: Twenty-five micrograms of total RNA was labeled in a total volume of 40 µl including 5 ng LuxA control RNA (Eurogentec), 1x first-strand buffer (Invitrogen), 0.2 pmol C. albicans-specific primer (Eurogentec), 1.5 mM (each) dATP, dTTP, and dGTP, 25 µM dCTP, 10 mM dithiothreitol, 1 µl RNasin, and 37.5 µM Cy5-dCTP (Amersham). The mixture was incubated at 65°C for 5 min and then at 42°C for 5 min. One microliter of RNasin (Promega) and 1 µl Superscript II reverse transcriptase (Invitrogen) were added and incubated at 42°C for 1 h. Following the addition of another 1 µl of Superscript II, the incubation was continued for 1 h at 42°C. The reaction was stopped by the addition of 5 mM EDTA, pH 8.0, and 0.5 M NaOH and incubation at 65°C for 20 min and was neutralized by adding 0.5 M acetic acid. The labeled cDNAs were purified using a QIAquick PCR purification kit (QIAGEN) and concentrated by drying under vacuum to a volume of approximately 2 µl.

extract_protocol: Ambion Yeast Ribopure kit

tag: ACE2 knockout strain (MK106)

tag: Cells in yeast form

source_name: Wildtype strain (SC5314)

label_protocol: As for Channel 1, but using  37.5 µM Cy3-dCTP (Amersham)

tag: Wildtype strain (SC5314)


title: Fibroblasts, technical replicate 1 at Oregon National Primate Research Center

description: Gene expression data from fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 7509

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-58


title: Pancreas, technical replicate 1 at Oregon National Primate Research Center

description: Gene expression data from pancreas


title: Cerebral cortex, technical replicate 2 at Oregon National Primate Research Center


title: Cerebral cortex, technical replicate 1 at Oregon National Primate Research Center


title: Yeast Replicate #6


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 7278

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-51

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7270

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-47


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7273

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-50

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36


title: Fibroblasts, technical replicate 2 at Oregon National Primate Research Center

description: Gene expression data from fibroblasts


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8227

description: IP sample of Cmyc tagged TFBg expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBg grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBg

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-112

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBg grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: whole cell extract of CCmyc tagged transcription factor TFBg grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

label: Alexa 546

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBg

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBg grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 6980

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-46


title: Yeast Replicate #3

description: Transcriptional comparison of WT and ACE2 knockout strains grown in yeast form

tag: Dyeswap

tag: ACE2 Knockout strain (MK106)


title: Yeast Replicate #4


title: Yeast Replicate #2


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8028

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-111


title: IP fraction of ChIP-Chip sample from Cmyc tagged TBPb, Halobacterium  GTF growth curve experiment, Array 6978

description: IP sample of Cmyc tagged TBPb expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TBPb grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TBPb

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TBPb grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TBPb grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TBPb

tag: whole cell extract of CCmyc tagged transcription factor TBPb grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: Yeast Replicate #5


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 6976

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-42

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


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8024

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-109


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8025

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-110


title: Yeast Replicate #1

label_protocol: Twenty-five micrograms of total RNA was labeled in a total volume of 40 µl including 5 ng LuxA control RNA (Eurogentec), 1x first-strand buffer (Invitrogen), 0.2 pmol C. albicans-specific primer (Eurogentec), 1.5 mM (each) dATP, dTTP, and dGTP, 25 µM dCTP, 10 mM dithiothreitol, 1 µl RNasin, and 37.5 µM Cy5-dCTP (Amersham). The mixture was incubated at 65°C for 5 min and then at 42°C for 5 min. One microliter of RNasin (Promega) and 1 µl Superscript II reverse transcriptase (Invitrogen) were added and incubated at 42°C for 1 h. Following the addition of another 1 µl of Superscript II, the incubation was continued for 1 h at 42°C. The reaction was stopped by the addition of 5 mM EDTA, pH 8.0, and 0.5 M NaOH and incubation at 65°C for 20 min and was neutralized by adding 0.5 M acetic acid. The labeled cDNAs were purified using a QIAquick PCR purification kit (QIAGEN) and concentrated by drying under vacuum to a volume of approximately 2 µl.


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 8487

description: IP sample of Cmyc tagged TFBd expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBd

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-108

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBd grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBd

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

tag: whole cell extract of CCmyc tagged transcription factor TFBd grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 8486

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-107

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 6979

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-45

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 9208

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-106


title: Hyphal Replicate #5

description: Transcriptional comparison of WT and ACE2 knockout strains grown in hyphal inducing conditions

hyb_protocol: Before hybridization, one of the labeled cDNA samples was resuspended in 45 µl of hybridization buffer (1x Dig Ease buffer [Roche] containing 0.5 mg ml–1 baker's tRNA and 0.5 mg ml–1 salmon sperm DNA) and then added to the second labeled cDNA. The mixture was heat denatured at 95°C for 2 min, quickly cooled on ice, applied to the DNA microarray, and covered with a 24-mm by 60-mm coverslip. Slides were placed in a hybridization chamber (Corning, Palo Alto, CA) with 9 µl of 3x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) in each of the wells and incubated at 37°C for 16 h by immersion in a water bath. Following hybridization, the slides were immersed in 1x SSC at 50°C until the coverslip fell off, washed twice for 15 min each in 1x SSC-0.1% sodium dodecyl sulfate (SDS) at 50°C and once in 0.1x SSC-0.1% SDS for 20 min at 50°C, and rinsed three times in 1x SSC at 50°C and, finally, once in 0.2x SSC at room temperature. The slides were dried by centrifugation at 900 rpm for 5 min.

source_name: ACE2 knockout strain (MK106) hyphal

tag: Hyphally induced in YPD+10% FCS @ 37C

source_name: Wildtype strain (SC5314) hyphal

label_protocol: As for Channel 1, but using  37.5 µM Cy3-dCTP (Amersham)


title: Hyphal Replicate #3


title: Hyphal Replicate #4


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 9207

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-105

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 6975

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-41


title: Hyphal Replicate #2


title: IP fraction of ChIP-Chip sample from Cmyc tagged TBPb, Halobacterium  GTF growth curve experiment, Array 6974


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 6971


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 8656

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-102


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 8665

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-103


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 8666

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-104

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36


title: Hyphal Replicate #1

hyb_protocol: Before hybridization, one of the labeled cDNA samples was resuspended in 45 ul of hybridization buffer (1x Dig Ease buffer [Roche] containing 0.5 mg ml-1 baker's tRNA and 0.5 mg ml-1 salmon sperm DNA) and then added to the second labeled cDNA. The mixture was heat denatured at 95C for 2 min, quickly cooled on ice, applied to the DNA microarray, and covered with a 24-mm by 60-mm coverslip. Slides were placed in a hybridization chamber (Corning, Palo Alto, CA) with 9 ul of 3x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) in each of the wells and incubated at 37C for 16 h by immersion in a water bath. Following hybridization, the slides were immersed in 1x SSC at 50C until the coverslip fell off, washed twice for 15 min each in 1x SSC-0.1% sodium dodecyl sulfate (SDS) at 50C and once in 0.1x SSC-0.1% SDS for 20 min at 50C, and rinsed three times in 1x SSC at 50C and, finally, once in 0.2x SSC at room temperature. The slides were dried by centrifugation at 900 rpm for 5 min.

scan_protocol: The microarrays were scanned using an Axon 4000B scanner at a 10 micrometer resolution

label_protocol: Twentyfive micrograms of total RNA was labeled in a total volume of 40 microlitres including 5 ng LuxA control RNA (Eurogentec), 1x first-strand buffer (Invitrogen), 0.2 pmol C. albicans-specific primer (Eurogentec), 1.5 mM (each) dATP, dTTP, and dGTP, 25 uM dCTP, 10 mM dithiothreitol, 1 ul RNasin, and 37.5 uM Cy5-dCTP (Amersham). The mixture was incubated at 65C for 5 min and then at 42C for 5 min. One microliter of RNasin (Promega) and 1 ul Superscript II reverse transcriptase (Invitrogen) were added and incubated at 42C for 1 h. Following the addition of another 1 ul of Superscript II, the incubation was continued for 1 h at 42C. The reaction was stopped by the addition of 5 mM EDTA, pH 8.0, and 0.5 M NaOH and incubation at 65C for 20 min and was neutralized by adding 0.5M acetic acid. The labeled cDNAs were purified using a QIAquick PCR purification kit (QIAGEN) and concentrated by drying under vacuum to a volume of approximately 2 ul.

label_protocol: As for Channel 1, but using  37.5 uM Cy3-dCTP (Amersham)


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 6965

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


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8601

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-97


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 8598

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBf

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-96


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBe, Halobacterium  GTF growth curve experiment, Array 8603

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBe

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-99

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBe grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBe

tag: whole cell extract of CCmyc tagged transcription factor TFBe grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8596

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-94

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBe, Halobacterium  GTF growth curve experiment, Array 8597

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-95


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8602

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-98


title: IP fraction of ChIP-Chip sample from Cmyc tagged TBPb, Halobacterium  GTF growth curve experiment, Array 8243

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-92

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 6966


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 6970

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBg, Halobacterium  GTF growth curve experiment, Array 8595

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-93

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 8604

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-100

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBf grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBf

tag: whole cell extract of CCmyc tagged transcription factor TFBf grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TBPb, Halobacterium  GTF growth curve experiment, Array 8239

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-90

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 8651

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-101


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 8062

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBc

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-89

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBc grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBc

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

tag: whole cell extract of CCmyc tagged transcription factor TFBc grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TBPb, Halobacterium  GTF growth curve experiment, Array 8242

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-91


title: TTE3 cells cultured at nonpermissive temperature for 24 h-2

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were cultured at nonpermissive temperature 39°C for 24 h.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: phycoerythrin

organism: Mus musculus

source_name: Mouse testicular Sertoli cell line TTE3

label_protocol: 5 μg of total RNA was used to synthesize double-strand cDNA with a GeneChip® Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). Biotin-labeled cRNA was then synthesized from the cDNA using GeneChip® Expression 3’-Amplification Reagents for IVT Labeling (Affymetrix).

extract_protocol: Total RNA was extracted from the cells using an RNeasy Total RNA Extraction Kit (Qiagen K.K., Tokyo, Japan). Then, RNA samples were treated with RNase-free DNase.

tag: Mouse testicular Sertoli cell line TTE3


title: TTE3 cells cultured at nonpermissive temperature for 12 h-1

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were cultured at nonpermissive temperature 39°C for 12 h.


title: TTE3 cells cultured at nonpermissive temperature for 12 h-2


title: TTE3 cells cultured at nonpermissive temperature for 24 h-1


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 8061

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-88


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBb, Halobacterium  GTF growth curve experiment, Array 8057

description: IP sample of Cmyc tagged TFBb expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBb grown to OD600 between 1.0 and 1.3 in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBb

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-84

growth_protocol: Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBb grown to OD600 between 1.0-1.3 in standard growth media with 20microgram/ml mevinolin

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBb grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBb

tag: whole cell extract of CCmyc tagged transcription factor TFBb grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBb, Halobacterium  GTF growth curve experiment, Array 8058

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-85


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 8060

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-87

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBc, Halobacterium  GTF growth curve experiment, Array 8059

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-86


title: TTE3 cells cultured at nonpermissive temperature for 6 h-1

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were cultured at nonpermissive temperature 39°C for 6 h.


title: TTE3 cells cultured at nonpermissive temperature for 0 h-2

description: A mouse testicular Sertoli cell line, TTE3, derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen was used. TTE3 cells were cultured at nonpermissive temperature 39°C for 0 h.


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 8023

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-83


title: TTE3 cells cultured at nonpermissive temperature for 6 h-2


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 8021

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-81


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBf, Halobacterium  GTF growth curve experiment, Array 8020

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-80

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38


title: TTE3 cells cultured at nonpermissive temperature for 0 h-1


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBb, Halobacterium  GTF growth curve experiment, Array 7967

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-78


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7965

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TFBa

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-76

tag: IP sample of ChIP-Chip experiment of plasmid based expression of Cmyc tagged transcription factor TFBa grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3

source_name: Halobacterium NRC1, whole cell extract (wce) from Cmyc tagged TFBa

tag: whole cell extract of CCmyc tagged transcription factor TFBa grown in standard growth media with mevinolin to OD600 between 1.0 and 1.3


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBb, Halobacterium  GTF growth curve experiment, Array 7968

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-79

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium  GTF growth curve experiment, Array 7962

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-73


title: IP fraction of ChIP-Chip sample from Cmyc tagged TFBa, Halobacterium  GTF growth curve experiment, Array 7963

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-74

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39


title: IP fraction of ChIP-Chip sample from Cmyc tagged TBPb, Halobacterium  GTF growth curve experiment, Array 6977

source_name: Halobacterium NRC1, IP fraction of ChIP-Chip sample from Cmyc tagged TBPb

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-43

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36