txid29292[Organism] - GEO DataSets - NCBI

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Items: 19

Select item 2000581311.

RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.

(Submitter supplied) The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. more...

Organism:: Pyrococcus abyssi

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL18745
1 Sample

Download data: GFF

Series

Accession:: GSE58131

ID:: 200058131

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000041042.

Origin of replication for Pyrococcus abyssi by ChIP-chip

(Submitter supplied) Recent advances in the study of archaeal DNA replication have uncovered defined replication origins (oriC) and demonstrated specific binding of the Cdc6/Orc1 protein and Mcm helicase to oriC in vivo and/or in vitro. The oriC of the hyperthermophilic archaeon Pyrococcus abyssi is characterized by 13 bp repeats, AT-rich regions and an inverted repeat whose precise roles remain unclear. We report here that the 13 bp repeats are widespread in the three Pyrococcus genomes. more...

Organism:: Pyrococcus abyssi

Type:: Genome binding/occupancy profiling by genome tiling array

Platform:: GPL3384
14 Samples

Download data: PDF, TXT

Series

Accession:: GSE4104

ID:: 200004104

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 1000187453.

Illumina Genome Analyzer IIx (Pyrococcus abyssi)

Organism:: Pyrococcus abyssi

1 Series
1 Sample

Platform

Accession:: GPL18745

ID:: 100018745

Select item 1000033844.

Origin of replication for Pyrococcus abyssi by ChIP-chip

(Submitter supplied) Chromatin immunopreciptation coupled with hybridization on a whole genome microarray (ChIP-chip) of P. abyssi. Protocol: Microarray preparation. The P. abyssi genome was divided into 353 regions, each of which is 5 kb in length. Each of the 353 DNA regions has a specific ID number. For example, the microarray region 25 corresponds to the genome coordinates 120 000 to 125 000. For the microarrays, each of the 353 regions was amplified with the BD Advantage 2 PCR kit (BD biosciences clontech). more...

Organism:: Pyrococcus abyssi

1 Series
14 Samples

Platform

Accession:: GPL3384

ID:: 100003384

PubMed Full text in PMC Similar studies

Select item 3014014885.

Organism:: Pyrococcus abyssi

Source name:: cells

Platform:: GPL18745
Series:: GSE58131

Download data: GFF

Sample

Accession:: GSM1401488

ID:: 301401488

SRA Run Selector

Select item 3000936286.

Mcm/ exponential phase/ replica 4

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in exponential phase, fourth replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in exponential phase, fourth replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93628

ID:: 300093628

Select item 3000936277.

Mcm/ exponential phase/ replica 2

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in exponential phase, second replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in exponential phase, second replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93627

ID:: 300093627

Select item 3000936268.

Mcm/ exponential phase/ replica 1

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in exponential phase, first replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in exponential phase, first replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93626

ID:: 300093626

Select item 3000936259.

Mcm/ stationary phase/ replica 4

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, fourth replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in stationary phase, fourth replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93625

ID:: 300093625

Select item 30009362410.

Mcm/ stationary phase/ replica 3

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, third replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in exponential phase, third replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93624

ID:: 300093624

Select item 30009362311.

Mcm/ stationary phase/ replica 2

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, second replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in stationary phase, second replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93623

ID:: 300093623

Select item 30009362212.

Mcm/ stationary phase/ replica 1

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Mcm antibody and archaebacteria in stationary phase, first replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in stationary phase, first replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93622

ID:: 300093622

Select item 30009362113.

Cdc 6/exponential phase replica 4

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, fourth replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in exponential phase, fourth replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93621

ID:: 300093621

Select item 30009362014.

Cdc 6/exponential phase replica 2

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, second replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in exponential phase, second replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93620

ID:: 300093620

Select item 30009361915.

Cdc 6/exponential phase replica 1

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in exponential phase, first replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in exponential phase, first replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93619

ID:: 300093619

Select item 30009361816.

Cdc 6/stationary phase replica 4

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, fourth replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in stationary phase, fourth replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93618

ID:: 300093618

Select item 30009361717.

Cdc 6/stationary phase replica 2

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, second replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in stationary phase, second replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93617

ID:: 300093617

Select item 30009361618.

Cdc 6/stationary phase

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria in stationary phase, first replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated in stationary phase, first replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93616

ID:: 300093616

Select item 30009356519.

Cdc 6/puromycin

Organism:: Pyrococcus abyssi

Source name:: ChIP co-immunoprecipitated DNA using Cdc 6 antibody and archaebacteria treated with puromycin, fourth replica (channel 1) DNA from mock-treated cell extract and archaebacteria treated with puromycin, fourth replica (channel 2)

Platform:: GPL3384
Series:: GSE4104

Sample

Accession:: GSM93565

ID:: 300093565

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