GEO DataSets

(Submitter supplied) RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation of heterocysts in filamentous cyanobacteria is an example of cell differentiation in prokaryotes. Although multiple non-coding transcripts are involved in this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation of RNA-protein complexes after RNase treatment in density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates in Nostoc sp. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Other

Platform:

GPL35010

6 Samples

Download data: XLSX

(Submitter supplied) Deletion of the global transcription factor PacR in Anabaena triggers heterocyst formation even in NO3- containing medium, likely due to impaired NO3- uptake and disrupted NH4+ assimilation in the GOGAT cycle. This phenotype may be exacerbated by reduced PSI-yield and reduced expression of ferredoxin, which may lead to less reducing equivalents for nitrogen uptake and fixation. These results highlight PacR’s role as a global regulator of carbon metabolism and photosynthesis while also establishing its involvement in regulating nitrogen metabolism.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35023

18 Samples

Download data: TXT

(Submitter supplied) In order to examine the response of Anabaena sp. PCC 7120 to an infection of the Cyanophage A1, we have used customized microarrays to identify genes potentially up- or downregulated by the infection. For this we compared cell culture before and after infection.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by array

Platform:

GPL25601

4 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analyses using high-throughput methods have revealed abundant antisense transcription in bacteria. Most frequently, antisense transcription is due to the overlap of mRNAs with long 5’ regions or 3’ ends that extend beyond the coding sequence. In addition, antisense RNAs that do not contain any coding sequence are also observed. Nostoc sp. PCC 7120 is a filamentous cyanobacterium that, under nitrogen limitation, behaves as a multicellular organism with division of labor among two different cell types that depend on each other, the vegetative CO2-fixing cells and the nitrogen-fixing heterocysts. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29232

6 Samples

Download data: GFF, TXT

(Submitter supplied) To investigate the function of All0854, we constructed the all0854 deletion mutant Mall0854, in which all0854 was knocked out by CRISPER-cpf1. We then performed gene expression profiling analysis using data obtained from RNA-seq of wide type Nostoc sp. PCC 7120 and Mall0854.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32888

6 Samples

Download data: FA, TXT

(Submitter supplied) To examine Alr3614 influence on the expression of Anabaena sp. PCC 7120, we have used customized microarrays to identify genes potentially regulated by this short DNA-binding protein. We compared the expression of an Alr3614-deletion strain with an Alr3614-complementation strain.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by array

Platform:

GPL25601

4 Samples

Download data: TXT

(Submitter supplied) As compared to Eukaryotes, Bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs, which are thought to act in concert for the maintenance of gene translation. Here we show that in some bacteria the tRNA gene set may be partitioned in a housekeeping sub-set that sustains translation, and an inducible one that is generally silent but can be largely induced to provide functionality under particular conditions. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29232

12 Samples

Download data: TSV

(Submitter supplied) Cell-cell communication is an essential attribute of multicellular organisms. We studied the effects of perturbed communication in multicellular filaments of mutant derivatives of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120, in which septal proteins were deleted. Filaments of sepJ and sepJ/fraC/fraD deleted strains showed marked differences in growth, pigment absorption spectra and spatial patterns of expression of the hetR gene encoding a master regulator of heterocyst differentiation. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29375

24 Samples

Download data: TXT

(Submitter supplied) In order to identify possible RNAs regulated by small RNA NsiR3 we have analyzed the responses to nitrogen removal in a mutant lacking nsiR3 (ΔnsiR3). RNA samples were isolated from cells growing in the presence of combined nitrogen (ammonium) or after 8 h of nitrogen deprivation.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by array

Platform:

GPL25601

4 Samples

Download data: TXT

(Submitter supplied) In order to analyze the responses of a heterocystous cyanobacterium to combined-nitrogen depletion/addition, we have used customized microarrays to identify genes potentially involved in heterocysts differentiation by comparing the responses in the control strain and a hetR mutant unable to differentiate heterocysts. RNA samples were isolated from cells growing in the presence of combined nitrogen (ammonium) or after 6, 8, 12 or 24 h of nitrogen deprivation. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by array

Platform:

GPL25601

20 Samples

Download data: TXT

(Submitter supplied) The whole regulon of the LTTR All3953 was determined at 3 h after Ci deficiency in the cyanobacterium Anabaena sp. PCC 7120 by ChIP-Seq analysis. A TAP-tagged version of the protein was used for the chromatin immunoprecipitation. A total of 142 peaks were found, mainly located in the chromosome of Anabaena.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11645

4 Samples

Download data: BED, TXT

(Submitter supplied) We employed chromatin pull-down and deep sequencing to globally identify HetR DNA targets in vivo at 6 hours after fixed-nitrogen deprivation. We identified novel DNA binding targets of tagged HetR-6xHis and defined a consensus HetR binding site from these HetR target sequences.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17863

2 Samples

Download data: TXT

(Submitter supplied) Here, we report the transcriptome of Anabaena sp. strain 7120, a cyanobacterium that forms specialized nitrogen-fixing cells called heterocysts. Our data suggests that cyanobacteria frequently have more complex transcripts than thought, with large 5' UTRs, numerous antisense transcripts, and multiple transcriptional start sites or processing sites.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11645

4 Samples

Download data: BAM

(Submitter supplied) Anabaena PCC7120 array for all features Arrays of this design have barcodes that begin with 16062842 or 2562842. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. more...

Organism:

Nostoc sp. PCC 7120 = FACHB-418

4 Series

32 Samples

Download data: TXT