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| Status |
Public on Nov 05, 2024 |
| Title |
6.6._CS_t=1 |
| Sample type |
SRA |
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| Source name |
all cells
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| Organism |
Nostoc sp. PCC 7120 = FACHB-418 |
| Characteristics |
tissue: all cells
cell type: all cell types
genotype: Anabaena sp. PCC7120 strain CSS77 containing C.S3 gene cassette
treatment: NO3- containing medium, 1h
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| Treatment protocol |
Experimental cultures were generated similar to precultures, however cells were harvested by filtration and washed twice with the new medium, and then grown in BG110 medium (pH 7.5) supplemented with either 3mM NH4+ or 17.6 mM NO3- as the nitrogen source.
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| Growth protocol |
The ΔpacR deletion mutant of the Anabaena sp. PCC7120 wild type strain (CSS74) and control strain with a spectinomycin resistance cassette (CSS77) were described previously (Picossi et al., 2015). The starting cultures were maintained in BG11 medium buffered with 20 mm HEPES-NaOH (pH 7.5) and supplemented with 25 ug/ml of spectinomycin. The cultures were grown at 30°C with 1% CO2, ~50 µmol photons m-2 s-1, and agitated at 80 rpm. Pre-cultures were generated by harvesting cells from starting cultures after 4 days and resuspending cells at OD750=0.1. Cells were then grown for 4 days in BG110 medium buffered with 20 mm HEPES-NaOH (pH 7.5) supplemented with 6mM NH4Cl on day 0, and additional 3mM NH4Cl was supplemented on days 2 and 3.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the hot-phenol method. DNAse treatment was performed with the Invitrogen kit. RNA concentration was measured with DS-11+ spectrophotometer (DeNovix) and 3ug of RNA from each sample was sent to BGI (China) for RNA-sequencing.
Library construction was performed as a service by BGI
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Data processing |
The sequencing platform used was DNBseq with a read length of PE 100bp. After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads (via the SOAPnuke software from BGI as a service).
The provided data was analyzed via the Chipster software
Initial Trimming of reads with FastX was performed
Alignment with TopHat2 for paired end reads and own genome (library type: first-strand, expected inner distance between mate pairs: 24, ignore novel junctions: yes, Sanger Phred+33, standard deviation for the inner distances between mate pairs: 85, how many hits is a read allowed to have: 20, number of mismatches allowed in final alignment: 2, minimum anchor length: 8, maximum number od mismatches allowed in anchor: 0, minim intron length: 70, maximum intron length: 500000, report only paired alignments: yes)
aligned reads per genes were counted with HTSeq using own GTF file (mode to handle reads overlapping more than one gene: union, minimum alignment quality: 10, feature type to count: exon, feature ID to use: gene_id)
Differential expression was analyzed using DESeq2 (cutoff p-value: 0.05, method for estimating size factors: ratio)
For experiential quality control, PCA analysis was performed. Principal component 1 (PC1) accounts for 83-86% of variance between the CS and ΔpacR replicates. When comparing CS or ΔpacR data between timepoints, 90-93% of variance was accounted for by PC1.
gene-body coverage at the 5’ end was higher than at the 3’ end, which could point towards a sequencing-bias in favor of the 5’ end of the RNA
Assembly: nostoc_sp_pcc_7120_fachb_418_gca_000009705, version ASM970v1_, current ENSEMBL release (October 2023)
Supplementary files format and content: tab-delimited text file with raw counts for each sample
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| Submission date |
Oct 27, 2024 |
| Last update date |
Nov 05, 2024 |
| Contact name |
Yagut Allahverdiyeva |
| E-mail(s) |
[email protected]
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| Organization name |
Turku University
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| Department |
Life Sciences
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| Lab |
Photomicrobes
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| Street address |
Tykistönkatu 6A
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| City |
Turku |
| ZIP/Postal code |
20520 |
| Country |
Finland |
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| Platform ID |
GPL35023 |
| Series (1) |
| GSE280386 |
The role of the LysR-type transcription factor PacR in regulating nitrogen metabolism in Anabaena sp. PCC7120 |
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| Relations |
| BioSample |
SAMN44467243 |
| SRA |
SRX26512702 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8596562_Count_14.txt.gz |
172.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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