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| Status |
Public on May 01, 2023 |
| Title |
Mall0854_3 |
| Sample type |
SRA |
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| Source name |
cyanobacterial cells
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| Organism |
Nostoc sp. PCC 7120 = FACHB-418 |
| Characteristics |
cell type: cyanobacterial cells
genotype: all0854 knockout
treatment: normal laboratory culture conditions
growth phase: logarithmic phase
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| Growth protocol |
Nostoc sp. PCC 7120 and its derivative Mall0854 were incubated with constant illumination (light density of 30 μmol·m-2·s-1) in BG11 medium. Cultures in flasks were shaken at 180 rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the hot phenol procedure. The quality of RNA samples was examined by Agilent 2100 Bioanalyzer (Agilent Technologies, PaloAlto, CA, USA), and the RNA integrity numbers (RIN) of all the samples were between 7.9–8.3.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Kit (Illumine, San Diego, CA, USA) following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
The reads matched to rRNA were removed by SOAP v2.21 (parameters: -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).
The adapter sequences and low-quality reads (those with more than 5% unknown bases or more than 20% of bases of which the quality scores were lower than 10) were discarded.
Trimmed sequence reads were mapped to Nostoc sp. PCC 7120 = FACHB-418 using Bowite2 v2.2.5 (parameters: -q–phred64 –sensitive –dpad 0 –gbar 99,999,999 –mp 1,1 –np 1 –score-min L,0, -0.1 -I 1 -X 1000 –no-mixed –no-discordant -p 1 -k 200)
Read count extraction and normalizaiton were performed using RSEM v1.2.12 (parameters: --forward-prob=0.0).
Assembly: Nostoc sp. PCC 7120 = FACHB-418
Supplementary files format and content: tab-delimited excel files include FPKM values for each Sample
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| Submission date |
Nov 28, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Zi-Qian Wang |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of Microbiology, Chinese Academy of Sciences
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| Street address |
NO.1 Beichen West Road, Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL32888 |
| Series (1) |
| GSE218875 |
Effect of deletion of all0854 on gene expression of Nostoc sp. PCC 7120 |
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| Relations |
| BioSample |
SAMN31891316 |
| SRA |
SRX18397558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6758094_Mall0854_3.gene.FPKM.txt.gz |
60.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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