|
| Status |
Public on May 01, 2024 |
| Title |
Cyano EM_2 |
| Sample type |
SRA |
| |
|
| Source name |
total cell
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
tissue: total cell
cell type: wild type
treatment: Erythromycin
|
| Treatment protocol |
with and without erythromycin
|
| Growth protocol |
BG11 medium cultured for 7 day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent (Life Technologies, Carlsbad, CA, USA) was used to extract RNA
In brief, RNA strand-specific RNA-Seq libraries were created using the QIAseq FastSelect RNA removal and QIAseq stranded total RNA library preparation kits (QIAGEN).
QIAseq stranded total RNA library preparation kits (QIAGEN
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Cyano EM_2: The Synechocystis cultivation under BG-11 with 5 µM of erythromycin addition_replicated 2
|
| Data processing |
cDNA libraries were quantified using a DeNovix fluorometer (DeNovix).
Pair-end 125 nucleotides read sequencing on an Illumina HiSeq sequencer was done with cluster creation.
The quality of the raw read data was examined using the FASTQC software.
Fastp software was used to delete adapters and low-quality reads.
Salmon software was used to compare high-quality reads to the reference genome sequence (Synechocystis sp. PCC 6803, accession number: ASM972v1). DESeq2 was used for the differential gene expression analysis (FDR 0.05, log2 fold change > 1.0)
Assembly: mm10, Synechocystis sp. PCC 6803, accession number: ASM972v1
Supplementary files format and content: fold-change
Supplementary files format and content: fold-change of transcript level
|
| |
|
| Submission date |
Feb 23, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Jidapa Leksingto |
| E-mail(s) |
[email protected]
|
| Phone |
0972405377
|
| Organization name |
Chulalongkorn
|
| Street address |
254
|
| City |
Bangkok |
| ZIP/Postal code |
10330 |
| Country |
Thailand |
| |
|
| Platform ID |
GPL28944 |
| Series (1) |
| GSE256451 |
Erythromycin mediates co-flocculation between cyanobacterium Synechocystis sp. PCC 6803 and filamentous fungi in liquid cultivation without organic compounds [C and CE] |
|
| Relations |
| BioSample |
SAMN35628456 |
| SRA |
SRX20644582 |
