|
| Status |
Public on Jun 30, 2024 |
| Title |
Aca2 |
| Sample type |
SRA |
| |
|
| Source name |
strain Aca13
|
| Organism |
Acinetobacter calcoaceticus |
| Characteristics |
strain: strain Aca13
treatment: control
|
| Treatment protocol |
Acinetobacter calcoaceticus strain Aca13 was incubated in the fresh LB broth until logarithmic growth period, add hexadecane or naphthalene, respectively. RNA protect-Bacteria- Reagent was used to protect RNA after 3 hours induction. Then bacteria were collected for total RNA extraction.
|
| Growth protocol |
LB
|
| Extracted molecule |
total RNA |
| Extraction protocol |
extraction of total RNA, detection of RNA integrity and total RNA content, then remove Ribosome RNA (rRNA) from total RNA to obtain mRNA. Subsequently, a fragmentation buffer was added to randomly break the obtained mRNA into short fragments and construct the library in a chain specific manner.
The cDNA libraries for RNA sequencing were constructed according to the chain specific library by the NEBNext Ultra Directional RNA Library Prep Kit for (Illumina) as per manufacturer’s instructions (NEB #E7420S)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Rockhopper was used to identify novel genes, operon, transcription start site (TSS), transcription terminal site (TTS) and Cis-natural antisense transcripts
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of Acinetobacter calcoaceticus strain Aca13 induced with substrates was performed using the DESeq R package.
KOBAS software was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: NZ_CP088954
Supplementary files format and content: bam file includes processed data file for each sample.
Supplementary files format and content: raw file includes raw data file for each sample.
|
| |
|
| Submission date |
Jun 23, 2023 |
| Last update date |
Jun 30, 2024 |
| Contact name |
Tingdi Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Jilin University
|
| Department |
college of new energy and environment
|
| Street address |
2519 Jiefang Road
|
| City |
Changchun city |
| State/province |
Jilin Province |
| ZIP/Postal code |
130021 |
| Country |
China |
| |
|
| Platform ID |
GPL33521 |
| Series (1) |
| GSE235642 |
Whole transcriptome analysis of Acinetobacter calcoaceticus Aca13 induced by n-hexadecane or naphthalene |
|
| Relations |
| BioSample |
SAMN35848693 |
| SRA |
SRX20759484 |
