|
| Status |
Public on Jan 29, 2021 |
| Title |
MFC-3 [RNA-seq K] |
| Sample type |
SRA |
| |
|
| Source name |
microbial fuel cell sample
|
| Organism |
Lysinibacillus varians |
| Characteristics |
strain: GY32
electron donor: Acetate
electron acceptor: Electrode in microbial fuel cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were collected, frozen in liquid nitrogen, and RNA was extracted by TRIzol-based method. Illumina TruSeq RNA Sample Prep Kit v2 (San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
FastQC (version 0.11.2) were used to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. Sequenced reads were trimmed for adaptor sequence with Trimmomatic (version 0.36), then mapped to the reference genome using Bowtie2 (version 2.3.2) with parameters‘-l 28 -n 2 -e 250 -M 1–best
The clean data were mapped on the annotated genomic objects identified in the genome of Lysinibacillus varians GY32 using TopHat (v2.0.11) and SAMtools (v0.1.18.0), yielding BAM files. Sorted and indexed BAM files were analyzed by Cufflinks (v2.0.0) to calculate the number of fragments per kilobase of transcript per million mapped reads (FPKM) and Transcripts Per Million (TPM) for all genes.
Genome_build: ASM60010v1
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include TPM and FPKM values.
|
| |
|
| Submission date |
Jan 28, 2021 |
| Last update date |
Jan 31, 2021 |
| Contact name |
kong guannan |
| E-mail(s) |
[email protected]
|
| Phone |
13822114616
|
| Organization name |
Guangdong Institute of Microbiology
|
| Street address |
100 Martyrs Central Road
|
| City |
Guang zhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL29670 |
| Series (2) |
| GSE165753 |
Transcriptomic analyses of Lysinibacillus varians GY32 respiring with electrode or oxygen [RNA-seq K] |
| GSE165755 |
Transcriptomic analyses of Lysinibacillus varians GY32 respiring with electrode or oxygen |
|
| Relations |
| BioSample |
SAMN17619841 |
| SRA |
SRX9973821 |
