|
| Status |
Public on May 08, 2024 |
| Title |
Myco Feriruminatoris 1_a |
| Sample type |
SRA |
| |
|
| Source name |
mycoplasma
|
| Organism |
Mycoplasma feriruminatoris |
| Characteristics |
cell type: mycoplasma
genotype: WT
treatment: Untreated
|
| Treatment protocol |
The cultures were untreated while growing.
|
| Growth protocol |
Grown in suspension at 37˚C in Hayflick media until exponential phase.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells separated from supernatant by centrifugation at 10,000 rpm and washed 3 times in PBS 1x. Bacterial pellet treated with RLT buffer (Rneasy kit, Qiagen) supplemented with 1:100 beta-mercaptoethanol. The rest of the protocol was followed as per the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
polyA-selected stranded RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Alignment to the reference genome using bowtie2 v. 2.3.5
SAM to BAM convertion using using samtools v. 1.9
Fragment counts per annotation region were computed using bedtools
Strand-specific per-base coverage was computed using bedtools
Assembly: NZ_CP091032.1
Supplementary files format and content: Files with raw read count and Transcripts per million (TPM) based on fragment count
|
| |
|
| Submission date |
Oct 20, 2023 |
| Last update date |
May 08, 2024 |
| Contact name |
Ludovica Ciampi |
| E-mail(s) |
ludovica.ciampi@crg.eu
|
| Phone |
657927674
|
| Organization name |
Centre for Genomic Regulation
|
| Street address |
Carrer del Doctor Aiguader 88
|
| City |
Barcelona |
| State/province |
Choose a State or Province |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL33858 |
| Series (1) |
| GSE245952 |
Mycoplasma feriruminatoris transcriptome |
|
| Relations |
| BioSample |
SAMN37909731 |
| SRA |
SRX22159491 |
