|
| Status |
Public on Sep 25, 2020 |
| Title |
Glyc_spo rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: 972h-
carbon source: Glycerol : sodium acetate (10 :1) 2%(w/v)
age: mid exponential growth culture
|
| Treatment protocol |
YE medium was used changed carbon source in each treatment : glucose 2% and Glycerol : sodium acetate (10 :1) 2%(w/v)
|
| Growth protocol |
liquid culture were incubated to mid exponential growth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in log phase and RNA later added and harvested to 5000g for 5 min. Pellet were frozen on -80°C. RNA was harvested using Trizol reagent and precipitated with isopropyl alcohol, samples were treated with DNAses an concentrate with RNA cleaner kit. RRNA were removed with Ribominus bacteria /yeast kit and Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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 NextSeq 500 |
| |
|
| Data processing |
Base-calling with bcl2fastq2-2.15
alignment done with bowtie version 0.12.7
filter and manipulation with samtools 1.3
Frecuency count htseq-count version 0.6.0.
last filter bedtools v2.25.0
Genome_build: E. coli K-12 MG1655 and S. pombe 972 h-
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest
|
| |
|
| Submission date |
Sep 26, 2019 |
| Last update date |
Sep 25, 2020 |
| Contact name |
Veronica Jimenez-Jacinto |
| E-mail(s) |
vjimenez@ibt.unam.mx
|
| Phone |
+52(777) 3291719
|
| Organization name |
Universidad Nacional Autonoma de Mexico
|
| Department |
Unidad Universitaria de Secuenciación Masiva y Bioinformática
|
| Street address |
Av. Universidad 2001. Col. chamilpa
|
| City |
Cuernavaca |
| State/province |
Morelos |
| ZIP/Postal code |
62130 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE138088 |
Comparative analysis of global transcriptional profile of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth: Inferring the evolution of analog circuits of post-transcriptional regulation |
|
| Relations |
| BioSample |
SAMN12859052 |
| SRA |
SRX6913126 |
