 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 11, 2021 |
| Title |
SM-28_2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Stenotrophomonas maltophilia |
| Characteristics |
strain: ATCC13637
growth phase: Mid log
growth temperature: 28 °C
|
| Growth protocol |
S. maltophilia strain MTCC 434T which is equivalent to the ATCC 13637T was grown in the 20 ml Luria Bertani Broth, Miller in 100 ml Erlenmeyer flask at either 37 °C and 28 °C under constant agitation at 200 RPM. Samples were withdrawn at intervals for optical density monitoring at 600 nm (OD600) and cells from both cultures were harvested at the mid log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by harvesting the cells and lysis by using TRIzol. Follwed by phase seperation and Dnase tretemnt using Direct-zol RNA MiniPrep kit (Zymo Research Corporation, Orange, CA, USA).
ScriptSeq complete kit (Epicenter, Illumina, Madison, WI USA) which is combined kit for the ribosomal (rRNA) depletion Ribo-Zero™ Kit (Bacteria) (Epicenter, Illumina, Madison, WI USA) and cDNA library construction kit ScriptSeq™ v2 RNA-Seq library preparation kit (Epicenter, Illumina, Madison, WI USA) was used as per manufacturer's guidlines.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Total RNA was isolated by growing cells at 28 °C and harvesting cells at mid log phase
|
| Data processing |
Basecalling, demultiplication and adaptor treaming was performed by Illumina MiSeq control software.
Quality of raw reads was assessed by using FastQC toolkit.
Aligning reads to the reference genome of S. maltophilia ATCC 13637 (NZ_CP008838) by using the Bowtie 2 (Langmead and Salzberg, 2012). The aligned SAM files generated by bowtie were sorted using samtools v1.4.1 (Li et al., 2009). The obtained BAM files were used as input to cufflinks v2.2.1 (Trapnell et al., 2013; Trapnell et al., 2012; Trapnell et al., 2010), which was used to assemble transcripts with FPKM (fragments per kilobase of transcript per million mapped reads) values. The data files for the replicates were merged into single transcript with Cuffmerge and differential gene expression was between both conditions was performed using the Cuffdiff, a packages of the cufflinks v2.2.1 (Trapnell et al., 2013; Trapnell et al., 2012; Trapnell et al., 2010).
Genome_build: NZ_CP008838
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each condition.
|
| |
|
| Submission date |
Jul 26, 2017 |
| Last update date |
May 11, 2021 |
| Contact name |
Prabhu B Patil |
| E-mail(s) |
[email protected]
|
| Organization name |
CSIR Institute of Microbial Technology Chandigarh
|
| Lab |
Bacterial Genomics and Evolution
|
| Street address |
Sector 39 A
|
| City |
Chandigarh |
| State/province |
Chandigarh |
| ZIP/Postal code |
160036 |
| Country |
India |
| |
|
| Platform ID |
GPL23835 |
| Series (1) |
| GSE101926 |
Global transcriptome analysis of Stenotrophomonas maltophilia in response to human body temperature |
|
| Relations |
| SRA |
SRX3040314 |
| BioSample |
SAMN07405720 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2718892_SM-28_2.txt.gz |
136.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
