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| Status |
Public on Mar 15, 2018 |
| Title |
D03: B2C, biol. repl. 1 |
| Sample type |
SRA |
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| Source name |
B2C (blood-C+Y, 5min)
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| Organism |
Streptococcus pneumoniae D39 |
| Characteristics |
strain: D39
tissue: cultured monoclonal bacteria
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| Growth protocol |
D39 was pre-cultured before innoculation in aforementioned liquid medium. After certain period, the cells were harvested for total RNA.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were harvested following phenol-chloroform separation, gDNA digestion and alcohol precipitation
Library were prepared according to manufacturer's protocol (Illumina), keeping stranded information
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
D03
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| Data processing |
trimming with Trimmomatic 0.36, single end mode, removing adapter sequences
alignment using STAR 2.5.3a, alignIntronMax 1
counting with featureCount from subread 1.5.3
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| Submission date |
Dec 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Rieza Aprianto |
| E-mail(s) |
[email protected]
|
| Phone |
+31503632409
|
| Organization name |
University of Groningen
|
| Department |
Molecular Genetics Department
|
| Lab |
Veening
|
| Street address |
Nijenborg 7
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| City |
Groningen |
| State/province |
Groningen |
| ZIP/Postal code |
9747AG |
| Country |
Netherlands |
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| Platform ID |
GPL24384 |
| Series (1) |
| GSE108031 |
High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions |
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| Relations |
| BioSample |
SAMN08169362 |
| SRA |
SRX3467963 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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