|
| Status |
Public on Jul 14, 2011 |
| Title |
[E-MTAB-502] ICC169-476, 3601_1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA from Citrobacter rodentium ICC169-476
|
| Organism |
Citrobacter rodentium |
| Characteristics |
material type: whole_organism
genotype: wild_type
|
| Growth protocol |
grow | Citrobacter rodentium strains were grown at 37 degrees C in Luria-Bertani (LB) medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
nucleic_acid_extraction | The whole genome transcriptome of Citrobacter rodentium ICC169-476 was sequenced using Illumina sequencing technology as previously described (Croucher NJ et al. (2009) A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res 37: e148). Removal of genomic DNA from the RNA sample and subsequent successful cDNA generation was confirmed by PCR using the four primer pairs NKP125-132 that generate amplicons internal to C. rodentium housekeeping genes.
sequencing | cDNA was made into a standard Illumina library with a fragment size of 200 to 250 bp. Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
bioassay_data_transformation | SRF files were generated using the standard method for the Illumina platform. Base calling was performed with phred quality scores at 64 levels using Illumina pipeline v1.3.4. There were 54 cycles of sequencing with 1 read per cluster.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Performer: SC
|
| Data processing |
processed data not provided
|
| |
|
| Submission date |
Jul 12, 2011 |
| Last update date |
May 15, 2019 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
[email protected]
|
| Lab |
ArrayExpress
|
| Street address |
Wellcome Trust Genome Campus
|
| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13894 |
| Series (1) |
| GSE30610 |
[E-MTAB-502] Citrobacter rodentium transcriptomics (Regulation) |
|
| Relations |
| SRA |
ERX009857 |
