|
| Status |
Public on Nov 02, 2018 |
| Title |
Impact of Escherichia coli K12 and O18 on human platelets: effects on platelet activation, spliced platelet RNAs and proteins |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We report RNA-sequencing data of 12 platelet samples isolated from four healthy individuals and incubated with either E. coli K12, E. coli O18 or no bacteria. This dataset highlights the differential effect of bacteria on spliced platelet RNA profiles.
|
| |
|
| Overall design |
Blood platelets were isolated from whole blood in citrate-coated BD Vacutainers by standard centrifugation and multiple washing steps. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the TruSeq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina HiSeq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the human reference genome using STAR, and intron-spanning reads were summarized using HTseq.
|
| |
|
| Contributor(s) |
Fejes AV, Best MG, Wurdinger T, Mannhalter C |
| Citation(s) |
30385858 |
| |
| Submission date |
May 21, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Myron Best |
| E-mail(s) |
m.best@vumc.nl
|
| Organization name |
VU University Medical Center
|
| Department |
Neurosurgery
|
| Lab |
Neuro-oncology Research Group
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (12)
|
| GSM3147985 |
Blood_Platelets_Vumc-bact-contrPLT-4 |
| GSM3147986 |
Blood_Platelets_Vumc-bact-PLTEcoliK12-1 |
| GSM3147987 |
Blood_Platelets_Vumc-bact-PLTEcoliK12-2 |
| GSM3147988 |
Blood_Platelets_Vumc-bact-PLTEcoliK12-3 |
| GSM3147989 |
Blood_Platelets_Vumc-bact-PLTEcoliK12-4 |
| GSM3147990 |
Blood_Platelets_Vumc-bact-PLTEcoliO18-1 |
| GSM3147991 |
Blood_Platelets_Vumc-bact-PLTEcoliO18-2 |
| GSM3147992 |
Blood_Platelets_Vumc-bact-PLTEcoliO18-3 |
| GSM3147993 |
Blood_Platelets_Vumc-bact-PLTEcoliO18-4 |
|
| Relations |
| BioProject |
PRJNA472350 |
| SRA |
SRP148569 |
Less...
More...