|
| Status |
Public on Aug 22, 2020 |
| Title |
0022V4D3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood RNA
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: post kala azar dermal leishmaniasis (PKDL)
tissue: whole blood
visit day: D3
treatment: 7.5x10^10 viral particles
age_group: adults
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PAXgene Blood RNA kit
Ion AmpliSeq™ Transcriptome Human Gene Expression Kit,, which employs an highly multiplexed PCR to amplify more than 20,000 human genes. Amplified products from each sample are then barcoded and sequenced on a Ion Proton machine. Amplified products from each sample are then barcoded and sequenced on a Ion Proton machine.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Raw data are processed on a Thermo Fisher server, basecalled and then reads are aligned to the fragments corresponding to the amplified PCR products. Aligned reads are then counted with samtools (For additional details: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681149/)
Genome_build: GRCh37
Supplementary_files_format_and_content: Counts_Leish2a_20191217.csv contains read counts for all the samples
|
| |
|
| Submission date |
Aug 21, 2020 |
| Last update date |
Aug 22, 2020 |
| Contact name |
Francesco Santoro |
| E-mail(s) |
santorof@unisi.it
|
| Organization name |
University of Siena
|
| Department |
Department of Medical Biotechnologies
|
| Lab |
Laboratory of Molecular Microbiology and Biotechnology
|
| Street address |
Viale Bracci, 16, V lotto, I piano
|
| City |
Siena |
| State/province |
SI |
| ZIP/Postal code |
53100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE156645 |
A chimpanzee adenovirus-vectored single dose therapeutic vaccine for post kala azar dermal leishmaniasis |
|
| Relations |
| BioSample |
SAMN15877914 |
| SRA |
SRX8984069 |
