|
| Status |
Public on Apr 10, 2017 |
| Title |
ProM (A) Sandfly 3 |
| Sample type |
SRA |
| |
|
| Source name |
Leishmania donovani
|
| Organism |
Leishmania donovani |
| Characteristics |
strain: BPK282
parasite developmental stage: Promastigotes
host cell type: cell culture
genotype: BPK282
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNASeq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep kit according to the manufacturer’s standard protocol apart from the PCR amplification, which was performed using KAPA Hifi Polymerase. 75 base pair paired-end reads were generated on the HiSeq 2000 v4 according to the manufacturer’s standard sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Standard Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to the Leishmania donovani reference using smalt 7.4
Reads per gene was extracted from read depth: ploidy normalization was performed based on median read depth
Deseq was used for the differential expression analysis
Genome_build: Leishmania donovani BPK282
Supplementary_files_format_and_content: tab-delimited text files include read count per gene values for each sample in one file
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hideo Imamura |
| E-mail(s) |
himamura@itg.be
|
| Organization name |
Institute of Tropical Medicine, Antwerp
|
| Lab |
Molecular Parasitology Unit
|
| Street address |
Nationalestraat 155
|
| City |
Antwerp |
| State/province |
Antwerp |
| ZIP/Postal code |
2000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL23261 |
| Series (1) |
| GSE97453 |
RNA Analysis for Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments, and its impact on gene expression |
|
| Relations |
| BioSample |
SAMEA4464693 |
| SRA |
ERX1914698 |
