|
| Status |
Public on Jun 30, 2023 |
| Title |
garid(-) gametocyte, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Gametocyte
|
| Organism |
Plasmodium berghei ANKA |
| Characteristics |
Stage: gametocyte
strain: ANKA
genotype: garid(-)
|
| Treatment protocol |
Infected mice were treated with sulfadiazine in their drinking water for 2 days in order to deplete asexual blood-stage parasites.
|
| Growth protocol |
Parasites were inoculated in Balb/c mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s instructions.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with DNBSEQ (Paired-end read - MGI DNBSEQ-G400),
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
garid(-)_RNA-seq_count.txt
|
| Data processing |
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” which was set to 1000. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Assembly: PlasmoDB, version 3
Supplementary files format and content: txt, raw read count
|
| |
|
| Submission date |
Jun 21, 2023 |
| Last update date |
Jun 30, 2023 |
| Contact name |
masao yuda |
| E-mail(s) |
m-yuda@doc.medic.mie-u.ac.jp
|
| Organization name |
mie university
|
| Street address |
edobashi 2-174
|
| City |
tsu |
| State/province |
mie |
| ZIP/Postal code |
514-0001 |
| Country |
Japan |
| |
|
| Platform ID |
GPL33514 |
| Series (2) |
| GSE235411 |
Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium [RNA-seq] |
| GSE235412 |
Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium |
|
| Relations |
| BioSample |
SAMN35816800 |
| SRA |
SRX20734714 |
