|
| Status |
Public on Feb 24, 2020 |
| Title |
419_11254_WT |
| Sample type |
SRA |
| |
|
| Source name |
mouse blood
|
| Organisms |
Plasmodium berghei; Mus musculus |
| Characteristics |
Sex: female
mouse strain: C57BL/6
plasmodium berghei strain: ANKA
agent: wild type Plasmodium berghei
|
| Treatment protocol |
9 weeks old female C57BL/6 mice were injected intraperitoneally with 200ul PBS containing 10^6 infected red blood cells
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
on the 9th day the mice were bled from the cheek and 250 ul blood was collected. The blood was immediately transferred to the eppendorf tubes containing 750ul Trizol LS.
RZ Globin/TruSeq mRNA Seq (Poly-dT)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
11254_scounts_no
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to mm10 and Plasmodium berghei whole genomes using hisat2
normalization and comparisons were run using deseq2. Matrix-mouse and matrix_Plasmodium are condensed files of the original with deseq2 normalized reads for each sample listed
Genome_build: mm10 with Plasmodium berghei (ANKA)
|
| |
|
| Submission date |
Mar 02, 2018 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
dsturdevant@niaid.nih.gov
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL24674 |
| Series (1) |
| GSE111333 |
A single nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity |
|
| Relations |
| BioSample |
SAMN08629690 |
| SRA |
SRX3757044 |
