|
| Status |
Public on May 21, 2024 |
| Title |
RNA-seq: Infected AGPAT2mut 2 |
| Sample type |
SRA |
| |
|
| Source name |
monocytes-derived macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: monocytes-derived macrophages
Sex: male
genotype: AGPAT2 mutated
treatment: Infected (Leishmania infantum)
|
| Treatment protocol |
Infection with L. infantum (Strain isolated from a patient diagnosed with VL in Natal, RN, Brazil) proceeded in the monocyte-derived macrophages. Leishmania stationary promastigotes at a 5 parasites/cell ratio were incubated for 2 hours. After the incubation, free parasites were washed with warm RPMI 1640. Infected MØ for sequencing were aliquoted at 72 hours after infection.
|
| Growth protocol |
PBMC were maintained in RPMI 1640 supplemented with 1.5μM L-glutamine, 1mM Hepes, 10% heat-inactivated AB human serum and 5ng/mL of M-CSF (Gibco, USA) to obtain monocytes-derived macrophages.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the standard Trizol protocol, followed by purification in the Qiagen column. The quality of the RNA was checked using the NanoDrop spectrometer (NanoDrop Technologies), Agilent Bioanalyzer (RNA Nano Chip, Agilent) and also by Qubit 2.0 / 3.0 fluorometer.
20 ul of total RNA (75-350 ng/ul) were submitted to the sequencing facility and default protocol was carried on.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
7.INF.lane1
7.INF.lane2
7.INF.lane3
|
| Data processing |
Illumina HiSeq 2000 (75 bp, paired-end), each sample with 3 experimental replicates (with the exception of participant 6, who has only an experimental duplicate in the infected sample.)
Aligmntent HISAT2 2.2.0 in default parameters
Files were compressed into BAM using Samtools 1.15
The counts assigned were accessed by FeatureCounts
Differential expression analysis: DESeq2 3.14 (Bioconductor)
Assembly: GRCh38
Supplementary files format and content: Gene counts matrix from FeatureCounts of all samples together
|
| |
|
| Submission date |
Aug 04, 2022 |
| Last update date |
May 21, 2024 |
| Contact name |
Selma MB Jeronimo |
| Organization name |
Federal University of Rio Grande do Norte (UFRN)
|
| Department |
Tropical Medicine Institute (IMT-RN)
|
| Street address |
655 Av Passeio dos Girassois, Capim Macio
|
| City |
Natal |
| State/province |
Rio Grande do Norte |
| ZIP/Postal code |
59078190 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE210555 |
Impaired signaling pathways on Berardinelli–Seip congenital lipodystrophy macrophages during Leishmania infantum infection |
|
| Relations |
| BioSample |
SAMN30154144 |
| SRA |
SRX16849001 |
