|
| Status |
Public on Jun 20, 2024 |
| Title |
MDMs co-cuclutre donor 1 replicate 1 HIV infected |
| Sample type |
SRA |
| |
|
| Source name |
PMBCs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PMBCs
cell type: MDMs
|
| Growth protocol |
MDMS were generated from freshly isolated CD14+ cells by cultiring in high attachment plates RPMI supplemented with human Ab serum for 5 days. Medium was changed for RPMI supplemented with IFNg and LPS for 48h before co-cuclture establishment. Freshly isolated PBMCs were culture for 24h in RPMI supplemented with FBS, GlutaMax and IL-2 before HIV infection with 0.1 MOI.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction kit: QIAGEN RNeasy mini kit. Protocol according to manufacturer instructions.
Illumina Stranded mRNA Prep, Ligation (https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/illumina-stranded-mrna-prep-data-sheet-m-gl-02143/illumina-stranded-mrna-prep-data-sheet-m-gl-02143.pdf)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Data processing |
The raw reads were first cleaned by removing adapter sequences and poly-x sequences (> 9 nt used for detection) using fastp (Version 0.23.4). Reads with length <18nt after trimming were additionally filtered out.
Sequence pseudo alignment of the resulting high-quality reads to the Human reference genome and quantification of gene level expression (gene model definition from GENCODE release 42) was carried out using Kallisto (Version 0.46.1)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited transcript abundances
|
| |
|
| Submission date |
Jun 06, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Genome Informatics |
| E-mail(s) |
fgcz.gi@gmail.com
|
| Organization name |
ETH ZURICH / University of Zurich
|
| Department |
Functional Genomics Center Zurich (FGCZ)
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE269285 |
Macrophages show unprecedented anti-HIV activity in HIV-infected iHMD-NSG mice |
|
| Relations |
| BioSample |
SAMN41720250 |
| SRA |
SRX24828834 |
