|
| Status |
Public on Dec 17, 2023 |
| Title |
human_study participant_2, acute |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cells
cell isolation: flow cytometry isolated cells
cell type: plasmacytoid dendritic cells
wheeze vs_ctrl: acute
wheeze phenotype: few
Sex: F
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Plasmacytoid dendritic cells (500 cells per tube) were sorted directly into PCR tubes each containing 2 µL of 1 mg/mL BSA (Ambion® Thermo Fisher Scientific) lysis buffer with 4 U/µL of recombinant RNase inhibitor (Takara Bio) and 1 µL of 10 mM dNTP mix, then stored at -80 °C
cDNA libraries were prepared using the SMART-seq2 protocol with the following modifications: (i) change in lysis buffer and cell collection as already described; (ii) addition of 20 μM TSO; (iii) use of 200 pg cDNA with 1/5 reaction of Nextera XT kit (Illumina)
All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq X system with 28-29 samples per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Five |
| |
|
| Description |
R12404
|
| Data processing |
The paired-end raw reads were mapped to the GRCh38 human genome build using the STAR aligner
Gene counts were computed using featureCounts based on GENCODEv31 gene annotation
Processed data was adjusted using RUVseq6 (k=4)
Assembly: GRCh38
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: processed_data.csv
|
| |
|
| Submission date |
Sep 13, 2023 |
| Last update date |
Dec 17, 2023 |
| Contact name |
Jonatan Leffler |
| E-mail(s) |
jonatan.leffler@telethonkids.org.au
|
| Phone |
0439246262
|
| Organization name |
Telethon Kids Institute
|
| Street address |
15 Hospital Ave
|
| City |
Nedlands |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL33758 |
| Series (1) |
| GSE243052 |
Impaired interferon response in plasmacytoid dendritic cells from children with persistent wheeze |
|
| Relations |
| BioSample |
SAMN37379562 |
| SRA |
SRX21765927 |
