|
| Status |
Public on Mar 28, 2023 |
| Title |
WB, post-COVID-19, control MC1_72 |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
age: 45
Sex: Female
dlco (%_of_predicted): 73.3
|
| Treatment protocol |
Venous blood samples were collected in Tempus TM blood RNA tubes by venipuncture after a night of fasting and before beginning pulmonary evaluation. Blood samples were stored at -80 °C for future analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 200 μL of preprocessed whole blood with the Maxwell® RSC simply RNA Blood Kit in combination with the Maxwell® RSC Instruments.
RNA was isolated from 1 μg of total RNA using Illumina´s Ribo-zero plus rRNA depletion kit. The RNA was fragmented into approximately 200 base pair (bp) pieces by using divalent cations under elevated temperature. Reverse transcriptase and random primers were used to generate first strand cDNA from cleaved RNA fragments. DNA polymerase I and RNase H were used to obtain the second strand. Double-stranded cDNA fragments were end-repaired by Klenow DNA polymerase and T4 DNA. cDNA was phosphorylated by T4 polynucleotide kinase and ligated to Illumina indexing adapters. Adapter-tagged libraries were amplified by using 15 cycles of PCR with DNA polymerase. Validation and quantification were performed using electrophoresis and qPCR. Pools of six indexed libraries were mixed at equimolar ratios to yield a total oligonucleotide mixture concentration of 10 nM.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
WB, post-COVID-19, control
MC1_72
|
| Data processing |
Raw sequence data in fastq format were processed using a sequential workflow:
(i) data were cleaned of adapters and low-quality sequences using TrimGalore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ accessed date April 1st, 2021).
(ii) reads were mapped to the reference genome (GRCh38.p12) by the aligner STAR (https://github.com/alexdobin/STAR).
(iii) mapped reads were counted using FeatureCounts (http://subread.sourceforge.net/ accessed date April 1st, 2021).
(iv) global distance analysis and normalization of reads were performed through DESeq2.
(v) differential expression analysis were performed using two different protocols derived from the R package SARTools: DESeq2 y EdgeR.
Assembly: GRCh38.p12
Supplementary files format and content: Tab-delimited text file including normalized counts for each gene per each sample.
Supplementary files format and content: Tab-delimited text file including raw counts for each gene per each sample.
|
| |
|
| Submission date |
Mar 27, 2023 |
| Last update date |
Apr 22, 2024 |
| Contact name |
David de Gonzalo-Calvo |
| E-mail(s) |
dgonzalo@irblleida.cat
|
| Phone |
973702201
|
| Organization name |
IRBLleida
|
| Street address |
Rovira Roure 80
|
| City |
Lleida |
| State/province |
Lleida |
| ZIP/Postal code |
25196 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE228320 |
Whole blood transcriptional profiling of pulmonary functional sequelae in ARDS- secondary to SARS-CoV-2 infection |
|
| Relations |
| BioSample |
SAMN33941575 |
| SRA |
SRX19788335 |
