|
| Status |
Public on Dec 11, 2020 |
| Title |
PC_9_RNA_TA |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Whole-Blood
|
| Organism |
Homo sapiens |
| Characteristics |
remission: Remission
gender: m
age: 56
pseudotime: 4
patient number: 009
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA sequencing libraries were prepared according to the Illumina TruSeq® messenger (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2). The resulting libraries were sequenced on the NovaSeq 6000 (2× 50 bp, S2 chemistry).
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base Calling perofmed by RTA1(MiSeq) and RTA3 (Novaseq 6000)
Transcriptome Processing: Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline. Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded. . The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b) (Dobin et al., 2013). featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
BCRseq Processing: Sequencing reads were aligned to BCR gene reference and clonotypes were identified and grouped using the software MiXCR (Bolotin et al., 2015). Relative proportions of IGH classes were calculated. Alpha diversity measures were calculated using the R packages vegan and tcR (versions 1.5-6 and 2.3.2).
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts and BCR Clonotype count tables
|
| |
|
| Submission date |
Nov 18, 2020 |
| Last update date |
Dec 11, 2020 |
| Contact name |
Neha Mishra |
| E-mail(s) |
n.mishra@ikmb.uni-kiel.de
|
| Organization name |
Institute of Clinical Molecular Biology
|
| Lab |
Cell biology Lab
|
| Street address |
Rosalind-Franklin-Str. 12
|
| City |
Kiel |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE161777 |
Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories [sequencing] |
| GSE161778 |
Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories |
|
| Relations |
| BioSample |
SAMN16829884 |
| SRA |
SRX9529554 |
