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Sample GSM4914308 Query DataSets for GSM4914308
Status Public on Dec 11, 2020
Title PC_13_RNA_TA
Sample type SRA
 
Source name Peripheral Whole-Blood
Organism Homo sapiens
Characteristics remission: Remission
gender: f
age: 69
pseudotime: 4
patient number: 013
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 SAMN16829867
SRA SRX9529571

Supplementary file Size Download File type/resource
GSM4914308_J14145-L1_S79_L001_R1_001Aligned.sortedByCoord.out_gene.featureCounts.txt.gz 4.7 Mb (ftp)(http) TXT
GSM4914308_J14145-L1_S79_L002_R1_001Aligned.sortedByCoord.out_gene.featureCounts.txt.gz 4.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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