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Sample GSM5628861 Query DataSets for GSM5628861
Status Public on Nov 18, 2021
Title Lung lymph node MBC 4
Sample type SRA
 
Source name Lung lymph node
Organism Homo sapiens
Characteristics tissue: Lung lymph node
cell type: Live-dead negative, CD14-, CD8-, CD16-, CD10-, Streptavidin-, CD20+ CD19+ IgD- IgG+
Extracted molecule total RNA
Extraction protocol RNA was isolated from sorted cells using a Zymo Research Direct-zol RNA Microprep Kit, as per manufacturer's protocol.
Ribosomal RNA depletion was performed using Nugen Ovation SoLo RNA-Seq system. Nugen Ovation SoLo library construction chemistry kit was use for library construction. RNA libraries were prepared for sequencing using standard manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model MGISEQ-2000RS
 
Data processing RNAseq analysis was performed using the web-based Galaxy platform maintained by Australian Galaxy Team (https://usegalaxy.org.au/).
Reads were mapped to the Homo sapiens reference genome (hg38) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: hg38
Supplementary_files_format_and_content: CSV/tab-delimited text files include raw counts or CPM values
 
Submission date Oct 15, 2021
Last update date Nov 18, 2021
Contact name Hyon Xhi Tan
E-mail(s) hxtan@unimelb.edu.au
Organization name The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity
Department Department of Microbiology and Immunology
Street address 792 Elizabeth St
City Melbourne
State/province Victoria
ZIP/Postal code 3010
Country Australia
 
Platform ID GPL30209
Series (1)
GSE186010 Transcriptional profile of human memory B cells isolated from lung, lung-draining lymph node and PBMCs
Relations
BioSample SAMN22330101
SRA SRX12634083

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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