|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|