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Sample GSM6598665 Query DataSets for GSM6598665
Status Public on Sep 27, 2023
Title Patient BE 26-5
Sample type SRA
 
Source name nasal epithelia
Organism Homo sapiens
Characteristics tissue: nasal epithelia
cell line: Primary cultures
genotype: TUBB4B p.P259L
treatment: Air Liquid Interface
Treatment protocol Apical fluid was then removed and cells were maintained in this air liquid interface (ALI) for at least 3 weeks until fully differentiated into multiciliated ciliated epithelium.
Growth protocol Primary human nasal epithelial cells were expanded at 37 °C in media selective for basal cells or specialized media until 80% confluency. Basal cells were then dissociated and seeded into transwell inserts until confluent.
Extracted molecule polyA RNA
Extraction protocol Cells were stored in RNALater until used. Total RNAas purified with miRNA Easy (Qiagen #74004)
Libraries were made with NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #E7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the providers protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Data processing Basecall data produced by the NextSeq 550 is automatically uploaded to BaseSpace, a cloud- based data management and analysis service provided by Illumina. Here it is converted into FASTQ files in order to allow analysis using a number of apps accessible directly through BaseSpace, or to download so that alternative analysis pipelines can be used.
Data was processed using the pipeline nf-core/rnaseq v3.0 (b892cc54e3b768dca93d19da30a907a) using Nextflow (20.12.0-edge)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene-level length corrected values for each Sample. Salmon (1.4.0) and bioconductor-tximeta (1.8.0)
 
Submission date Sep 23, 2022
Last update date Sep 27, 2023
Contact name Graeme Richard Grimes
E-mail(s) graeme.grimes@ed.ac.uk
Organization name University of Edinburgh, The Institute of Genetics and Cancer
Department Human Genetics Unit
Lab Bioinformatics Analysis Core
Street address Western General Hospital, Crewe Road
City Edinburgh
ZIP/Postal code EH4 2XU
Country United Kingdom
 
Platform ID GPL21697
Series (1)
GSE214070 Distinct spectrum of ciliopathic diseases results from de novoTUBB4B variants through differential effects on organelle-specific microtubules
Relations
BioSample SAMN30986173
SRA SRX17682778

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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