|
Status |
Public on Sep 27, 2023 |
Title |
Patient BE 26-6 |
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 |
SAMN30986172 |
SRA |
SRX17682779 |