|
| Status |
Public on Jul 05, 2022 |
| Title |
CTR [WTCHG_823226_70945070] |
| Sample type |
SRA |
| |
|
| Source name |
CTR M3 36S
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CTR M3 36S
cell type: keratinocytes iPSCs
genotype: wt
treatment: untreated
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Qiagen RNeasy Mini PLUS Kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Preparation Kit (Illumina) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
adult, neurotypical
|
| Data processing |
QC using FastQC v0.11.5.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v1.13.
Trimmed sequence reads were aligned to GRCh37 using BWA-MEM v0.7.15.
Read count extraction and normalization were summarised to the gene-level using the summarizeOverlaps function of the GenomicAlignments R package. Normalised counts using the median of ratios method (estimateSizeFactors function) implemented in DESeq2 v1.28.1.
Assembly: GRCh37.EBVB95-8wt.ERCC
Supplementary files format and content: tab-delimited text files include normalised counts using the median of ratios.
|
| |
|
| Submission date |
Jul 05, 2022 |
| Last update date |
Jul 05, 2022 |
| Contact name |
Marco Fernandes |
| E-mail(s) |
marco.fernandes@psych.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Department of Psychiatry, Warneford Ln, Headington
|
| Street address |
Department of Psychiatry, Warneford Ln, Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7JX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE207466 |
Glycosylated clusterin species facilitate amyloid beta toxicity in human neurons. |
|
| Relations |
| BioSample |
SAMN29500365 |
| SRA |
SRX16019912 |
