|
| Status |
Public on Nov 22, 2024 |
| Title |
300.12_HCB8_4w |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-neuron
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: iPSC-neuron
cell line: 300.12-HCB8
cell type: iPSC-neuron
genotype: S305N/S305N
age: 4 weeks
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Neurons and astrocytes were differentiated as previously published (Bowles et al, 2019; TCW et al, 2017)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from neuron and astrocyte cultures using the Qiagen Rneasy miniprep kit
Libraries were prepared and sequenced as paired-end 150bp reads on the Illumina HiSeq 4000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome using the STAR aligner (v2.5.2b)
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files of raw read counts
|
| |
|
| Submission date |
Feb 28, 2024 |
| Last update date |
Nov 22, 2024 |
| Contact name |
Kathryn R Bowles |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Edinburgh
|
| Street address |
49 Little France Crescent
|
| City |
Edinburgh |
| ZIP/Postal code |
EH16 4SB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE260517 |
Development of MAPT S305 mutation models exhibiting elevated 4R tau expression, resulting in altered neuronal and astrocytic function [bulkRNA-seq] |
| GSE279322 |
Development of MAPT S305 mutation models exhibiting elevated 4R tau expression, resulting in altered neuronal and astrocytic function |
|
| Relations |
| BioSample |
SAMN40193973 |
| SRA |
SRX23786531 |
