|
| Status |
Public on Nov 22, 2024 |
| Title |
GP1.1_SH1G8_6w |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-neuron
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: iPSC-neuron
cell line: GP1.1-SH1G8
cell type: iPSC-neuron
genotype: S305S/S305S
age: 6 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
MAPT RNA was isolated using the following primers: Forward 5’-ATG GAA GAT CAC GCT GGG AC-3’, Reverse 5’-GAG GCA GAC ACC TCG TCA G-3’ and submitted for single molecule real time (SMRT) sequencing on the RS II platform
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
| |
|
| Data processing |
Raw sequencing reads were passed through the ISOseq3 pipeline to detect full-length transcripts
Single consensus sequences were generated for each MAPT amplicon with a SMRT adapter on both ends of the molecule
SMRT adapter sequences were removed and MAPT-specific primer sequences were identified to orient isoforms
Isoforms were trimmed of poly(A) tails, and concatemers identified and removed.
Isoform consensus sequences were predicted using hierarchical alignment and iterative cluster merging to align imcomplete reads to longer sequences
Clustered isoform sequences were polished using the arrrow model and binned into groups, then aligned to hg38 with GMAP aligner
Assembly: hg38
Supplementary files format and content: csv fille of isoform counts per sample
Library strategy: Targeted MAPT ISO-seq
|
| |
|
| Submission date |
Oct 11, 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 |
GPL21311 |
| Series (2) |
| GSE279321 |
Development of MAPT S305 mutation models exhibiting elevated 4R tau expression, resulting in altered neuronal and astrocytic function [Targeted MAPT ISO-seq] |
| GSE279322 |
Development of MAPT S305 mutation models exhibiting elevated 4R tau expression, resulting in altered neuronal and astrocytic function |
|
| Relations |
| BioSample |
SAMN44256854 |
| SRA |
SRX26355863 |
