|
| Status |
Public on Apr 24, 2023 |
| Title |
SR0030_03_b |
| Sample type |
SRA |
| |
|
| Source name |
Gene-corrected patient derived iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Gene-corrected patient derived iPSCs
cell type: iPSCs
genotype: Variant-corrected clone derived from Sample2
treatment: Undifferentiation state
|
| Growth protocol |
iPSCs were maintained in StemFitAK02N (Takara Bio) on plates coated with iMatrix-511 (Matrixome).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Rneasy Mini Kit (Qaigen) and purified using NucleoSpin RNA Kit (Takara Bio). The amount of total RNA was determined using Nanodrop, and the quality of RNA was checked using BioAnalyzer.
cDNA was synthesized using NEBNext Single Cell/Low cDNA Synthesis and Amplification Module (NEB) and Iso-Seq Express Oligo Kit. Libraries were then prepared using SMARTbell Express Template Prep Kit 2.0 and Barcoded Overhang Adapter Kit A/B according to the procedure and Checklist-Oso-Seq Express Template Preparation for Sequel and Sequel II Systems Version 02.
Iso-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Sequel II |
| |
|
| Data processing |
The isoseq3 tool was used to remove polyA tail sequences and concatemer reads, and high quality full-length reads were obtained after clustering.
The high-quality full-lengths were mapped to GRCh38.primary_assembly.genome using minimap2 software.
The cDNA_Cupcake was used to isolate isoforms by clustering and to qualify expression.
The annotation was attached to the isoforms using the SQANTI3 tool.
Assembly: GRCh38
Supplementary files format and content: The Excel file containing the count number and TPM value of each sample.
|
| |
|
| Submission date |
Apr 13, 2023 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Tsukasa Ohmori |
| E-mail(s) |
tohmori@jichi.ac.jp
|
| Phone |
+81-285-58-7324
|
| Organization name |
Jichi Medical University
|
| Street address |
3311-1 Yakushiji, Shimotsuke,
|
| City |
Tochigi |
| State/province |
--- |
| ZIP/Postal code |
329-0498 |
| Country |
Japan |
| |
|
| Platform ID |
GPL28352 |
| Series (1) |
| GSE229621 |
Long-read RNA-Seq analysis of the full-length F8 transcript in iPSCs |
|
| Relations |
| SRA |
SRX19952032 |
| BioSample |
SAMN34165157 |
