|
| Status |
Public on Dec 25, 2023 |
| Title |
H1 cells, FINE, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
H1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: Embryonic stem cells
genotype: WT
treatment: Naïve ESCs were grown in FINE culture condition after research 50% confluency
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent and purified.
Library was prepared according to theNanopore Ligation Sequencing Kit 1D (PM).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Sequence reads were mapped to GRCh38 using minimap2 (parameters: -ax splice --MD)
Read counts extraction were performed using featureCounts basd on the GRCh38.105 reference annotation (parameters: -L -M -O -g: transcript_id -t: transcript)
Assembly: human NCBI genome build 38
Supplementary files format and content: tab-delimited text files include expression raw count values for each sample
|
| |
|
| Submission date |
Mar 22, 2023 |
| Last update date |
Dec 25, 2023 |
| Contact name |
Yaqi Su |
| Organization name |
Zhejiang University-University of Edinburgh Institute, Zhejiang University
|
| Street address |
ZJU-UoE Institute,718 East Haizhou Rd.
|
| City |
Haining |
| State/province |
Zhejiang |
| ZIP/Postal code |
314400 |
| Country |
China |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE227911 |
Comprehensive Assessment of Isoform Detection Methods for Third-Generation Sequencing Data |
|
| Relations |
| BioSample |
SAMN33850103 |
| SRA |
SRX19746659 |
