|
| Status |
Public on May 26, 2023 |
| Title |
Thyroid, PolyA RNA |
| Sample type |
SRA |
| |
|
| Source name |
Thyroid
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thyroid
cell type: Thyrocytes
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from freshly dissected thyroids which were immediately placed in ice cold TriZol and homogenized using an ultra-turrax dispersing tool (IKA).
The sequencing library was created using the cDNA-PCR Sequencing Kit (Oxford Nanopore Technologies) according to the manufacter’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Basecalling was performed using Guppy 6.4.6
Read quality was checked using pycoQC 2.5.2
Sequence alignment to the mm10 genome was performed using minimap2 (parameters: -ax splice)
Genome coverage was processed using Bedtools (v2.30.0) genomecov (parameters: -trackline -bg -split -ibam)
Assembly: mm10
Supplementary files format and content: BedGraph file
|
| |
|
| Submission date |
May 25, 2023 |
| Last update date |
May 26, 2023 |
| Contact name |
Irina Solovei |
| E-mail(s) |
irina.solovei@lrz.uni-muenchen.de
|
| Organization name |
LMU Munich
|
| Street address |
Großhaderner Str. 2
|
| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26624 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN35365639 |
| SRA |
SRX20516352 |
