|
| Status |
Public on Sep 04, 2023 |
| Title |
Mediobasal hypothalamus - Q3 |
| Sample type |
SRA |
| |
|
| Source name |
Mediobasal hypothalamus
|
| Organism |
Coturnix japonica |
| Characteristics |
tissue: Mediobasal hypothalamus
treatment: 16La
|
| Treatment protocol |
Tissue was dissected, frozen on powdered dry ice and stored at -80C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using QIAGEN RNEasy Plus Mini Kit
RNA was synthesized into cDNA using Oxford Nanopore Direct cDNA Native Barcoding (SQK-DCS109 and EXP-NBD104) and followed the manufacturers protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
Photoperiod
|
| Data processing |
fast5 files were demultiplex and basecalled by Guppy 4.2.1
Porechop v0.2.4 was conducted to remove adapters from reads
Filtlong v0.2.0 to filter long reads with minimum 25 bases and mean q weight of 9
Transcripts were aligned to the Japanese quail reference genome and transcriptome using Minimap2 v2.17
Transcript expression levels were determined using Salmon v0.14.2 and EdgeR v3.24.3 for normalisation and differential expression
Assembly: Minimap2 v2.17
Supplementary files format and content: tab-delimited text files and includes raw counts for each sample
Supplementary files format and content: tab-delmiinted text files and includes normalized values for each sample
|
| |
|
| Submission date |
Aug 28, 2023 |
| Last update date |
Jan 23, 2024 |
| Contact name |
Tyler Stevenson |
| E-mail(s) |
tyler.stevenson@glasgow.ac.uk
|
| Phone |
01413305793
|
| Organization name |
University of Glasgow
|
| Street address |
Jarrett building
|
| City |
Glasgow |
| ZIP/Postal code |
G611QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL34121 |
| Series (2) |
| GSE241772 |
FSHβ links photoperiodic signalling in the mediobasal hypothalamus to seasonal reproduction in Japanese quail. |
| GSE241775 |
FSHβ links photoperiodic signalling in the mediobasal hypothalamus and pituitary gland to seasonal reproduction in Japanese quail. |
|
| Relations |
| BioSample |
SAMN37171557 |
| SRA |
SRX21487964 |
