|
| Status |
Public on May 01, 2024 |
| Title |
Sham Hip-1, mRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Canis lupus familiaris |
| Characteristics |
breed: beagle
tissue: hippocampus
treatment: sham operation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Description |
Hippocampus All_samples_rpkm.txt
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI.
The de-duplicated consensus sequences were mapped to CanFam 3.1 using STAR software (version 2.5.3a)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）
Assembly: CanFam 3.1
Supplementary files format and content: tab-delimited text files include RPKM values/TPM values for each Sample
|
| |
|
| Submission date |
Aug 14, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
wang xuewen |
| E-mail(s) |
wangxuewen@whu.edu.cn
|
| Phone |
+8618372030240
|
| Organization name |
Renmin Hospital of Wuhan University
|
| Department |
Department of Cardiology
|
| Lab |
Cardiovascular Research Institute
|
| Street address |
238 Jiefang Road, Wuhan 430060, China
|
| City |
Wuhan |
| State/province |
中国 (+86) |
| ZIP/Postal code |
430060 |
| Country |
China |
| |
|
| Platform ID |
GPL33670 |
| Series (1) |
| GSE240776 |
Extracellular vesicles from epicardial fat mediate long-distance heart-brain communication and promote atrial fibrillation associated cognitive impairment (EAT exosomal miRNA-seq and hippocampal mRNA-seq) |
|
| Relations |
| BioSample |
SAMN36983671 |
| SRA |
SRX21360786 |
