|
| Status |
Public on Mar 31, 2021 |
| Title |
Brain_Young_LL_P22547 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Peromyscus leucopus |
| Characteristics |
stock: LL
tissue: Brain
age of animal at termination: 7 months
|
| Treatment protocol |
Brain tissues of 7-months-old and 2- to 3-years-old outbred deer mice P. maniculatus and P. leucopus were collected at sacrifice.
|
| Growth protocol |
Deer mice, P. maniculatus were obtained from the Peromyscus Genetic Stock Center (PGSC), University of South Carolina (USC), Columbia, SC (RRID:SCR_002769). P. maniculatus bairdii (BW Stock), was closed colony bred in captivity since 1948 and descended from 40 ancestors wild-caught near Ann Arbor, Michigan. P. leucopus (LL Stock) was derived from 38 wild ancestors captured between 1982 and 1985.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from brain using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB#E7490/NEB#E7760).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
S05
RNASeqCounts_LL.txt
|
| Data processing |
Indexed sequences were checked by FastQC | version: 0.11.5.
Trimmed adapter by TrimGalore-0.4.5.
Reads were mapped to the P. maniculatus and P. leucopus reference genome using STAR | version 2.7.2b with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes Peromyscus_maniculatus_bairdii.HU_Pman_2.1.101.gtf and GCF_004664715.1_Pero_0.1_genomic.gtf were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -T 10.
Genome_build: Peromyscus_maniculatus_bairdii.HU_Pman_2.1 and GCF_004664715.1_Pero_0.1_genomic
Supplementary_files_format_and_content: RNASeqCounts_*.txt: Tab-delimited text files include gene counts for each sample.
|
| |
|
| Submission date |
Feb 08, 2021 |
| Last update date |
Mar 31, 2021 |
| Contact name |
HAO JI |
| E-mail(s) |
ji5@email.sc.edu
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL29708 |
| Series (1) |
| GSE166394 |
Whole Transcriptome RNA-seq in Brain Tissue of Young and Old Peromyscus maniculatus and P. leucopus |
|
| Relations |
| BioSample |
SAMN17836388 |
| SRA |
SRX10052164 |
