|
| Status |
Public on Jun 30, 2021 |
| Title |
CA3 subfield rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Hipocampal subfield
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
tissue: brain
age: three-month-old animals
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from tissue was harvested using Trizol reagent. IlluminaTruSeq Stranded Total RNA LT was used with 200 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard IlluminaTruSeq Stranded Total RNA LT protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
n2_ca3
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
All sequenced reads were aligned with the StarAligner 2.6 program (https://github.com/alexdobin/STAR, RRID:SCR_004463) with the Rattus norvegicus genome 3.1 (Rnor6 Ensembl release 6.0 - https://www.ensembl.org/Rattus_norvegicus/Info/Index).
Subsequently, DESeq2 package version 3.12(http://bioconductor.org/packages/release/bioc/html/DESeq2.html, RRID:SCR_015687) was used to calculate all differentially expressed genes(DEGs) between subfields and carry statistical analysis.
Genome_build: rnor6
Supplementary_files_format_and_content: comma-delimited text files include counts values for each pairwise comparison
Supplementary_files_format_and_content: countData.csv: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 29, 2021 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Andre Schwambach Vieira |
| E-mail(s) |
asv@unicamp.br
|
| Phone |
1935216197
|
| Organization name |
State University of Campinas
|
| Street address |
Rua Monteiro Lobato, 255 - Bloco J - 1 piso - Sala 3
|
| City |
Campinas |
| State/province |
SP |
| ZIP/Postal code |
13083-862 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE179101 |
The transcriptome of rat hippocampal subfields |
|
| Relations |
| BioSample |
SAMN19945486 |
| SRA |
SRX11248237 |
