|
| Status |
Public on Jan 28, 2022 |
| Title |
Deprivated-326-L-LGN |
| Sample type |
SRA |
| |
|
| Source name |
LGN
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissues: LGN
age: 3 months old
treatment: monocular visual deprivation of left eye
|
| Treatment protocol |
The left eye of deprivated group was sutured by surgery from 1 month old to 3 month old.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LGN of Macaca Fascicularis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Then we used Agilent Bioanalyzer 2100 to test the quality of RNA. We used 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Only the left LGN of monocular deprivated Macaca Fascicularis was sequencing owing to the low quality of the right LGN examined using Agilent Bioanalyzer 2100
|
| Data processing |
lllumina GA Pipeline v1.5 software used for basecalling.
Reads were further filtered by fastp(version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
Alignment with reference genome: an index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISA T2 (version 2.1.0) with “-rna-strandness RF” and other parameters set as a default.
Transcripts Reconstruction: the reconstruction of transcripts was carried out with software Stringtie(version 1.3.4), which together with HISA T2, allow biologists to identify new genes and new splice variants of known ones.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NC_022273.1 Chromosome 2 Reference Macaca_fascicularis_5.0 Primary Assembly
Supplementary_files_format_and_content: "xlsx" excel files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw mRNA transcript counts for every mRNA transcript and every sample
|
| |
|
| Submission date |
Nov 24, 2021 |
| Last update date |
Jan 29, 2022 |
| Contact name |
Zhongshu Tang |
| Organization name |
Sun Yat-sen University
|
| Street address |
54 South Xianlie Road
|
| City |
GuangZhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL23096 |
| Series (1) |
| GSE189488 |
Monocular Visual Deprivation in Macaca Fascicularis: A mRNA Sequencing Profile of LGN Tissues. |
|
| Relations |
| BioSample |
SAMN23424293 |
| SRA |
SRX13217283 |
