|
| Status |
Public on Apr 09, 2022 |
| Title |
Choroid - PAPA-NONOate (control) [L3] |
| Sample type |
SRA |
| |
|
| Source name |
Choroid - PAPA-NONOate (control)
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Whole tissue homogenate
strain: Domesticus
age: Post hatch day 15
|
| Treatment protocol |
Choroids were incubated with 1.5 mM PAPA-NONOate for 24 hours at 37 °C with 5% CO2
|
| Growth protocol |
Chicks were maintained in standard animal housing with a 12-hour light/dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Choroids were removed, snap frozen in liquid nitrogen, and RNA was extracted using TRIzol reagent. Illumina NEBNext poly(A) mRNA isolation kit and SWIFT RNA Library kit were used with 100ng of total RNA for the construction of sequencing libraries
Swift directional mRNA prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality trim to a minimum of Q15
gsnap -D ./ -d Chicken_GRCg6a --use-splicing=chicken.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t${num_processors} --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $outfile_R1 $outfile_R2 | samtools view -bS -@ ${num_processors} - | samtools sort -@ ${num_processors} -o ./Illumina_data/${j}.sorted.bam -; samtools index ./Illumina_data/${j}.sorted.bam
split forward and reverse reads using SAMTOOLS
call FPKM using CUFFLINKS, applying anti-sense reads to sense genes, and sense reads to anti-sense genes
Assembly: GRCg6a
Supplementary files format and content: Excel file containing FPKM values
|
| |
|
| Submission date |
Apr 06, 2022 |
| Last update date |
Apr 09, 2022 |
| Contact name |
Kenneth L Jones |
| Organization name |
Bioinformatic Solutions LLC
|
| Street address |
1309 Coffeen Avenue STE 10090
|
| City |
Sheridan |
| State/province |
Wyoming |
| ZIP/Postal code |
82801 |
| Country |
USA |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE200347 |
The Effects of Nitric Oxide on Choroidal Gene Expression |
|
| Relations |
| BioSample |
SAMN27393677 |
| SRA |
SRX14770490 |
