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| Status |
Public on Aug 28, 2020 |
| Title |
C1_F |
| Sample type |
SRA |
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| Source name |
Amygdala
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Amygdala
treatment: Control
gender: Female
age: 22 day old
feeding: Nursed
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| Extracted molecule |
total RNA |
| Extraction protocol |
Amygdala was obtained and RNA extracted using standards protocols: TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
RNA was extracted from all samples using standards protocols. TRIzol reagent (Life Technologies, Grand Island, New York) was used to isolate total RNA and the QIAGEN RNeasy kit (Qiagen, Valencia, California) was use for purification
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were quantitated by qPCR and sequenced on 4 lanes first and 5 lanes later for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1. Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
150 nt paired-end reads were assembled into transcript isoforms and mapped to the pig genome (version GRCm38) using Kallisto v0.43 (Bray et al., 2016)
Genome_build: Sus scrofa genome (version xxx)
Supplementary_files_format_and_content: csv format, comma delimited columns, including transcripts per million (TPM) values for each sample, one column per sample
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| Submission date |
May 01, 2020 |
| Last update date |
Aug 28, 2020 |
| Contact name |
Sandra Rodriguez Zas |
| Organization name |
University of Illinois at Urbana
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| Street address |
1207 W. Gregory Dr.
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| City |
Urbana |
| State/province |
IL - Illinois |
| ZIP/Postal code |
61801 |
| Country |
USA |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE149695 |
Comparison between PRRS and control in female and male pig amygdala in 22 day old pigs |
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| Relations |
| BioSample |
SAMN14791310 |
| SRA |
SRX8241172 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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