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| Status |
Public on Jan 15, 2024 |
| Title |
WCF_27 |
| Sample type |
SRA |
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| Source name |
Amygdala
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| Organism |
Sus scrofa |
| Characteristics |
feeding: Weaned
treatment: C
Sex: Female
age: 22 day old
tissue: Amygdala
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| Extracted molecule |
total RNA |
| Extraction protocol |
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 Inc, San Diego, CA, USA). Read 1 aligns to the antisense strand and read 2 aligns to the sense strand. The libraries were sequenced on a NovaSeq 6000. Pair-ended reads of length 150bp were sequenced. 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 10)
Supplementary_files_format_and_content: xls format, transcripts per million (TPM) values for each sample, one column per sample
rodriguez_wean22amy48_counts.xlsx
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| Submission date |
Jan 18, 2021 |
| Last update date |
Jan 15, 2024 |
| 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) |
| GSE165059 |
Evaluation of the effect of stresses due to weaning and immune activation on pigs |
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| Relations |
| BioSample |
SAMN17376647 |
| SRA |
SRX9892461 |
| 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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