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| Status |
Public on Sep 24, 2020 |
| Title |
RNA-seq from UC Davis FAANG pig spleen rep P350 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Sus scrofa |
| Characteristics |
tissue: spleen
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. DNase I (Ambion, Austin, TX) digestion was carried out after RNA isolation and the RNA concentration and purity were determined by measuring absorbance at 260 nm and A260/A280 ratio using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). RNA samples were stored at − 80 °C until further use. Total RNA (1 μg) was subjected to two rounds of hybridization to oligo (dT) beads (Invitrogen, Carlsbad, CA) to enrich poly-adenylated transcripts.
Stranded RNA-seq libraries were prepared using the TruSeq RNA Illumina protocol, and libraries were sequenced on an Illumina HiSeq-3000 using 100 bp PE
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
SAMEA4454575
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| Data processing |
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with STAR 2.5.4a to the galGal6, Sscrofa11.2, and ARS-UCD1.2 genomes with the arguments --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20
Alignments were filtered with Samtools 1.10 using argument -q 30
Gene counts were obtained with htseq-count 0.11.1 using the Ensembl 99 annotations with arguments -r pos --stranded=reverse
Genome_build: galGal6,susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: 2-column tsv, Ensembl gene ID and raw read count
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| Submission date |
Sep 23, 2020 |
| Last update date |
Sep 24, 2020 |
| Contact name |
Colin Kern |
| Organization name |
UC San Diego
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL24486 |
| Series (2) |
| GSE158412 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility (RNA-Seq) |
| GSE158430 |
Comparative functional genome annotation of livestock species identifies core amniote regulatory features and avian enhancer versatility |
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| Relations |
| BioSample |
SAMN16245090 |
| SRA |
SRX9176756 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4799587_RNASeq_Spleen_P350.txt.gz |
106.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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