RNA seq of bowfin gill, spleen, intestine - SRA

SRX20884979: RNA seq of bowfin gill, spleen, intestine
1 ILLUMINA (Illumina NovaSeq 6000) run: 33.7M spots, 10.2G bases, 4Gb downloads

Design: Library preparation and next-gen sequencing (2 150 bp paired end reads) was performed on a NovaSeq 6000 instrument (Illumina). mRNA was enriched using oligo(dT) beads. rRNA was removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

Submitted by: North Carolina State University

Study: A survey of ray finned fish PSMB8 sequences reveal novel holostean alleles that may impact MHCI function

PRJNA990750 • SRP447125 • All experiments • All runs

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The evolutionary history and scope of haplotypic diversity of this critical piece of the immunoproteasome is only beginning to be understood. Based on a significant amino acid difference at the 31st residue of the mature protein, PSMB8 haplotypes are classified into A and F types. All jawed vertebrates possess PSMB8A. In contrast, the PSMB8F lineage has been lost by most vertebrates except for chondrichthyans and early diverging actinopterygians, leading to type conversions in multiple species that lost the F lineage. Here we investigate type conversions in 68 ray-finned fishes, and identify two new PSMB8 types, PSMB8S and PSMB8K. These previously unknown types are exclusive to holosteans (gar and bowfin), and introduce novel biochemical changes to the binding pocket suggesting altered cleavage properties. These results expand our knowledge of vertebrate PSMB8 haplotypes and the processing of peptide antigens for display by MHC class I.

Sample:

SAMN36292784 • SRS18163442 • All experiments • All runs

Organism: Amia calva

Library:

Name: Ami_cal_0013

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: Oligo-dT

Layout: PAIRED

Runs: 1 run, 33.7M spots, 10.2G bases, 4Gb

Run	# of Spots	# of Bases	Size	Published
SRR25133147	33,712,337	10.2G	4Gb	2024-08-01

ID:: 28317329

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