U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX18222224: GSM6722701: Telencephalon, building, biol rep 2, capture area C; Mchenga conophoros; RNA-Seq
2 ILLUMINA (Illumina NovaSeq 6000) runs: 70.2M spots, 8.3G bases, 2.5Gb downloads

External Id: GSM6722701_r1
Submitted by: Streelman, School of Biological Sciences, Georgia Institute of Technology
Study: Cellular profiling of a recently-evolved social behavior [spatial transcriptomics]
show Abstracthide Abstract
Social behaviors are essential for survival and reproduction and vary strongly among individuals, species, and heritable brain diseases. The molecular and cellular bases of this variation are poorly resolved, and discovering them is necessary to understand how neural circuit and behavioral functions—and dysfunctions—vary in social contexts. Here we integrate single nucleus RNA-sequencing (snRNA-seq) with comparative genomics and automated behavior analysis to investigate the neurobiology of castle-building, a recently-evolved social, spatial, goal-directed, and repetitive construction behavior in Lake Malawi cichlid fishes. We simultaneously control for and analyze two biological variables correlated with castle-building behavior: quivering, a courtship “dance” behavior, and relative gonadal mass. We find signatures of building-, quivering-, and gonadal-associated neuronal excitation, gene expression, and neurogenesis in distinct cell populations. Converging lines of evidence support the involvement of estrogen, TrkB, and CCK signaling systems, and specific pallial excitatory neuronal subpopulations, in castle-building behavior. We show additional evidence that castle-building has evolved in part through genomic divergence in a gene module that is selectively expressed in stem-like quiescent radial glial cells (RGCs) lining the ventricular zone of the pallium. This RGC subpopulation exhibits signatures of a building-associated departure from quiescence, which in turn is associated with neuronal rebalancing in the putative fish homologue of the hippocampus. Our work supports an unexpected role for glia and neurogenesis in the evolution of social behavior, and more broadly shows how snRNA-seq can be used to systematically profile the cellular bases of previously unstudied social behaviors in new species systems. Overall design: Spatial transcriptomics analysis was performed on coronal telencephalic sections sampled from Mchenga conophoros during bower-building behavior and 'control' fish that were not building.
Sample: Telencephalon, building, biol rep 2, capture area C
SAMN31670019 • SRS15718638 • All experiments • All runs
Library:
Name: GSM6722701
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC SINGLE CELL
Selection: cDNA
Layout: PAIRED
Construction protocol: Telencephalon tissue samples were embedded in cryomolds (7mm x 7mm x 7mm) containing chilled OCT (Optimal Cutting Temperature embedding compound) and snap frozen. OCT-embedded tissue blocks were cryosectioned at 10 m thickness at -20C (CryoStar NX70). Tissue sections were mounted onto 6.5 mm2 capture areas on Visium Spatial Gene Expression Slides (10X Genomics). There are four capture areas per slide, each containing 5000 spatially-barcoded 55m-diameter spots. RNA quality of the tissue sections (RIN > 7) was confirmed using the Agilent RNA 6000 Nano Kit on the Bioanalyzer 2100 system (Agilent). Gene Expression slides containing tissue sections were processed according to manufacturer instructions (Methanol Fixation, H&E Staining, and Imaging – Visium Spatial Protocol (10X Genomics)). Slides were fixed in methanol for 30 minutes at -20C and stained with Hematoxylin and Eosin (H&E). Brightfield images of H&E-stained slides were taken at 1.33 m/pixel resolution (5X objective, Zeiss AxioObserver Z1 Fluorescent Microscope) and stitched using Zen 2 software (blue edition, Zeiss) prior to library construction. Dual-index Illumina paired-end spatial gene expression libraries were prepared according to manufacturer instructions (Visium Spatial Gene Expression Reagent Kits User Guide (10X Genomics)). Fixed and stained tissue sections were permeabilized for 18 minutes and poly-adenylated mRNA released from cells was captured by primers on the underlying gene expression spots. Primers include a 10X spatial barcode, unique molecular identifier (UMI) and an Illumina read 1 sequencing primer. Incubation with reverse transcription (RT) reagents produced spatially barcoded, full-length cDNA. Barcoded cDNA was denatured, transferred into tubes, and amplified via PCR. Amplified cDNA was size-selected with SPRIselect. During final library construction, P5 and P7 paired-end construct sequences, i5 and i7 sample indices, and an Illumina read 2 primer sequence were added. Quality was assessed using high sensitivity DNA analysis on the Bioanalyzer 2100 system (Agilent).
Runs: 2 runs, 70.2M spots, 8.3G bases, 2.5Gb
Run# of Spots# of BasesSizePublished
SRR2224550335,548,3514.2G1.3Gb2023-06-14
SRR2224550434,605,7544.1G1.2Gb2023-06-14

ID:
25205328

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...