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| Status |
Public on Jul 01, 2023 |
| Title |
female Poecilia latipinna 19, whole brain, Ff treatment |
| Sample type |
SRA |
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| Source name |
whole brain
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| Organism |
Poecilia latipinna |
| Characteristics |
tissue: whole brain
preference behavior: Ff social context
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| Treatment protocol |
Sexually experienced P. latipinna females were collected from a semi-natural environment and socially isolated for two weeks to ensure sexual receptivity. Each female was subjected to short-term (30min) non-contact dichotomous choice assays. Females were randomly assigned to one of two social choice treatment groups (mate preference with male stimuli to female shoaling partner with female stimuli) without a non-social control. Focal females made preference decisions based on stimuli size differences in both treatments.Each focal female was acclimatized in an opaque cylinder for 5 minutes in the central neutral zone before being released. Following release from habituation, focal females were observed for 15 minutes and position and behavior in tank recorded. After the first 15 minutes of observations, focal females were brought back to the neutral area and placed in the opaque habituation cylinder while the stimulus fish were switched to opposite sides to ensure that our preference measures were directed at a specific fish rather than a location preference in our experimental tank. Following the stimulus switch, focal females were observed for an additional 15 minutes.
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| Growth protocol |
Fish were maintained in semi-natural on-campus outdoor ponds at the Brakenridgen Field Laboratory at the University of Texas, Austin
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| Extracted molecule |
total RNA |
| Extraction protocol |
Immediately following the 30-minute behavioral trial, focal females were immediately decapitated, whole brains were removed and individually immersed in RNAlater solution (Applied Biosystems, Carlsbad, CA, USA) at 4˚ Celsius with gentle shaking for 24 hours, then stored at -80 C (without RNAlater) for subsequent RNA profiling. 1-4 μg of total RNA were used as input for RNA library preparation and sequencing.
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq mRNA Sample Prep Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Libraries were demultiplexed using a custom python script. Raw 101 bp reads were trimmed to remove low quality base pairs (Phred quality score < 20), reads with few contiguous high-quality base pairs (fewer than 30 bp) using a python script.
python script (http://genomics-pubs.princeton.edu/prv/resources/scripts/TQSfastq.py)
Adapter sequences were trimmed using the program cutadapt (https://cutadapt.readthedocs.io/en/stable/).
To evaluate the quality of the trimmed reads, we ran FastQC (Andrew, 2010) using TACC (Texas Advanced Computing, The University of Texas at Austin).
Reads were pseudoaligned to the Sailfin molly Poecilia latipinna (assembly GCA_001443285.1, retrieved from Ensembl January 2019) with Kallisto (version 0.43.0) using the single-end reads option with a length of 100bp (-l 100), standard deviation of 20 (-s 20).
Assembly: GCA_001443285.1
Supplementary files format and content: tab-delimited Kalisto abundance text files include estimated counts and transcripts per million
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| Submission date |
May 26, 2023 |
| Last update date |
Jul 01, 2023 |
| Contact name |
Rebecca L Young |
| E-mail(s) |
youngrl@utexas.edu
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| Organization name |
University of Texas at Austin
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| Department |
Integrative Biology
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| Street address |
2415 Speedway
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platform ID |
GPL33433 |
| Series (1) |
| GSE233523 |
Individual variation in preference behavior in sailfin fish refines the neurotranscriptomic pathway for mate preference |
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| Relations |
| BioSample |
SAMN35418716 |
| SRA |
SRX20521823 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7429874_FPL19.abundance.tsv.gz |
397.8 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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