Welcome to the Songbird Brain Transcriptome Database

A Comprehensive Resource for Zebra Finch Brain cDNA Clones, Bioinformatics, and Biotechnological Research

Our database is dedicated to the extensive cataloging and analysis of cDNA clones derived from the brains of zebra finches (Taeniopygia guttata) — one of the most important animal models for studying vocal learning, neural circuits, and behavior. This rich dataset supports researchers working at the intersection of bioinformatics, neurogenomics, and biotechnology, providing detailed genetic sequences, annotations, and analytical tools.

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What We Offer:

Data, Annotation, and Tools

High-Quality cDNA Clone Sequences

Full-length clones with consensus sequences built from multiple sequencing reads to ensure accuracy.

Detailed clone and subcluster grouping to identify alternatively spliced or closely related gene family members.

Raw sequencing reads available for quality inspection and independent verification

Rich Annotations

Annotation with gene names, functional descriptions, and homology to other species’ genes.
Integration with external databases such as UniGene, LocusLink, and Gene Ontology (GO) for biological process, cellular component, and molecular function insights.
Both machine-generated and expert-curated annotations provide a reliable understanding of gene function.

Bioinformatics Search and Analysis Tools

Search at multiple hierarchical levels: clusters, subclusters, clones, and reads.

Advanced text-based searches including partial and wildcard queries for gene names and functional annotations.

BLAST search against various databases for sequence similarity and homology assessment.

Gene Ontology browsing with a hierarchical tree to find functionally related genes.

Biotechnological Applications

Data enables design of primers for RT-PCR, in vitro transcription, and gene cloning.

Insights into RNA editing and alternative splicing relevant to functional studies.

Resource for development of biotechnological tools in neuroscience and behavior genetics.

Extraction of cDNA from Zebra Finch Brain Tissue

The extraction of cDNA (complementary DNA) from zebra finch brains is a crucial step in studying gene expression patterns involved in vocal learning, neuroplasticity, and brain development. Below is an overview of the typical workflow used in generating high-quality cDNA libraries from zebra finch neural tissue.

Key Steps in Zebra Finch cDNA Extraction

1️⃣ Tissue Collection

Brain regions involved in vocal learning (e.g., HVC, RA, Area X) are carefully dissected from adult or juvenile zebra finches under RNase-free conditions.
Tissue samples are immediately flash-frozen in liquid nitrogen or preserved in RNA stabilization reagents (e.g., RNAlater).

2️⃣ Total RNA Extraction

Total RNA is isolated using phenol-chloroform extraction (e.g., TRIzol reagent) or column-based kits designed for high-quality RNA recovery.
RNA integrity is verified using Bioanalyzer or agarose gel electrophoresis, ensuring high RNA integrity numbers (RIN ≥ 8).

3️⃣ mRNA Enrichment / Purification

Poly(A)+ mRNA is purified from total RNA using oligo(dT) beads or columns to selectively capture messenger RNAs, removing ribosomal and other non-coding RNAs.

4️⃣ First-Strand cDNA Synthesis

Reverse transcription is performed using reverse transcriptase enzymes (e.g., M-MLV, SuperScript) with oligo(dT) or random primers to generate first-strand cDNA.

5️⃣ Second-Strand cDNA Synthesis & Cloning

The second DNA strand is synthesized, and the double-stranded cDNA is ligated into cloning vectors.
Libraries are often normalized and subtracted to reduce over-representation of abundant transcripts and enrich rare or novel transcripts.

6️⃣ Library Validation and Sequencing

cDNA clones are arrayed, sequenced, and annotated. Sequencing reads are assembled into consensus sequences to confirm clone identity and quality.
Clones are cross-referenced with homologous genes in other species for comparative genomics studies.

🚀 Applications of Zebra Finch Brain cDNA

✅ Transcriptome analysis of vocal learning and neuroplasticity

✅ Identification of novel genes and splice isoforms

✅ Functional genomics and evolutionary biology studies

✅ Gene cloning for biotechnological applications

Explore the full scientific publication that inspired our database click here to access the study.