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| Status |
Public on Jan 11, 2021 |
| Title |
Pekin duck, Replicate 1 |
| Sample type |
SRA |
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| Source name |
Bill Skin
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| Organism |
Anas platyrhynchos |
| Characteristics |
tissue: Bill skin
developmental stage: Embryonic Day 24-26
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| Growth protocol |
Eggs of bird species were incubated at 37°C and 55%-75% humidity. Embryos were extracted for dissection when they had broken through the inner shell membrane (24-48 hrs before hatching).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bill skin was dissected from duck embryos, flash-frozen and stored at -80°C until RNA isolation. Total RNA was isolated from the stored bill skin tissue using the TRIzol reagent (ThermoFisher, Waltham, MA) according to manufacturer’s instructions. RNA quality and integrity were confirmed by running on Agilent Bioanalyzer.
mRNA was purified from ~200 ng total RNA with oligo-dT beads. Strand-specific sequencing libraries were prepared using the KAPA mRNA Hyper Prep kit (Roche Sequencing, Pleasanton, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Pekin duck
RNASeq_Nikolaev_et_al_2020_Duck_Bill_Skin.xlsx
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| Data processing |
Primary analysis performed using Illumina's CASAVA 1.8.2 software suite.
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.36 (Bolger et al., 2014) with default parameters.
Filtered high-quality reads from all samples were aligned to duck reference genome using STAR aligner v2.5.4b with default parameters (Dobin et al., 2013).
Aligned reads were counted by featureCounts program within the Subread package v1.6.2 with default parameters (Liao et al., 2014).
Raw read counts were processed and converted to ‘‘mRNA fragments per kilobase of exon per million mapped fragments’’ (FPKM) values by EdgeR v3.22.3 (Robinson et al., 2010).
Genome_build: Anas platyrhynchos [assembly BGI_duck_1.0], ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.fna.gz ; annotation: NCBI Release 102, ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.gff.gz ; files accessed on 8/5/2018. The gene annotation was filtered to include only protein-coding genes.
Supplementary_files_format_and_content: Processed data file contains raw read counts and FPKM values for 3 replicates/sample for protein-coding genes in the annotation.
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| Submission date |
Aug 01, 2020 |
| Last update date |
Jan 11, 2021 |
| Contact name |
Viktor Feketa |
| E-mail(s) |
viktor.feketa@yale.edu
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| Organization name |
Yale University
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| Department |
Cellular & Molecular Physiology
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| Lab |
Sensory Physiology lab
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| Street address |
333 Cedar St SHM BE58
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06510 |
| Country |
USA |
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| Platform ID |
GPL28134 |
| Series (1) |
| GSE155529 |
Lamellar cells from Pacinian and Meissner corpuscles are touch sensors |
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| Relations |
| BioSample |
SAMN15693837 |
| SRA |
SRX8864021 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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