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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 17, 2019 |
| Title |
chicken caudal cntrl rep 1 |
| Sample type |
SRA |
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| Source name |
Embryonic brainstem
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| Organism |
Gallus gallus |
| Characteristics |
age: embryonic day 7.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
Vestibulospinal neurons were retrogradely labeled for manual cell isolation with tetramethylrhodamine-conjugated dextran amine, acutely dissociated, and manually sorted.
RNA was isolated using the PicoPure RNA Isolation kit (Applied Biosystems), cDNA was synthesized and amplified using Ovation RNA-seq System v2 (Nugen), and RNA-seq libraries were prepared using the Ovation Ultralow DR Multiplex System (Nugen)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
lunde_et_al_2019_chicken_counts.txt
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| Data processing |
Illumina CASAVA 1.8.2 for HiSeq 2000 or RTA 2.4.6 for NextSeq500
Sequencing data in FASTQ format were aligned to the mouse genome (mm9) using the RUM pipeline (version 1.11 (Grant et al., 2011)) or to the chicken genome (Galgal5) using the STAR aligner (Dobin et al., 2013).
Genome feature quantification for mouse data was performed with RUM, using RefSeq annotations, and for chicken data with STAR using the Gallus_gallus.Gallus_gallus-5.0.93.gtf annotation file downloaded from Ensembl.org
Genome_build: mm9 for mouse, Galgal5 for chicken
Supplementary_files_format_and_content: counts
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| Submission date |
Jan 16, 2019 |
| Last update date |
Jan 17, 2019 |
| Contact name |
Benjamin Okaty |
| E-mail(s) |
bokaty@genetics.med.harvard.edu
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| Organization name |
Harvard Medical School
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19787 |
| Series (1) |
| GSE125197 |
Molecular Profiling defines evolutionarily conserved transcription factor signatures of major vestibulospinal neuron groups |
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| Relations |
| BioSample |
SAMN10756464 |
| SRA |
SRX5255283 |
| 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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