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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 04, 2011 |
| Title |
Vampire-TG |
| Sample type |
SRA |
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| Source name |
Vampire bat TG
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| Organism |
Desmodus rotundus |
| Characteristics |
bat type: Vampire
tissue: trigeminal ganglia (TG)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Paraformaldehyde fixation, trizol extraction, poly-(A)+ enrichment, cDNA synthesis, Illumina library generation from dsDNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Desmodus_rotundus_tg
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| Data processing |
Alignment files (*vs_bos.txt): blastx against Bos taurus genome build bt3.
Alignment file column headers are the standard blastx tabular output:
1. qseqid--Query Seq-id (sequencing read name) 2. sseqid--Subject Seq-id (RefSeq protein ID) 3. pident--Percentage of identical matches 4. length--Alignment length 5. mismatch--Number of mismatches 6. gapopen--Number of gap openings 7. qstart--Start of alignment in query (nucleotide coordinates) 8. qend--End of alignment in query (nucleotide coordinates) 9. sstart--Start of alignment in subject (amino acid coordinates) 10. send--End of alignment in subject (amino acid coordinates) 11. evalue--Expect value 12. bitscore--Bit score
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Counts files (*bos_hits.txt): We used a custom script (described in the associated manuscript), that counts the number of reads whose best BlastX alignment is a hit on the RefSeq protein in question.
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| Submission date |
Mar 29, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas T Ingolia |
| E-mail(s) |
nick@ingolia.org
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| Phone |
410 246 3025
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| Organization name |
Carnegie Institution
|
| Department |
Embryology
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| Lab |
Ingolia
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| Street address |
3520 San Martin Drive
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21218 |
| Country |
USA |
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| Platform ID |
GPL13343 |
| Series (1) |
| GSE28243 |
Alternative splicing of the TRPV1 gene underlies infrared sensation in vampire bats |
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| Relations |
| SRA |
SRX089368 |
| BioSample |
SAMN00696772 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM699148_Desmodus_rotundus_tg1_bos_hits.txt.gz |
76.7 Kb |
(ftp)(http) |
TXT |
| GSM699148_Desmodus_rotundus_tg1_vs_bos.txt.gz |
59.6 Mb |
(ftp)(http) |
TXT |
| GSM699148_Desmodus_rotundus_tg2_bos_hits.txt.gz |
76.7 Kb |
(ftp)(http) |
TXT |
| GSM699148_Desmodus_rotundus_tg2_vs_bos.txt.gz |
58.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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