 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 04, 2011 |
| Title |
Non-Pit-TG |
| Sample type |
SRA |
| |
|
| Source name |
Non-vampire bat TG
|
| Organism |
Carollia brevicauda |
| Characteristics |
bat type: Non-vampire
tissue: trigeminal ganglia (TG)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Paraformaldehyde fixation, trizol extraction, poly-(A)+ enrichment, cDNA synthesis, Illumina library generation from dsDNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Carollia_brevicauda_tg
|
| 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
.
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.
|
| |
|
| Submission date |
Mar 29, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas T Ingolia |
| E-mail(s) |
nick@ingolia.org
|
| Phone |
410 246 3025
|
| Organization name |
Carnegie Institution
|
| Department |
Embryology
|
| Lab |
Ingolia
|
| Street address |
3520 San Martin Drive
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21218 |
| Country |
USA |
| |
|
| Platform ID |
GPL13344 |
| Series (1) |
| GSE28243 |
Alternative splicing of the TRPV1 gene underlies infrared sensation in vampire bats |
|
| Relations |
| SRA |
SRX089370 |
| BioSample |
SAMN00696774 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM699150_Carollia_brevicauda_tgs_bos_hits.txt.gz |
80.2 Kb |
(ftp)(http) |
TXT |
| GSM699150_Carollia_brevicauda_tgs_vs_bos.txt.gz |
287.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
