 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 21, 2018 |
| Title |
wildtype4 |
| Sample type |
SRA |
| |
|
| Source name |
WT_larval dorsal organ
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: third instar
genotype: Orco-Gal4 > UAS-mCD-8GFP
tissue: dorsal organ
quantity: 20 organs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thoracic segments containing chemosensory organs were dissected from third instar larvae, enzymatically treated with type I collagenase, and GFP-positive dorsal organs were manually separated from neighboring tissue and snap frozen in RNAqueous lysis buffer (Fisher). RNA was isolated using the RNAqueous Micro Kit, diluted to 0.2ng/ul, and converted to pre-amplified cDNA libraries using Smart-seq2 template-switching reverse transcription.
RNA libraries were prepared for sequencing following Illumina protocols. cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq4000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Each sample isolated independently
|
| Data processing |
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2
Reads were filtered for the presence of adapters using Cutadapt version 1.9.1
Reads were aligned to the transcriptome using Kallisto version 0.43.0 with default parameters.
Transcript-level counts were condensed to gene-level counts using tximport
Genome_build: FlyBase genome release 6.10
Supplementary_files_format_and_content: Tab delimited text files showing estimated counts for all isoforms for each sample
Supplementary_files_format_and_content: Tab delimited text files showing estimated counts for all genes for each sample
|
| |
|
| Submission date |
Mar 02, 2018 |
| Last update date |
Jun 22, 2018 |
| Contact name |
Jay Parrish |
| E-mail(s) |
jzp2@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Department of Biology
|
| Lab |
Parrish Lab
|
| Street address |
Box 351800
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL21306 |
| Series (1) |
| GSE111334 |
Prior activity of olfactory receptor neurons is required for proper sensory processing and behavior in Drosophila larvae |
|
| Relations |
| BioSample |
SAMN08629712 |
| SRA |
SRX3757060 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3028688_wildtype4Genes.txt.gz |
135.2 Kb |
(ftp)(http) |
TXT |
| GSM3028688_wildtype4Isoforms.txt.gz |
282.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
