|
| Status |
Public on Jun 27, 2013 |
| Title |
Dscam isoforms Profiling for S2 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cell line
|
| Organism |
Drosophila melanogaster |
| Characteristics |
sample type: cell line derived from embryonic hemocytes
gene: Dscam
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNAs were extracted using Trizol reagent following manufacturer's protocol.
Libraries were prepared using customized pipeline for our Circularization-Assisted Multi-Segment Sequencing. In brief, first, using RT-PCR with the barcode-indexed primers targeting constitutive exon 3 and exon 10, Dscam mRNA was reverse-transcribed and amplified. After circularization of the 2kb RT-PCR products and another round of PCR with the primers targeting constitutive exon 7 and exon 8, the amplification product of approximately 1kb in length was then sequenced.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Library strategy: Circularization-Assisted Multi-Segment Sequencing
The bases were called from the raw images using the offline base caller OLB-1.9.0. Note that due to our special multiple-segment sequencing protocol, the control lane produced output only for the first segment which contained the barcodes. Therefore the quality values of the produced fastq files are not reliable.
The read files were demultiplexed according to the barcodes. The barcodes consist of two parts which are ligated during the circularization step and then sequenced as one segment. A read was only retained if both parts of the barcode matched to the same reference sequence with at most one mismatch.
The three exonic segments of each read were aligned separately to the drosophila melanogaster dscam exon sequences using bowtie2 (parameters: --very-sensitive-local -5 3). Only the reads for which all three segments could uniquely be mapped to exons from the respective cluster were retained.
Genome_build: dm3
Supplementary_files_format_and_content: The processed data files contain the number of reads for each combination of exon 4 (1..12), exon 6 (1..48) and exon 9 (1..33).
|
| |
|
| Submission date |
Mar 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Andreas Gogol-Döring |
| E-mail(s) |
andreas.gogol-doering@mni.thm.de
|
| Organization name |
Technische Hochschule MIttelhessen
|
| Department |
MNI
|
| Street address |
Wiesenstraße 14
|
| City |
Gießen |
| ZIP/Postal code |
35390 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE45167 |
Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing |
|
| Relations |
| SRA |
SRX249389 |
| BioSample |
SAMN01978275 |
