|
| Status |
Public on Jul 01, 2012 |
| Title |
LacZ_control_RNAseq, 1 |
| Sample type |
SRA |
| |
|
| Source name |
central nervous system, LacZ expression control
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: D42>LacZ
tissue: central nervous system
developmental stage: 3rd instar larva
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq libraries were constructed using Illumina mRNA sequencing kits. Total RNA was subjected to two rounds of oligo-dT purification to extract the poly(A)+ component. Purified mRNA was then chemically fragmented to approximately 200 bases. Fragmented RNA was used as template for first strand cDNA synthesis using random primers and SuperScript II. The second strand was then synthesized using RNAseH and DNA Pol I. Fragment ends were repaired using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. A single 'A' was added to the 3' ends of each fragment using Klenow fragment (3' to 5' exo minus). Adaptors were ligated to the fragments and the final product was run on a 2% sizing gel. The region corresponding to 300 bp was then recovered. Templates were enriched by 15 cycles of polymerase chain reaction (PCR) using Phusion DNA polymerase. The PCR primers also included indexing sequences to "barcode" the samples. PCR was followed by a second gel to separate PCR product from unincorporated primers. Libraries were validated by examining their profiles on the Agilent Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNA-Seq of polyA-selected RNA.
|
| Data processing |
Sequences were aligned to a reference Drosophila sequence (FlyBase r5.23) using Illumina's CASAVA package.
|
| |
|
| Submission date |
Aug 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Dennis J Hazelett |
| Organization name |
OHSU
|
| Department |
Integrative Biosciences
|
| Lab |
David Morton
|
| Street address |
611 SW Campus Dr
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE31194 |
Parallel high-throughput RNA-sequencing suggests little overlap of differential gene expression between knockout of TDP-43 and its over-expression in central nervous system in Drosophila |
|
| Relations |
| Reanalyzed by |
GSM3275865 |
| SRA |
SRX105244 |
| BioSample |
SAMN00752466 |
