|
| Status |
Public on Nov 30, 2018 |
| Title |
GMR_PRP4-RNAi_GD_9-15-SampleA_S1 |
| Sample type |
SRA |
| |
|
| Source name |
fly head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: adult head
genotype/variation: prp4 knockdown sample (GMR>prp4-RNAi (GD))
|
| Growth protocol |
3-5 day old flies were entrained for at least 3 full cycles in 12h:12h light:dark conditions and all frozen at ZT12 for subsequent RNA isolation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fly heads were then collected on dry ice and homogenized with Trizol (Life Technologies) on ice using standard protocols. Following the phase separation, the aqueous phase was transferred into a new tube, mixed with an equal volume of 70% ethanol and loaded directly onto the RNeasy mini kit columns (Qiagen). The rest of RNA isolation was done according to the manufacturer’s protocol. On-column DNase digestion (Qiagen) for 15 minutes at RT was always included.
Samples were prepared with Lexogen’s SENSE mRNA-Seq library Prep Kit. Illumina Next-Generation Sequencing (NextSeq 500) with 300pb paired-end high output run (at ~50M reads per sample) was performed by the Genomics Facility at the Wistar Institute.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
gene_quant.txt
junction_counts.txt
exon_counts.txt
|
| Data processing |
Raw RNA-Seq reads were aligned to the BDGP6.v88 build of the fruitfly genome using STAR v2.5.3a. STAR was provided with gene models from the Ensembl v88 genome annotation.
The Pipeline of RNA-Seq Transformations (PORT) v0.8.2a-beta was used to perform gene-level and exon-level normalization and quantification of the aligned data. PORT is an implementation of the re-sampling approach for normalization proposed by Li and Tibshirani. Briefly, PORT accounts for potential confounding factors like reads mapping to rRNA and mitochondrial DNA. Next, PORT determines the input samples with the fewest number of gene-mapping reads and re-samples all datasets to the same number of reads. Lastly, PORT quantifies the normalized gene-level reads counts for each sample.
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample
|
| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
Iryna Shakhmantsir |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennsylvania
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE115163 |
Identification of gene expression and splicing changes upon eye-specific downregulation of tri-snRNP components in Drosophila |
|
| Relations |
| BioSample |
SAMN09296162 |
| SRA |
SRX4155527 |
