|
| Status |
Public on Jul 20, 2021 |
| Title |
TBI_1h_Rep1_Lib2 |
| Sample type |
SRA |
| |
|
| Source name |
whole heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w[1118]; Bloomington stock 5905
post-injury timepoint: 1h
condition: TBI
library: library 2
tissue: whole heads
|
| Treatment protocol |
3d old male flies were subjected to sham or severe dTBI injury. control animals are 3d old males.
|
| Growth protocol |
reared at 25C; 12 hour light-dark cycle; standard medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
whole flies were flash frozen in liquod nitrogen; heads (n=20/sample) were dissociated by vortexing then collected. Total RNA was extracted by TRIzol/chloroform.
sample libraries were prepared in two batches (separate days) using the same Illumina TruSeq Stranderd Sample Kit (Cat# RS-122-2103)
RNA-seq; sequenced on Illumina NextSeq using NextSeq® 500/550 High Output Kit v2 (75 cycles; FC-404-2005)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Severe TBI injured males, 1 h post-injury, biological replicate 1
|
| Data processing |
demultiplexed fastq files were obtained from Illumina's BaseSpace and quality checked with fastqc/multiqc
sequenced reads were were mapped to the fly genome (FlyBase d. mel build 6.17) using HISAT2 with parameter --rna-strandness R; index reference was created using hisat2-build
aligned reads were converted to bam files sorted by aligned position
sample bam files were merged across sequencing runs using Picard
Htseq-count was used to generate unnormalized read count table (with parameters: htseq-count --format bam --order pos --mode union --stranded reverse --minaqual 1 --type exon --idattr gene_id --nonunique=none) for differential expression analysis with DESeq2
Genome_build: Flybase dmel r6.17
Supplementary_files_format_and_content: matrix table (.csv) with raw gene counts for every gene (FlyBase gene ID) and every sample
|
| |
|
| Submission date |
Mar 30, 2021 |
| Last update date |
Jul 20, 2021 |
| Contact name |
Nancy M Bonini |
| Organization name |
University of Pennsylvania
|
| Street address |
433 South University Ave
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE171185 |
Timecourse RNAseq for Drosophila TBI |
|
| Relations |
| BioSample |
SAMN18542737 |
| SRA |
SRX10484335 |
