|
Status |
Public on Jul 20, 2021 |
Title |
sham_3d_Rep1_Lib1 |
Sample type |
SRA |
|
|
Source name |
whole heads
|
Organism |
Drosophila melanogaster |
Characteristics |
strain: w[1118]; Bloomington stock 5905 post-injury timepoint: 3d condition: sham library: library 1 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 |
Sham injured males, 3 d 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
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|
|
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 |
SAMN18542761 |
SRA |
SRX10484310 |