 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 20, 2021 |
| Title |
Post 3 |
| Sample type |
SRA |
| |
|
| Source name |
lymph gland
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: w1118
tissue: Blood
age: third instar larvae
position: posterior
|
| Treatment protocol |
Third instar larval lymph glands were dissected in ice cold PBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted with Arcturus PicoPure RNA kit and samples were converted to cDNA using Nugen’s Ovation RNA-Seq System.
Library preparation was performed using Kapa Biosystems library preparation kit. Samples were multiplexed using the following barcodes: Ant1 (CAGATC), Ant2 ( ACTTGA), Ant3 (GATCAG), Post1 (TAGCTT), Post2 (GGCTAC), Post3 (CTTGTA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalling was performed with Casava (v1.8).
Quality score trimming and filtering were performed with Trimmomatic (v0.32).
Trimmed reads were aligned to Drosophila melanogaster rRNA gene sequences using Bowtie2 (v2.1.0) to filter out reads originating from rRNA
rRNA filtered reads were aligned to the annotated Dm genome (build BDGP5, Ensembl release 70) using TopHat (v2.0.10)
Per gene read counts were calculated from the TopHat output using htseq-count (v0.5.4p5)
RPKM (Reads Per Kilobase of exon per Megabase of library size) were caclulated using Cufflinks (2.2.1)
Differential gene expression was analyzed using the R package DESeq2 (v1.2.8)
Genome_build: BDGP dm6
Supplementary_files_format_and_content: tab-delimited text files include FBGN number and RPKM values for each sample.
|
| |
|
| Submission date |
Jun 13, 2020 |
| Last update date |
Feb 20, 2021 |
| Contact name |
yoan renaud |
| E-mail(s) |
yoan.renaud@uca.fr
|
| Organization name |
igred
|
| Street address |
place henri dunand
|
| City |
clermont ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE152416 |
Transcriptomic analysis of Drosophila larval lymph glands |
|
| Relations |
| BioSample |
SAMN15230099 |
| SRA |
SRX8540988 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
