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| Status |
Public on Feb 01, 2022 |
| Title |
total RNA from Lam Dm0 and Lam C KD testes, rep 1 |
| Sample type |
SRA |
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| Source name |
3rd instar larvae testes
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Testes
developmental stage: third instar larvae
strain: UAS-LamDm0-RNAi/bam-Gal4-VP16; UAS-LamC-RNAi/+
biological replicate: 1
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| Growth protocol |
Flies were grown according to standard protocols.
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNAs from ~200 testes per replicate (in three biological replicates), dissected from third instar larvae of UAS-LamDm0-RNAi/bam-Gal4-VP16; UAS-LamC-RNAi/+ (Lam-KD) males, were isolated using Trizol (Invitrogen). RNA was isolated using Trizol reagent (Invitrogen).
RNA samples were subjected to poly(A)+ selection, cDNA synthesis and deep sequencing on Illumina NovaSeq in the GENEWIZ (USA; www.GENEWIZ.com), resulting in 33-40 million 150-nt paired-end reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RNA-seq_Lam-KD_rep1
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| Data processing |
sequencing reads from three biological replicates of Lam-KD and control testes were adapter clipped, uniquely mapped to dm3/R5 genome assembly and low quality reads with the length of less than 20 nt were filtered out. Since replicates were highly correlated, they were merged, reads were counted for genes of BDGP5.78 annotation and converted to TPM values using Salmon (Patro et al. 2017).
Genome_build: dm3
Supplementary_files_format_and_content: sf.txt files for RNA-seq replicates represent read counts per gene (in TPM) obtained in Salmon.
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| Submission date |
Sep 06, 2020 |
| Last update date |
Feb 01, 2022 |
| Contact name |
Artem Ilin |
| E-mail(s) |
artem.ilin@su.se
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| Organization name |
Stockholm University
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| Department |
MBW
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| Street address |
Svante Arrhenius väg 20C
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| City |
Stockholm |
| ZIP/Postal code |
11418 |
| Country |
Sweden |
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| Platform ID |
GPL25244 |
| Series (1) |
| GSE157565 |
Comparison of genome architecture at two stages of male germline cell differentiation in Drosophila |
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| Relations |
| BioSample |
SAMN16070788 |
| SRA |
SRX9084990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4770614_7_quant.genes.sf.txt.gz |
200.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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