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| Status |
Public on Feb 12, 2024 |
| Title |
wildtype, adult trachea, replicate 4 |
| Sample type |
SRA |
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| Source name |
trachea
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: trachea
cell line: adult
genotype: w1118
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNAmagic after manufacturer's protocol (Bio-Budget Technologies GmbH, Germany). cDNA synthesis was performed after Hagemann-Jensen et al. 2020 with minor modifications. Due to low cDNA amount whole length cDNA was amplified via PCR by controlling cycle number to avoid overamplification with LA Taq polymerase (TAKARA BIO INC., Japan).
Library preparation was done adopted to Picelli et al. 2014. The samples were equimolar pooled and quantified (with Agilent Bioanalyzer, DNA 7500). Sequencing was done on the NextSeq 500 (Illumina) using the High Output Kit v2.5 (75 cycles)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
S04Adult Trachea_4
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| Data processing |
CLC Genomics Workbench 9.5.2
Imported using Illumina Single Read import (FastQ); Quality Score = NCBI/Sanger or Illumina Pipeline 1.8 and later; failed reads were removed
Sequence reads were mapped to gene regions only using the Drosophila melanogaster genome (assembly Release 6 plus ISO1 MT) (parameters: mismatch cost = 2, insertion cost = 2, deletion cost = 2, length fraction = 0.8, similarity fraction = 0.85, global alignment = no, strand specific = both, maximum number of hits for a read = 10, count paired reads as two = no, expression value = RPKM, calculate RPKM for genes without transcripts = no, use EM estimation = yes)
Differential expression for RNA-Seq was perfomed compairing to a control group (WholeAdults, Larval Trachea )
Assembly: assembly Release 6 plus ISO1 MT
Supplementary files format and content: xlsx files include RPKM values for each Sample
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| Submission date |
Feb 10, 2023 |
| Last update date |
Feb 12, 2024 |
| Contact name |
Judith Bossen |
| E-mail(s) |
jbossen@zoologie.uni-kiel.de
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| Organization name |
CAU Kiel, Zoological Institute
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| Department |
Molecular Physiology
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| Lab |
Roeder
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| Street address |
Am Botanischen Garten 3-9
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| City |
Kiel |
| ZIP/Postal code |
24118 |
| Country |
Germany |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE225000 |
Adult and larval tracheal systems exhibit different molecular architectures in Drosophila |
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| Relations |
| BioSample |
SAMN33238819 |
| SRA |
SRX19329737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7036834_RPKM-values_AdultTrachea_4.xlsx |
2.2 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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