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| Status |
Public on Jun 27, 2023 |
| Title |
U29_3 |
| Sample type |
SRA |
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| Source name |
female reproductive tract, unmated, 29C, biol rep 3
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: female reproductive tract
Sex: female
genotype: Oregon-R-P2
treatment: unmated
time: collected in parallel with mated samples
temperature: 29
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| Treatment protocol |
Females either remained virgin or were collected 10-15 after mating with a wildtype control male (w1118 or esgts F/O w1118), or Dad male (esgts F/O UAS-Dad). Reproductive tracts of females were dissected in 1X PBS. The digestive system and the upper part of the common ovidcut were removed.
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| Growth protocol |
D. melanogaster stocks were maintained at 21 or 29C on yeast/glucose food in a 12 hour light/dark cycle.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from on average 64 female reproductive tracts per sample. For males, RNA was extracted from 3 whole males. RNA was extracted using the Direct-zol RNA microprep kit according to the manufacturer's instructions (Zymo, CA)
To sequence mRNAs and non-polyadenylated long noncoding RNAs, we used the Ovation Universal Drosophila RNA-Seq Kit, which allows for the depletion of abundant ribosomal RNAs (Tecan, CA). We prepared the libraries according to the manufacturer’s instructions (Tecan, CA). For the optional fragmentation step in the protocol, we fragmented cDNA using Covaris to obtain a fragment size of 400 bases.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
U29_3
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| Data processing |
We used Trimmomatic to remove overrepresented sequences and to filter reads (Bolger, Lohse, and Usadel 2014). Specifically, bases at the end of a read with a Phred quality score less than 20 were clipped off. The read was also clipped once, in a window of 5 bases, the average read quality dropped below a Phred score of 20. After trimming, we kept only reads with a minimum length of 30 bases.
Reads were aligned to dm6 using STAR (Dobin et al. 2013).
Read counts were obtained using HTSeq (Anders, Pyl, and Huber 2015).
Assembly: dm6
Supplementary files format and content: The processed data files contains raw read counts for each sample (output from HTSeq).
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| Submission date |
Oct 19, 2022 |
| Last update date |
Jun 27, 2023 |
| Contact name |
Sofie Delbare |
| Organization name |
NYU Langone
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| Street address |
435 East 30th Street
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE216083 |
Mating activates transcriptional programs and represses microRNAs in the Drosophila melanogaster female reproductive tract [mRNA-seq] |
| GSE216085 |
Mating activates transcriptional programs and represses microRNAs in the Drosophila melanogaster female reproductive tract |
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| Relations |
| BioSample |
SAMN31366441 |
| SRA |
SRX17955528 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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