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| Status |
Public on May 01, 2023 |
| Title |
Act5C-GS>Ras attP-GFP-LI-Clone2_rep2 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Act5C-GS>Ras attP-GFP-LI-Clone2
tissue specificity: neuronal-like
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| Growth protocol |
Cell cultures were grown and expanded in their respective media. All cell lines were cultured in Schneiders Drosophila Medium (Gibco Cat # 21720001), supplemented with 10% Fetal Bovine Serum (Cytiva Hyclone Cat SH30070.03). For Act5C-GS>Ras attP-GFP-LI-Clone 2, Act5C-GS>Ras attP-GFP-LI-Clone 3 and Act5C-GS>Ras attP-GFP-LB-Clone 6 cultures were grown in the same basal media supplemented with 10 nM of Mifepristone (Thermofisher Cat# H11001).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from the pellets using the TRIzolTM reagent (Life technologies (Ambion), Cat#:15596018) as per manufacturer’s instructions. The isolated total RNA was subjected to a cleanup using the RNeasy Mini Kit (Qiagen, Cat#74104) and the RNA post-cleanup was eluted in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
330A1-2
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| Data processing |
FastQC was used for sequencing data quality control and MultiQC was used to aggregate the results.
Raw data processing was performed using STAR sequence aligner, the reads from 3 runs are added.
featureCounts were used to get gene counts from all samples into a single counts' matrix
Differential gene expression testing was performed by DESeq2
Assembly: Drosophila, FlyBase release r6.48
Supplementary files format and content: text file including read counts of each sample
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| Submission date |
Nov 30, 2022 |
| Last update date |
May 01, 2023 |
| Contact name |
Yanhui Hu |
| E-mail(s) |
[email protected]
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| Phone |
617-432-6546
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
Norbert Perrimon
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE219105 |
Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research |
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| Relations |
| BioSample |
SAMN31950771 |
| SRA |
SRX18438954 |
| 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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