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| Status |
Public on Aug 19, 2017 |
| Title |
FMRP_HyperTRIBE_s2_rep2 |
| Sample type |
SRA |
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| Source name |
S2 Cell
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| Organism |
Drosophila melanogaster |
| Characteristics |
selection method: Transient tranfection-FACS sorting
tribe expression: induced
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| Treatment protocol |
S2 cells were treated with CuSO4 to induce protein expression, neuron expression was induced by RU486
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from FACS-sorting cells are extracted by TRIZOL, RNA from manual sorted neurons are prepared using the method described in Abruzzi et al, 2015.
s2 cell mRNA libraries were prepared using Illumina Truseq kits according to manufacturers protocol. Neuronal cell sorting libraries were prepared according to Abruzzi et al, 2015.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA sequencing data were analyzed as described in (Rodriguez et al., 2012; McMahon et al., 2016), with minor modifications.
Scripts available on GitHub (https://github.com/rosbashlab/TRIBE).
Alignment to dm3 genome was done with Tophat v2.1.1 with referenence annotation in gtf format. Multimapped reads are removed.
PCR duplicate is removed with Picard v2.8.2
Genome_build: Release 5/dm3
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format, (Chromosome, co-ordinate, co-ordinate, edit %, edit%_number of total reads)
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| Submission date |
Aug 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Weijin Xu |
| E-mail(s) |
[email protected]
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| Organization name |
Brandeis University
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| Street address |
415 South st.
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| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02453 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE102814 |
Mechanistic Implications of Enhanced Editing by a HyperTRIBE RNA-binding protein |
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| Relations |
| BioSample |
SAMN07519225 |
| SRA |
SRX3103151 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2746742_FMRP_HyperTRIBE_s2_rep2.bedgraph.gz |
211.7 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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