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| Status |
Public on Mar 24, 2017 |
| Title |
low detergent rep 2 |
| Sample type |
SRA |
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| Source name |
Fly heads
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: fly heads
treatment: low detergent
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| Extracted molecule |
total RNA |
| Extraction protocol |
For head1 and 2 samples we followed the original fly head homogenization protocol (Huang et al 2013 Pbio PMID: 24348200). For the Heads 3 and 4 sample 200 heads were frozen and lysed in 500ul of lysis buffer (30 mM HEPES KOH at pH 7.4, 100 mM KAcetate, 2 mM MgAcetate, 5% glycerol, 0.1% Triton X-100, 1 mM EGTA, 5 mM DTT, 0.4 U/μL murine RNase inhibitor [NEB], protease inhibitors (Complete mini, Roche), and 100ug/ml CHX). ribosome-protected RNA fragments were isolated using previously publish protocol (Calviello L et al 2015 nature methods PMID: 26657557)
RNA libraries were prepared using previously publish protocol (Calviello L et al 2015 nature methods PMID: 26657557)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ribosome bound RNA
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| Data processing |
Illumina adaptors were removed using cutadapt 1.9.1
Removing PCR duplications
Trimming four bases from both ends of the reads (these are UMIs)
Removing ribosoal RNA reads from the files
Alignment aginst circRNA dataset
Genome_build: dm3
Supplementary_files_format_and_content: Table with list of circRNA detected in the footprinting data
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| Submission date |
Mar 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sebastian Kadener |
| E-mail(s) |
[email protected]
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| Organization name |
Brandeis University
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| Street address |
415 South Street
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| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
9190401 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE79626 |
Ribosome footprinting of fly heads |
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| Relations |
| Reanalyzed by |
GSM3278860 |
| BioSample |
SAMN04580878 |
| SRA |
SRX1663881 |
| 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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