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Status |
Public on Aug 19, 2015 |
Title |
small RNAs in complex with Smaug from Drosophila melanogaster 0-2h embryos |
Sample type |
SRA |
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Source name |
embryos
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Organism |
Drosophila melanogaster |
Characteristics |
Stage: 0-2h embryos genotype: Smaug IP antibody: Guinea pig anti-Smaug
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Treatment protocol |
after RNA extraction from Smaug immunoprecipitates, small RNAs between 18 and 30 nucleotides were selected on an acrylamide gel.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was prepared using Trizol (Invitrogen)
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Library strategy |
RIP-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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Description |
RIP-seq
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Data processing |
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAAT) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch. Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs. Supplementary_files_format_and_content: table of sequences matching release 5 of the genome; indicating sequence and read count. For small RNA-seq, sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3' end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) using Bowtie, with up to one mismatch (-v 1 -a --best --strata). Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. For piRNA identification, we selected reads that were 23-29nt in length and not annotated either as abundant cellular species (tRNAs, rRNAs, snoRNA and snRNA) nor as miRNAs. For iCLIP-seq, the sample- and random barcode sequence were removed from 5’ end following linker sequence trimming at the 3’ end. Trimmed sequence reads were aligned to the genome sequence of Drosophila melanogaster using Bowtie, with up to 2 mismatches for unique mapper reads and 0 mismatch for multi mapper reads. Genome_build: dm5 Supplementary_files_format_and_content: For small RNA-seq, tab-delimited texts containing mapped non-redundant sequences (first column) and corresponding count in the library (second column)
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Submission date |
Jul 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Simonelig Martine |
E-mail(s) |
martine.simonelig@igh.cnrs.fr
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Organization name |
Institut de Genetique Humaine - CNRS
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Department |
Genetics and Development
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Lab |
mRNA Regulation and Development
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Street address |
141, rue de la Cardonille
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City |
MONTPELLIER |
ZIP/Postal code |
34396 |
Country |
France |
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Platform ID |
GPL13304 |
Series (2) |
GSE70777 |
Aubergine iCLIP reveals direct regulation of mRNAs involved in germ cell development by piRNAs in the early embryo |
GSE70778 |
Aubergine iCLIP and expression |
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Relations |
BioSample |
SAMN03854472 |
SRA |
SRX1091849 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1818088_Smaug_IP.txt.gz |
100.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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