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Sample GSM1818088 Query DataSets for GSM1818088
Status Public on Aug 19, 2015
Title small RNAs in complex with Smaug from Drosophila melanogaster 0-2h embryos
Sample type SRA
 
Source name embryos
Organism Drosophila melanogaster
Characteristics Stage: 0-2h embryos
genotype: Smaug IP
antibody: Guinea pig anti-Smaug
Treatment protocol after RNA extraction from Smaug immunoprecipitates, small RNAs between 18 and 30 nucleotides were selected on an acrylamide gel.
Extracted molecule total RNA
Extraction protocol RNA was prepared using Trizol (Invitrogen)
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description RIP-seq
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)
 
Submission date Jul 10, 2015
Last update date May 15, 2019
Contact name Simonelig Martine
E-mail(s) martine.simonelig@igh.cnrs.fr
Organization name Institut de Genetique Humaine - CNRS
Department Genetics and Development
Lab mRNA Regulation and Development
Street address 141, rue de la Cardonille
City MONTPELLIER
ZIP/Postal code 34396
Country France
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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