|
| Status |
Public on Jun 13, 2013 |
| Title |
Manual HiTrapQ small RNAs |
| Sample type |
SRA |
| |
|
| Source name |
3 day-old ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: MG derived
tissue: Ovaries
developmental stage: 3 day-old
gender: female
purification procedure: Manual anion-exchange chromatography (HiTrapQ column) purification
|
| Treatment protocol |
MG_Size isolation: Small RNAs (18-30nt) were isolated using Trizol and size-isolation procedure
MG_HQ: Small RNAs (18-30nt) were isolated by anion exchange chromatography using AKTA FPLC purifier system
MG_manualHQ: Small RNAs (18-30nt) were isolated by manual anion exchange chromatography procedure
|
| Growth protocol |
Flies were grown at 21 degrees C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted small RNAs were cloned by Fasteris SA (Switzerland) after being selected on acrylamide gel between 18 and 30 nucleotides
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Manual anion-exchange chromatography (HiTrapQ column) purification
|
| Data processing |
Base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.)
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) according to sequencing quality using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed (one mismatch was nevertheless allowed on low-sequencing quality nucleotides, -e 20 option).
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode (http://www.modencode.org/ (Celniker et al. 2009)), miRNAs from miRBase (http://www.mirbase.org/ (Kozomara and Griffiths-Jones 2011)), transcripts from Flybase (http://flybase.org/) and transposable elements from Repbase (http://www.girinst.org/repbase/index.html (Jurka et al. 2005)).
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNAs, the remainders, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.
Genome_build: dm5
Supplementary_files_format_and_content: Read counts (second column) for each bona fide sequence (first column)
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
SEVERINE CHAMBEYRON |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Department |
Institute of Human Genetics
|
| Lab |
Non-coding RNA, epigenetics and genome stability
|
| Street address |
141, rue de la Cardonille
|
| City |
MONTPELLIER |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE40748 |
A user-friendly chromatographic method to purify small regulatory RNAs |
|
| Relations |
| SRA |
SRX185891 |
| BioSample |
SAMN01163908 |
