|
| Status |
Public on Jun 20, 2013 |
| Title |
AGO1-isolated RNA |
| Sample type |
SRA |
| |
|
| Source name |
cell culture, purified AGO1
|
| Organism |
Trichoplusia ni |
| Characteristics |
cell line: Hive Five
infection: AGO1 baculovirus
rna source: purified AGO1 protein
|
| Treatment protocol |
Baculovirus infection for recombinant protein expression.
|
| Growth protocol |
Approximately 1 million High Five (T. ni) uninfected or infected (with AGO1 baculovirus) cells were used for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard Trizol (Invitrogen) RNA extraction, per manufacturer's instructions. Additionally, 10 μg of purified hAGO proteins were subjected to Trizol RNA extraction.
Barcoded small RNA sequencing was performed essentially as described (Hafner et al., 2011 (PMID 21775473)). RNA inputs of 2 μg (from T. ni cells) or 20 ng (AGO-isolated RNAs) were used per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Barcoded sample, single HiSeq sequencing lane.
|
| Data processing |
Alignment was performed using Bowtie2 (Langmead and Salzberg, 2012) and standalone BLAST (NCBI).
Annotation was accomplished using custom Perl scripts with the following reference sequence sources: ACMPNV genome (Ayres et al., 1994), D. melanogaster genome (FB2013_03, except for rRNA which was added from ENTREZ NCBI), and an internally curated human tRNA database (based originally on (Lowe and Eddy, 1997)).
Genome_build: FlyBase FB2013_03 (Drosophila melanogaster)
Supplementary_files_format_and_content: Tab-delimited text files containing sequences and counts. See the GSE48076_README.txt file for details.
|
| |
|
| Submission date |
Jun 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Pavel Morozov |
| Organization name |
Rockefeller University
|
| Department |
Tuschl Lab
|
| Lab |
RNA biology Lab.
|
| Street address |
1230
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17310 |
| Series (1) |
| GSE48076 |
Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity |
|
| Relations |
| BioSample |
SAMN02208076 |
| SRA |
SRX310407 |
