|
| Status |
Public on Nov 14, 2014 |
| Title |
ddm1-ago6_mock_FLAG-IP_Replicate_A |
| Sample type |
SRA |
| |
|
| Source name |
ddm1-ago6_mock_FLAG-IP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Columbia-0
genotype/variation: ddm1-ago6 mutant
tissue: unopened flower buds
ip antibody: FLAG Antibody
ip antibody vendor: Sigma
ip antibody vendor: M8823
molecule subtype: Immunoprecipitated small RNA
|
| Growth protocol |
Plants were grown on soil in 18 hour long days at 23C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the total RNA libraries, total RNA was extracted using Trizol reagent and enriched using the MirVana microRNA isolation kit. For the IP libraries, mock and IPs were performed as in MuCue et al (in preparation). Small RNAs were extracted from proteins using Trizol LS.
Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mock control: FLAG-IP without the FLAG antigen
|
| Data processing |
Illumina software was used for basecalling. Sequenced reads de-multiplexed and were trimmed for adaptor sequence. Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, tRNA and rRNA-matching reads were removed, and only small RNAs that perfectly match the genome are reported (UEA small RNA tool v 2.5.0 used).
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
R. Keith Slotkin |
| E-mail(s) |
kslotkin@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 North Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE57191 |
Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes |
|
| Relations |
| BioSample |
SAMN02741300 |
| SRA |
SRX529422 |
