|
| Status |
Public on Nov 01, 2013 |
| Title |
nrpe1 sRNA |
| Sample type |
SRA |
| |
|
| Source name |
floral tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: nrpe1-11
ecotype: Columbia
|
| Growth protocol |
All plants were grown at 22 degrees celsius in constant light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction followed by PEG and then urea-PAGE fractionation
Illumina TruSeq small RNA
18-28nt isolated small RNAs from total RNA Trizol preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/8 lane
RNA-seq (size fractionation) - Reads were demultiplexed (perfect matches to each index were required). Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >18 nt and <28 nt in length after trimming were retained. Reads with no identifiable adapter were discarded. Reads were mapped with Bowtie (Langmead et al. 2009 Genome Biol) to the nuclear genome, allowing for 1 mismatch. Both unique and non-uniquely mapping reads were retained for normalization purposes but only uniquely mapping reads were used for downstream analysis. For downstream analyses up to 100 identical mapping reads were allowed to be counted at any given region, locations with more than 100 siblings were flattened to 100 mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome for 24nt class of small RNAs with each bin given a value corresponding to the relative 24 nt read density at that location (24nt reads in 25bp bins / total mapping small RNA reads of all size classes - unique and non-uniquely mapping)
|
| |
|
| Submission date |
Jul 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Joel Hale |
| E-mail(s) |
chris.joel.hale@gmail.com
|
| Organization name |
University of Washington
|
| Department |
Pathology
|
| Lab |
Center for Precision Diagnostics
|
| Street address |
1959 NE Pacific St., HSC H-458
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE49090 |
Interplay Between Active Chromatin Marks and RNA-directed DNA Methylation in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN02261602 |
| SRA |
SRX326959 |
