|
| Status |
Public on May 03, 2012 |
| Title |
Col small RNA |
| Sample type |
SRA |
| |
|
| Source name |
floral tissue, wild type, small RNA
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: wild type (eco. Columbia)
tissue: floral
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated small RNAs from total RNA Trizol preparation.
Illumina TruSeq small RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Purified 15-30nt small RNAs.
|
| Data processing |
Small RNA reads were demultiplexed (perfect matches to each index were required) and then filtered for average QC score > 30. Adapter sequences (identified by at least a 13 nt perfect match) were trimmed and reads >15 nt in length after trimming were retained. Reads with no identifiable adapter were discarded. Reads were then mapped with Bowtie to TAIR8 chr1..5/C/M, allowing for 2 mismatches and retaining only uniquely-mapping reads.
Supplementary_files_format_and_content: Each processed file gives 50-basepair resolution small RNA counts normalized by total number of uniquely-mapping reads as a UCSC Genome Browser wiggle file in plain text format with UNIX-style line endings (single `fixedStep start=1 step=50 span=50' header per chromosome in order chr1..5; non-negative decimal values).
Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/3 lane.
Genome_build: TAIR8
|
| |
|
| Submission date |
May 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn J. Cokus |
| Organization name |
UCLA
|
| Street address |
UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE37644 |
MORC family ATPases required for heterochromatin condensation and gene silencing |
|
| Relations |
| SRA |
SRX145410 |
| BioSample |
SAMN00990535 |
| Named Annotation |
GSM925641_Col_sRNA_processed.linCvg50bpResolution.UCSCwigToAthTAIR8chr12345.wig.gz |
