|
| Status |
Public on Jun 30, 2015 |
| Title |
mDCL_Apr2B |
| Sample type |
SRA |
| |
|
| Source name |
10 day-old protonemata
|
| Organism |
Physcomitrium patens |
| Characteristics |
genotype: mDCL
tissue: protonemal tissue
|
| Treatment protocol |
None
|
| Growth protocol |
protonemal tissue was grown on cellophane-overlaid BCD media {Ashton, 1977} supplemented with 50mM ammonium tartarate under 16hr days, 8hr nights at 22ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Tri-Reagent (Sigma) per the manufacturer's instructions
small RNA-seq libraries for the Illumina HiSeq2500 were prepared using the Illumina TruSeq Small RNA protocol, as described by the manufacturer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FASTQ data were groomed by removal of 3' adapter sequences using ShortStack (version 1.1.0) with adapter sequence "ATCTCGTA". The right-most exact match to this sequence was inferred to be the 3' adapter junction, and was the site of trimming. Reads < 15 after trimming, and reads where the adapter was not found were discarded.
Trimmed FASTQ data was counted to make a table giving the frequencies of each unique small RNA sequence in tab-delimited text format.
Genome_build: n/a
Supplementary_files_format_and_content: Processed data files are tab-delimited text files giving 1) Small RNA sequences, 2) Frequencies
|
| |
|
| Submission date |
Oct 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael J Axtell |
| E-mail(s) |
[email protected]
|
| Organization name |
Pennsylvania State University
|
| Department |
Biology
|
| Lab |
Axtell
|
| Street address |
280 Mueller Lab
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL17793 |
| Series (1) |
| GSE51419 |
small RNA-seq of Physcomitrella patens small RNA mutants |
|
| Relations |
| BioSample |
SAMN02377983 |
| SRA |
SRX365413 |
