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Sample GSM1245136 Query DataSets for GSM1245136
Status Public on Jun 30, 2015
Title dcl4_Apr2F
Sample type SRA
 
Source name 10 day-old protonemata
Organism Physcomitrium patens
Characteristics genotype: dcl4
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 22ÂșC.
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 SAMN02377969
SRA SRX365405

Supplementary file Size Download File type/resource
GSM1245136_dcl4_Apr2F_table.txt.gz 13.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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