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Sample GSM2171659 Query DataSets for GSM2171659
Status Public on Feb 16, 2017
Title hrde-1;HC125 #2 Small RNA-seq
Sample type SRA
 
Source name C. elegans
Organism Caenorhabditis elegans
Characteristics strain: hrde-1;HC125 (HC995)
developmental stage: Young adult
Growth protocol Synchronized to young adults by timed egg lay
Extracted molecule total RNA
Extraction protocol Trizol/chroloroform, isopropanol precipitation, DNaseI treatment, 5' polyphosphatase treatment, purification and concentration
(In SAMPLES section)
Small RNA libraries made with Apollo 324 NGS Library Prep System (Small RNA 8 Protocol), amplified for 12 cycles, size selected on Pippin Prep, purified and concentrated.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description 5'-independent
Data processing Filter 21-26nt reads (custom script)
Align to C. elegans genome WS235 using Bowtie2, allowing 0 mismatches (--score-min L,0,0) and up to four alignments per read (-k 4)
Generate small RNA counts per gene using HTseq
Genome_build: C. elegans WS235
 
Submission date May 20, 2016
Last update date May 15, 2019
Contact name Olga Minkina
E-mail(s) ominkina@gmail.com
Organization name Harvard University
Department Molecular and Cellular Biology
Lab Craig P. Hunter
Street address 16 Divinity Ave.
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL19757
Series (2)
GSE81706 Germline- and soma-specific heritable epigenetic silencing at an endogenous locus (small RNA-Seq)
GSE81708 Germline- and soma-specific heritable epigenetic silencing at an endogenous locus
Relations
BioSample SAMN05157444
SRA SRX1787472

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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