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Sample GSM2585327 Query DataSets for GSM2585327
Status Public on May 21, 2018
Title E14G rep1
Sample type SRA
 
Source name E14 male gonads
Organism Gallus gallus
Characteristics breed: Cobb 500
tissue: Male gonads
developmental stage: E14
Growth protocol Fertilized eggs incubated at 37oC at 60% humidity to desired date
Extracted molecule total RNA
Extraction protocol Samples are homogenized and small RNAs are collected via miRNeasy Mini Kit (Qiagen, CA, USA) according to manufacturers’ instructions
Sodium periodate oxidation treatment on small RNA samples, followed by library preparation using Illumina TruSeq Small RNA sample preparation kit (Illumina, San Diego, CA, USA) accordint to manufactures' iinstruction
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina MiSeq
 
Description periodate oxidation treated
Data processing Base-calling via real time analysis in Illumina HiSeq 2000 systems
adapter trimmed small RNAs are aligned to gga4 genome assembly using tophat2, with options: -g 1 -N 0 --read-gap-length 0 --read-edit-dist 0 --read-realign-edit-dist 0 --max-insertion-length 0 --max-deletion-length 0
filtering out potential rRNA/tRNA based on Rfam record, and filtering out potential miRNA based on miRBase record, using bowtie v1.2.0 with options: --norc -v 0; piRNA candidates are selected at range of 24nt to 34nt
piRNA cluster prediction via proTRAC v2.0.5, with options: -pdens 0.05 -1Tor10A 0.01 -1Tand10A 0.01 -distr 1-90 -clsize 3000 -clsplit 0.2 -pimin 24 -pimax 34 -rpm -nh -nr -noimage -nofaspi; the proTRAC v2.0.5 was slightly modfied for identifying dual-strand piRNA clusters
Genome_build: gga5
Supplementary_files_format_and_content: proTRAC output that list piRNA clusters identified in each sample
 
Submission date Apr 20, 2017
Last update date May 15, 2019
Contact name Shau-Ping Lin
E-mail(s) shaupinglin@ntu.edu.tw
Organization name National Taiwan University
Department Institute of Biotechnology
Street address No. 81, Chang-Xing St.
City Taipei City
ZIP/Postal code 10672
Country Taiwan
 
Platform ID GPL19064
Series (1)
GSE98005 Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development
Relations
BioSample SAMN06768588
SRA SRX2748823

Supplementary file Size Download File type/resource
GSM2585327_E14G_1.proTRAC.table.txt.gz 81.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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