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Sample GSM2871144 Query DataSets for GSM2871144
Status Public on May 21, 2018
Title E7PGC rep2
Sample type SRA
 
Source name E7 cultured male PGC
Organism Gallus gallus
Characteristics breed: Arbor Acres broiler
tissue: Male gonads
developmental stage: E7
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 HiSeq 2000
 
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 Nov 30, 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 GPL16133
Series (1)
GSE98005 Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development
Relations
BioSample SAMN08115081
SRA SRX3434284

Supplementary file Size Download File type/resource
GSM2871144_E7PGC_2.proTRAC.table.txt.gz 124.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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