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| Status |
Public on May 21, 2018 |
| Title |
BC rep2 |
| Sample type |
SRA |
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| Source name |
Blastodermal cells
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| Organism |
Gallus gallus |
| Characteristics |
breed: Leghorn
tissue: Blastodermal cells
developmental stage: fresh fertilized eggs
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| Growth protocol |
Fertilized eggs incubated at 37oC at 60% humidity to desired date
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| 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
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
periodate oxidation treated
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| 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
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| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shau-Ping Lin |
| E-mail(s) |
shaupinglin@ntu.edu.tw
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| Organization name |
National Taiwan University
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| Department |
Institute of Biotechnology
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| Street address |
No. 81, Chang-Xing St.
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| City |
Taipei City |
| ZIP/Postal code |
10672 |
| Country |
Taiwan |
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| Platform ID |
GPL16133 |
| Series (1) |
| GSE98005 |
Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development |
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| Relations |
| BioSample |
SAMN06768591 |
| SRA |
SRX2748820 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2585324_BC_2.proTRAC.table.txt.gz |
79.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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