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Sample GSM3729282 Query DataSets for GSM3729282
Status Public on Feb 02, 2020
Title DE2-3
Sample type SRA
 
Source name gonadal fragments
Organism Oryzias latipes
Characteristics strain: offspring of d-rR-Tg(olvas-GFP) and Qurt
tissue: gonadal fragments,(include gonads, intestines, and body trunks)
developmental stage: stage 39
treatment: in 28 ◦C fresh water, 14 h light and 10 h dark
Extracted molecule total RNA
Extraction protocol RNA extraction using Both TRIzol and Qiagen RNeasy Micro Kit
Decode-seq: Reverse transcription and template switching using SuperScript II Reverse Transcriptase, library preparation using Illumina Nextera XT DNA Library Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description DE2_count.tsv
Data processing sequencing reads processing and filtering, customized data processing pipeline (python)
genome mapping, STAR(v2.5.2a) using default parameters, and customized data processing pipeline (python)
quantification based on barcode counts, customized data processing pipeline (python)
Genome_build: ENSEMBL human GRCh38, mouse GRCm38, and medaka ASM223467v1
Supplementary_files_format_and_content: plain text,quantification count matrix based on barcode counts, raws are genes and columns are samples (sample name_barcode_sample)
 
Submission date Apr 18, 2019
Last update date Feb 02, 2020
Contact name Qiang Tu
E-mail(s) qtu@genetics.ac.cn
Organization name Institute of Genetics and Developmental Biology
Street address No.1 West Beichen Road,Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL25587
Series (1)
GSE130014 Decode-seq: a practical approach to improve differential gene expression analysis
Relations
BioSample SAMN11461703
SRA SRX5708053

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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