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| Status |
Public on Feb 02, 2020 |
| Title |
DE2-3 |
| Sample type |
SRA |
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| Source name |
gonadal fragments
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| 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
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
DE2_count.tsv
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| 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)
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| Submission date |
Apr 18, 2019 |
| Last update date |
Feb 02, 2020 |
| Contact name |
Qiang Tu |
| E-mail(s) |
qtu@genetics.ac.cn
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| Organization name |
Institute of Genetics and Developmental Biology
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| Street address |
No.1 West Beichen Road,Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL25587 |
| Series (1) |
| GSE130014 |
Decode-seq: a practical approach to improve differential gene expression analysis |
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| Relations |
| BioSample |
SAMN11461703 |
| SRA |
SRX5708053 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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