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| Status |
Public on Mar 17, 2016 |
| Title |
miGh3c rep3 |
| Sample type |
SRA |
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| Source name |
stem tip
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| Organism |
Gossypium hirsutum |
| Characteristics |
strain: Huazhong 94-3130
tissue: shoot apical
age: the budding stage,eight pieces of leaf
genotype: normal branch
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Plant RNA EASYspin Plus Kit(Aidlab, Peking, China).
RNA and miRNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were aligned to cotton genome no more than 5 mismatches using the SOAP aligner/SOAP2 software after low-quality reads (reads with unknown sequences ‘N’), adaptor sequence fragments, and empty reads were removed
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
The GeneIDs in the processed data files represent (e.g. CotAD_22466, CotAD_64340, etc.), The cotton genome and cds sequences we download form http://cgp.genomics.org.cn (Free to register to use). The reference :(Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J et al: Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution.
Genome_build: ASM98774v1; NCBI WGS Project: LBLM01 (Gossypium hirsutum)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
May 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
quan sun |
| E-mail(s) |
sunquan@cqupt.edu.cn
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| Organization name |
Chongqing University of Posts and Telecommunications
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| Department |
College of Bioinformation
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| Street address |
Chongwen road 2#
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| City |
Chongqing |
| ZIP/Postal code |
400065 |
| Country |
China |
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| Platform ID |
GPL16485 |
| Series (1) |
| GSE69025 |
To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages |
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| Relations |
| BioSample |
SAMN03701522 |
| SRA |
SRX1032945 |
| 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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