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| Status |
Public on Jun 12, 2017 |
| Title |
sj-DK |
| Sample type |
SRA |
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| Source name |
blade of sporophyte
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| Organism |
Saccharina japonica |
| Characteristics |
treatment: dark
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from blade of S. japonica using the improved method of Cetyl Trimethylammonium Bromide (CTAB), RNA integrity, quantity and size were detected by Agilent 2100 Bioanalyzer. Requirements for constructing library are as follows: content>200 ng/μl, total amount >10 μg, OD260/280 is 1.8-2.2, RIN≥8. Then, sRNAs were separated by size fractionation on denaturing polyacrylamide gels. Fragments of 18-30 nt were purified and ligated with 5’ and 3’ RNA adaptor and then amplified by reverse transcription PCR (RT-PCR). Thereafter the purified products were sequenced on a Solexa sequencer (Illumina) according to the manufacturer’s protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
small RNA sequencing
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| Data processing |
Raw data files: sj-BL.fq and sj-DK.fq are raw reads produeced by Solexa sequencing machine, fastq format.
Processed data files: known_miRNAs_in_BL_and_DK_samples.txt and differentially_expressed_known_miRNAs.txt [linked as supplementary files on Series record]
Software = Beijing Genomics Institute (BGI) "tag2miRNA".
Remove low qulity reads strictly
Trim 3' adaptor sequence, Remove 5' adaptor contaminants
Plot data length distribution
Remove too small and polyA
Genome_build: model brown alga Ectocarpus siliculosus [EMBL: CABU01000001-CABU01013533, FN647682-FN649242]
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| Submission date |
Mar 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Li |
| E-mail(s) |
liwei0309@gmail.com
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| Organization name |
Institute of Oceanology, Chinese Academy of Sciences
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| Street address |
No 7 Nanhai Road
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| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266071 |
| Country |
China |
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| Platform ID |
GPL14911 |
| Series (1) |
| GSE36704 |
Identification of microRNAs in response to blue light irridiation by high-throughput sequencing in Saccharina japonica |
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| Relations |
| SRA |
SRX130871 |
| BioSample |
SAMN00829600 |
| 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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