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| Status |
Public on Feb 16, 2017 |
| Title |
NonArrayF6 #1 Small RNA-seq |
| Sample type |
SRA |
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| Source name |
C. elegans
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: HC83 non-array F6
developmental stage: Young adult
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| Growth protocol |
Synchronized to young adults by timed egg lay
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol/chroloroform, isopropanol precipitation, DNaseI treatment, 5' polyphosphatase treatment, purification and concentration
(In SAMPLES section)
Small RNA libraries made with Apollo 324 NGS Library Prep System (Small RNA 8 Protocol), amplified for 12 cycles, size selected on Pippin Prep, purified and concentrated.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
5'-independent
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| Data processing |
Filter 21-26nt reads (custom script)
Align to C. elegans genome WS235 using Bowtie2, allowing 0 mismatches (--score-min L,0,0) and up to four alignments per read (-k 4)
Generate small RNA counts per gene using HTseq
Genome_build: C. elegans WS235
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| Submission date |
May 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Olga Minkina |
| E-mail(s) |
ominkina@gmail.com
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| Organization name |
Harvard University
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| Department |
Molecular and Cellular Biology
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| Lab |
Craig P. Hunter
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| Street address |
16 Divinity Ave.
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL19757 |
| Series (2) |
| GSE81706 |
Germline- and soma-specific heritable epigenetic silencing at an endogenous locus (small RNA-Seq) |
| GSE81708 |
Germline- and soma-specific heritable epigenetic silencing at an endogenous locus |
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| Relations |
| BioSample |
SAMN05157445 |
| SRA |
SRX1787473 |
| 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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