|
Status |
Public on Feb 16, 2017 |
Title |
HC125 5' dependent #1 Small RNA-seq |
Sample type |
SRA |
|
|
Source name |
C. elegans
|
Organism |
Caenorhabditis elegans |
Characteristics |
strain: HC125 developmental stage: Young adult
|
Growth protocol |
Synchronized to young adults by timed egg lay
|
Extracted molecule |
total RNA |
Extraction protocol |
Trizol/chroloroform, isopropanol precipitation, DNaseI 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.
|
|
|
Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
5'-dependent
|
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
|
|
|
Submission date |
May 20, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Olga Minkina |
E-mail(s) |
ominkina@gmail.com
|
Organization name |
Harvard University
|
Department |
Molecular and Cellular Biology
|
Lab |
Craig P. Hunter
|
Street address |
16 Divinity Ave.
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02138 |
Country |
USA |
|
|
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 |
|
Relations |
BioSample |
SAMN05157449 |
SRA |
SRX1787477 |