characteristics.text: 2018-04-06
characteristics.characteristic: Date_sequenced
characteristics.text: sRNA-seq
characteristics.characteristic: Experiment_type
characteristics.text: SAMN32942858
characteristics.characteristic: External Id
characteristics.text: University of Chicago
characteristics.characteristic: INSDC center name
characteristics.text: 2023-01-27T00:00:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-01-27T18:01:14.480Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS16610873
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: Model organism or animal
characteristics.characteristic: NCBI submission model
characteristics.text: Model.organism.animal.1.0
characteristics.characteristic: NCBI submission package
characteristics.text: npp-7
characteristics.characteristic: RNAi treatment
characteristics.text: SRS16610873
characteristics.characteristic: SRA accession
characteristics.text: Total RNA was extracted from whole animals of ~100,000 synchronized young adults. Small (<200nt) RNAs were enriched with mirVana miRNA Isolation Kit (Ambion). In brief, 80 μL (200-300 μg) of total RNA, 400 μl of mirVana lysis/binding buffer and 48 μL of mirVana homogenate buffer were mixed well and incubated at room temperature for 5 minutes. Then 176 μL of 100% ethanol was added and samples spun at 2500 x g for 4 minutes at room temperature to pellet large (>200nt) RNAs. The supernatant was transferred to a new tube and small (<200nt) RNAs were precipitated with pre-cooled isopropanol at -70°C. Small RNAs were pelleted at 20,000 x g at 4°C for 30 minutes, washed once with 70% pre-cooled ethanol, and dissolved with nuclease-free water. 10 μg of small RNA was fractionated on a 15% PAGE/7M urea gel, and RNA from 17 nt to 40 nt was excised from the gel. RNA was extracted by soaking the gel in 2 gel volumes of NaCl TE buffer (0.3 M NaCl, 10 mM Tris-HCl, 1 mM EDTA pH 7.5) overnight. The supernatant was collected through a gel filtration column. RNA was precipitated with isopropanol, washed once with 70% ethanol, and resuspended with 15 μL nuclease-free water. RNA samples were treated with RppH to convert 22G-RNA 5’ triphosphate to monophosphate in 1x reaction buffer, 10U RppH (New England Biolabs), and 20U SUPERase-In RNase Inhibitor (Invitrogen) for 3 hours at 37°C, followed by 5 minutes at 65°C to inactivate RppH. RNA was then concentrated with the RNA Clean and Concentrator-5 Kit (Zymo Research). Small RNA libraries were prepared according to the manufacturer’s protocol of the NEBNext Multiplex Small RNA Sample Prep Set for Illumina-Library Preparation (New England Biolabs). NEBNext Multiplex Oligos for Illumina Index Primers were used for library preparation (New England Biolabs). Libraries were sequenced using an Illumina HiSeq4000 at the University of Chicago Genomic Facility.
characteristics.characteristic: description
characteristics.text: young adult
characteristics.characteristic: dev_stage
characteristics.text: oma-1::gfp I; cdk-1::gfp II; 21ur-anti-gfp(type I) IV.
characteristics.characteristic: genotype
characteristics.text: Staged worms from parents grown on npp-7 RNAi food were grown from L1 to YA at 20C
characteristics.characteristic: growth_protocol
characteristics.text: Caenorhabditis elegans
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_6239
characteristics.characteristic: organism
characteristics.text: 1
characteristics.characteristic: replicate
characteristics.text: hermaphrodite
characteristics.characteristic: sex
characteristics.text: HCL134
characteristics.characteristic: strain
characteristics.text: whole worm
characteristics.characteristic: tissue
characteristics.text: npp7_sRNA.fastq.gz
characteristics.characteristic: title