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Sample GSM4978174 Query DataSets for GSM4978174
Status Public on Dec 18, 2020
Title sRNA S2 zswim8/Dora knockout clone 3
Sample type SRA
 
Source name sRNA S2 zswim8/Dora knockout
Organism Drosophila melanogaster
Characteristics cell type: Drosophila S2
genotype/variation: Knockout
Extracted molecule total RNA
Extraction protocol Cells were washed with PBS, and RNA was harvested using TRI-Reagent.
Small-RNA sequencing libraries were prepared as described (Kingston and Bartel, 2019). A step-by-step protocol is available at http://bartellab.wi.mit.edu/protocols.html. Libraries were prepared from 5 ug total RNA extracted from cells.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description TTAGGC-s_1_1
S2_sRNA_DESeq2_output_zswim8.txt
Data processing Standard base calls were made using the Illumina HiSeq platform protocol.
Adapter sequences were trimmed using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’ to ensure that all bases had an accuracy of 99.9%.
Counting of miRNAs was performed by string-matching the first 19 nt of each read to a dictionary derived from mature miRNA sequences. These dictionaries were generated from sets of mature miRNA sequences downloaded from TargetScan7 (Agarwal et. al, 2015) in the case of human, mouse, and fly miRNAs, or as reported (Jan et. al, 2011) in the case of worm miRNAs. These sequences were filtered to retain only those for which the first 19 nt were distinct. This matching method had the advantage of reducing the ambiguity in assigning miRNA isoforms, which exhibited heterogeneity at their 3′ ends, to a single mature miRNA.
Count files were merged to generate tables of counts for each cell line, organized by the gRNA expressed for knockdown/knockout.
Differential expression and significance levels were determined using DESeq2 (1.18.1) (Love et. al, 2014) without the lfcShrink() function.
Genome_build: TargetScanHuman release 7.2 or TargetScanFly release 7.2.
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 contain normalized counts for each library, log2-fold changes, adjusted p-values, and other output.
 
Submission date Dec 16, 2020
Last update date Dec 20, 2020
Contact name Charlie Y. Shi
E-mail(s) [email protected]
Organization name Whitehead Institute / MIT
Department Biology
Lab Bartel Lab
Street address 455 Main St.
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL17275
Series (2)
GSE160304 The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation
GSE163388 The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset3]
Relations
BioSample SAMN17099193
SRA SRX9695096

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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