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| Status |
Public on Apr 10, 2014 |
| Title |
dsRNA in wt cells |
| Sample type |
SRA |
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| Source name |
HEK 293 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK 293
dicer status: wt
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was prepared using Trizol reagent, digested using T1 nuclease and resulting dsRNA was sequenced
100ng of sample was phosphatase and PNK treated, as in the Illumina mRNA Directional protocol. All clean ups (post-PNK, post-PCR) were done using Ampure XP beads. Following steps were carried out using the NEBNext Small RNA Library Prep Kit but with custom indexes designed by the WTCHG facility (Reference: Improved workflows for high throughput library preparation using the transposome-based nextera system <http://www.biomedcentral.com/1472-6750/13/104> Sarah Lamble, Elizabeth Batty, Moustafa Attar, David Buck, Rory Bowden, Gerton Lunter, Derrick Crook, Bassam El-Fahmawi, Paolo Piazza BMC Biotechnology 2013, 13:104, 20 November 2013). The concentration of each library was determined by realtime using Agilent qPCR Library and a MX3005P instrument (Agilent). Sequencing was performed on an Illumina HiSeq2000, using 50bp paired end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
total RNA was digested using T1 nuclease and resulting dsRNA was sequenced
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| Data processing |
Basecalling was by Illumina's bcl2fastq v1.8.4, with internal chastity filter. Parameters for configureBclToFastq:.pl --ignore-missing-bcl --fastq-cluster-count 0 --no-eamss --use-bases-mask "Y*,I8,Y*" --mismatches 1 --ignore-missing-stats --ignore-missing-control
Mapping was by BWA v0.7 followed by stampy v1.0.21. Parameters for bwa: -t 8 -q10 Parameters for stampy: defaults, except: -t 8 --bamkeepgoodreads
Processed bam file of WTCHG_64954_282 and WTCHG_64954_283 to wiggle type format. Multiple peaks from set 282 were combined into one, if they overlayed one peak in 283 and vice versa. This was done iteratively until the peaks remained constant. "Top peaks" refers to the peaks where the maximum coverage is >1500 in 282 and 283 data simultaneously.
genome build hg19
supplementary files format and content: peak coordinates from overlay step and top peaks
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| Submission date |
Apr 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kinga Kamieniarz-Gdula |
| Organization name |
University of Oxford
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| Department |
Sir William Dunn School of Pathology
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| Street address |
South Parks Road
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| City |
Oxford |
| ZIP/Postal code |
OX1 3RE |
| Country |
United Kingdom |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE56648 |
Human nuclear Dicer restricts the deleterious accumulation of endogenous double strand RNA |
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| Relations |
| BioSample |
SAMN02724791 |
| SRA |
SRX514565 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1366346_dsRNA_coordinates.xlsx.gz |
9.9 Mb |
(ftp)(http) |
XLSX |
| GSM1366346_file282_v2.bedGraph.gz |
37.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1366346_finalset.xlsx.gz |
24.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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