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GEO help: Mouse over screen elements for information. |
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Status |
Public on Oct 22, 2018 |
Title |
HeLa cells, control siRNA, no I-PpoI, Cordycepin treated [25_siCont_unc_Cord] |
Sample type |
SRA |
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Source name |
HeLa
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Organism |
Homo sapiens |
Characteristics |
cell line: HeLa growth protocol: DMEM + FBS + Pen/Strep incubation after plasmid or mock transfection: 36hrs sirna: 25nM of control siRNA (Thermo Fisher, CatNo: 4390844) was transfected with Lipofectamine RNAiMAX 12 hrs prior to I-PpoI transfection ip, antibody: none i-ppoi transfection: Mock miRNA spike-ins (exiqon): recommended amount
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Extracted molecule |
total RNA |
Extraction protocol |
TRIZOL TruSeq small RNA library preparation, Illumina, using 1ug of total RNA as input, addition of Exiqon small RNA spike-ins
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Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
removing adatper, pre-mapping to a hand-curated list of ribosomal cDNA and miRNA libraries and collapsing reads with identical sequence using an in-house pipeline allowing one mismatch and discarding reads below 18nt remapping to ribosomal RNA (custom cDNA library) using bowtie (version 1.12) with the options “-v 0 –q –k 1 –best” Genome_build: custom Supplementary_files_format_and_content: standard bowtie output format, reads mapped to ribosomal cDNA library
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Submission date |
Mar 23, 2018 |
Last update date |
Oct 22, 2018 |
Contact name |
Franziska Bonath |
E-mail(s) |
franziska.bonath@scilifelab.se
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Organization name |
Stockholm University
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Department |
Department for Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratories
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Lab |
Visa/Friedländer
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Street address |
Tomtebodavägen 23A
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City |
Solna |
State/province |
Stockholm |
ZIP/Postal code |
17165 |
Country |
Sweden |
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Platform ID |
GPL18573 |
Series (1) |
GSE106764 |
Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks |
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Relations |
BioSample |
SAMN08783723 |
SRA |
SRX3837316 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3063053_25_siCont_unc_Cord_rrna.bowtie.gz |
582.6 Kb |
(ftp)(http) |
BOWTIE |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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