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| Status |
Public on Oct 22, 2018 |
| Title |
DGCR8 KO mESC, no I-PpoI [13_DGCR8KO_unc] |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
growth protocol: LIF+Serum, gelatin coated wells
incubation after plasmid or mock transfection: 36hrs
sirna: 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: The reference we used to map was not from a genome build but from a curated ribosomal RNA library:We curated a ribosomal RNA library based on RNA sequences retrieved from NCBI (www.ncbi.nlm.nih.gov, accessed: 2015-02-17), Silva (https://www.arb-silva.de, 23193283) and the Ensembl database (www.ensembl.org, accessed: 2015-02-17).
Supplementary_files_format_and_content: standard bowtie output format, reads mapped to ribosomal cDNA library
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| Submission date |
Nov 10, 2017 |
| 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 |
GPL19057 |
| 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 |
SAMN08011079 |
| SRA |
SRX3383514 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2850028_13_DGCR8KO_unc.bowtie.gz |
525.7 Kb |
(ftp)(http) |
BOWTIE |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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