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Sample GSM2850025 Query DataSets for GSM2850025
Status Public on Oct 22, 2018
Title parental line of Drosha KO mESC, no I-PpoI [2_mESC_unc]
Sample type SRA
 
Source name mouse embryonic stem cells
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
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
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
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
 
Submission date Nov 10, 2017
Last update date Oct 22, 2018
Contact name Franziska Bonath
E-mail(s) franziska.bonath@scilifelab.se
Organization name Stockholm University
Department Department for Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratories
Lab Visa/Friedländer
Street address Tomtebodavägen 23A
City Solna
State/province Stockholm
ZIP/Postal code 17165
Country Sweden
 
Platform ID GPL19057
Series (1)
GSE106764 Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks
Relations
BioSample SAMN08011082
SRA SRX3383511

Supplementary file Size Download File type/resource
GSM2850025_2_mESC_unc.bowtie.gz 438.1 Kb (ftp)(http) BOWTIE
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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