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Sample GSM3063047 Query DataSets for GSM3063047
Status Public on Oct 22, 2018
Title AgoRIP 3, antibody A, no I-PpoI [unc-AgoIP-abc-5]
Sample type SRA
 
Source name HeLa
Organism Homo sapiens
Characteristics cell line: HeLa
growth protocol: DMEM + FBS + Pen/Strep
incubation after plasmid or mock transfection: 36hrs
sirna: none
ip, antibody: abcam (ab57113)
i-ppoi transfection: Mock
miRNA spike-ins (exiqon): none
Extracted molecule total RNA
Extraction protocol Magna RIP RNA-Binding Protein Immunoprecipitation Kit
TruSeq small RNA library preparation, Illumina, using RNA returned from RIP as input
 
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: custom
Supplementary_files_format_and_content: standard bowtie output format, reads mapped to ribosomal cDNA library
 
Submission date Mar 23, 2018
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 GPL18573
Series (1)
GSE106764 Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks
Relations
BioSample SAMN08783732
SRA SRX3837310

Supplementary file Size Download File type/resource
GSM3063047_unc-AgoIP-abc-5.rrna.bowtie.gz 110.0 Kb (ftp)(http) BOWTIE
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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