|
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 |