|
| Status |
Public on Oct 22, 2018 |
| Title |
AgoRIP 3, antibody B, no I-PpoI [unc-AgoIP-dia-10] |
| 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: diagenode (Cat. No. C15200167)
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 |
SAMN08783730 |
| SRA |
SRX3837312 |
