|
| Status |
Public on Jul 05, 2012 |
| Title |
Exp1 Control AID |
| Sample type |
SRA |
| |
|
| Source name |
Co-transduced NIH-3T3 cells
|
| Organism |
Mus musculus |
| Characteristics |
vector 1: mOrangeSTOP
vector 2: AID-ER
vector 3: Empty
|
| Growth protocol |
Retroviral supernatants were produced in 293T cells by transient calcium phosphate cotransfection with pCL-ECO (Imgenex) and a combination of AID-ER, AIDE58Q-ER, pMX-PIE-OrangeSTOP,adn pBABE-Ugi, pBABE-UNG or pBabe-Empty retroviral vectors. NIH-3T3 cells were transduced with retroviral supernatants for 16 h in the presence of 8 µg/ml polybrene (Sigma-Aldrich) and selected with 0.4 µg/ml puromycin or 100 µg/ml hygromycin. Transduced NIH-3T3 cells were cultured in the presence of 1 µM OHT for 11 days. Orange sequence was PCR-ed with Pfu Ultra for 25 cycles.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
PCR products were fragmented to a range of 100-300 pb (Covaris S2). DNA was processed through successive enzymatic treatments of end repair, dA tailing, and ligation to adapters according to the manufacturer’s instructions (Illumina). Adapter-ligated libraries were further amplified by PCR with Phusion High-Fidelity DNA Polymerase (Finnzymes) using Illumina PE primers for 10 cycles.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
PCR amplified mOrangeSTOP
|
| Data processing |
Base calling was done with Illumina's Casava 1.7
Reads were aligned with Novoalign v2.07.04
SAM alignments were processed with samtools 0.1.11 into pileup format
A custom perl script was used to filter the positions with Q<20 and compile statistics for each sequence position
Supplementary_files_format_and_content: Complete mutation data in Excel format, description of the columns in the Legend tab
|
| |
|
| Submission date |
Jul 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Pablo Perez-Duran |
| Organization name |
Centro Nacional de Investigaciones Cardiovasculares (CNIC)
|
| Street address |
Melchor Fernandez Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28002 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE39108 |
UNG shapes the specifity of AID-induced somatic hypermutation in non B cells |
| GSE39115 |
UNG shapes the specificity of AID-induced somatic hypermutation |
|
| Relations |
| SRA |
SRX157695 |
| BioSample |
SAMN01085836 |
