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Sample GSM956231 Query DataSets for GSM956231
Status Public on Jul 05, 2012
Title Exp3 Control AID-E58Q
Sample type SRA
Source name Co-transduced NIH-3T3 cells
Organism Mus musculus
Characteristics vector 1: mOrangeSTOP
vector 2: AID-E58Q-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
SRA SRX157710
BioSample SAMN01085851

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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