|
| Status |
Public on Nov 12, 2015 |
| Title |
M. musculus kidney input replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
M. musculus kidney input
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57B6
gender: male
developmental stage: adult
tissue: kidney
|
| Growth protocol |
Freshly isolated tissue was used
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted using Phenol and Quiagen Dneasy Blood and Tissue Kit
Libraries were prepared accroding to Ford et al (BMC Res. Notes 7, 312, 2014). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12-18 cycles and library fragments of 250-350 bp ) were band isolated with Agencourt beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
DIP-Seq
All reads were trimmed using sickle and the fastx toolkit (removing bases with <Q20).
M. musculus reads were mapped to mm9 with variations as in publication using bwa 0.6.2
X. laevis reads were mapped to LAEVIS7.1 with variaitions as in publication using bwa 0.6.2
E. coli reads were mapped to the K12 genome (NCBI Reference NC_000913.2) using bwa 0.6.2
bigwigs were generated by extending the reads to 300 bases and binned to 50 bases.
Genome_build: E.coli NC_000913.2; mm9;
X. laevis 7.1 at ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla7.1/
Supplementary_files_format_and_content: bigwigs - binned tracks for visualisation
|
| |
|
| Submission date |
Oct 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Bradshaw |
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE74184 |
Methylome analysis of deoxyadenosines in higher eukaryotes |
|
| Relations |
| BioSample |
SAMN04196524 |
| SRA |
SRX1356594 |
