|
| Status |
Public on Nov 01, 2013 |
| Title |
Young_3_MeDIP |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Haematopoietic Stem Cells
strain: C57BL/6
age: Young - 8 - 12 weeks
medip antibody: 5-mC monoclonal antibody 33D3 (Diagenode, catalog# mAb-081, lot# 03000A)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We sorted lower side population cells (LSPs) from adult female wild-type C57b/6 mice at different time points and extracted DNA and RNA simultaneously from the same cells. DNA library prep was performed using NEB library prep kits for illumina and mRNA library prep was completed using the Illumina Tru-seq library prep kit
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DNA IP against 5-Methylcytosine
|
| Data processing |
The MeDIP-seq data were analysed within the MeDUSA pipeline (Wilson et al. 2012)
Alignment was performed using BWA v0.5.8 with default parameters
Filtering was performed using SAMtools to remove reads with low alignment score. Only those forming a correctly aligned pair were kept. A final filtering step removed potential PCR artefacts by discarding all but one read-pair within groups of non-unique fragments.
Wig files were created using the MEDIPS v1.0 bioconductor package. Bigwig files generated by converting wig files generated in MEDIPS using wigToBigWig from UCSC.
The RNA-Seq data were analysed using RSEM v1.1.21
RNA-seq data was aligned against a transcriptome library using BOWTIE v0.12.7 with default parameters. Transcript library built using RSEM v1.1.21 utilising UCSC mm9 annotation (from UCSC table 'knownGene')
Isoform counts were generated from the aligned RNA-seq data using RSEM (http://deweylab.biostat.wisc.edu/rsem/) utilising the UCSC known gene table for mm9.
Gene counts and isoform counts .results files output from RSEM
Genome_build: mm9
Supplementary_files_format_and_content: .bw file scores represent normalised (reads per million) read depth across the genome.
Supplementary_files_format_and_content: .results files represent gene counts and isoform counts. Headers for the output genes.results are 'internal_gene_id', 'expected_counts', 'tau_value', 'ucsc_transcript_id_list'. Headers for the output isoforms.results are 'ucsc transcript_id', 'expected_counts', 'tau_value', 'internal_gene_id'.
|
| |
|
| Submission date |
Oct 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gareth Wilson |
| E-mail(s) |
gareth.wilson@ucl.ac.uk
|
| Organization name |
UCL Cancer Institute
|
| Street address |
23 Huntley Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE41658 |
Methylomic analysis identifies the involvement of migration and adhesion genes in the ageing of primary haematopoietic stem cells |
|
| Relations |
| SRA |
SRX196440 |
| BioSample |
SAMN01766991 |
