|
| Status |
Public on May 01, 2013 |
| Title |
Single cell #3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse liver single cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57BL/6
|
| Treatment protocol |
Liver tissue was perfused with collagenase
|
| Growth protocol |
C57BL/6 mice were obtained from the National Institute of Aging (NIA) and liver cells were collected and sequenced without growth
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single hepatocytes were collected using hand-held capillaries under an inverted microscope
Library construction for RRBS sequencing was done as described by Meissner 2005 (PubMed: PMC1258174), but with MseI as digest vector and add adding 2 ng salmon DNA (samples H1,H2) or 2 ng tRNA cDNA (samples H3,H4) as buffer DNA to stabilize single-cell samples.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H3
Reduced Representation BS-Seq (RRBS)
|
| Data processing |
Library strategy: RRBS-Seq
Basecalls were performed using CASAVA version 1.4
BS-Seq reads were preprocessed for better alignment quality using FASTX-toolkit 0.0.13, trimgalore 0.2.2 and cutadapt 1.0
BS-Seq reads were aligned to the mm10 genome using Bowtie2 2.0.0 and Bismark 0.7.6
CpG-Methylation calling was done using Bismark 0.7.6
CpG sites were grouped into regions of 1000 nt's with a minimum coverage of 10 CG sites using R 2.13 with custom scripts
Methylation status and differential methylation between single-cells and reference H1 were assessed using bayesian estimation for a beta-binomial model using R 2.13
Methylating epimutations were called on regions showing low methylation in the reference L1 but high methylation in a single-cell sample using R 2.13
Demethylating epimutations were called on regions showing high methylation in the reference L1 but low methylation in a single-cell sample using R 2.13
Genome_build: mm10
Supplementary_files_format_and_content: GFF listing all regions with methylation and demethylating epimutation were generated using R 2.13
Supplementary_files_format_and_content: GFF scores represent the CG methylation level of each region with epimutations
|
| |
|
| Submission date |
Oct 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kemal Akman |
| E-mail(s) |
kemal.akman@campus.lmu.de
|
| Phone |
+492215062161
|
| Fax |
+492215062163
|
| URL |
http://www.treschgroup.de
|
| Organization name |
Max Planck Institute Cologne
|
| Department |
Plant Breeding Research
|
| Lab |
Tresch Group
|
| Street address |
Carl-von-Linné-Weg 10
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE41379 |
Single-cell DNA methylation analysis of epimutations in mouse liver cells. |
|
| Relations |
| SRA |
SRX192133 |
| BioSample |
SAMN01758881 |
