 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 14, 2018 |
| Title |
PTR1/N+ |
| Sample type |
SRA |
| |
|
| Source name |
chimpanzee_neuronal cells of Brodmann area 10 (Cortex)
|
| Organism |
Pan troglodytes |
| Characteristics |
gender: female
tissue: Fresh-frozen frontal cortex sample (Brodmann area BA10)
cell type: neuronal cells
|
| Treatment protocol |
Cortex tissue was fluorescence-activated cell sorted into neuronal and non-neuronal cells using a NeuN-specific antibody, as described previously (Wagner et al., 2015).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from sorted cell fractions was isolated with the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).
Genomic DNA was digested with the methylation sensitive restriction enzyme MspI (New England BioLabs, Frankfurt a. M., Germany). End repair of the resulting 3’ overhangs and A-tailing were performed to enable adaptor ligation. After purification with AMPure XP beads (Beckmann Coulter, Krefeld, Germany) and ligation of the methylated universal adaptors (Illumina, San Diego, USA), an additional bead wash step was conducted. Bisulfite conversion was performed with the EpiTect Bisulfite Kit (Qiagen, Hilden, Germany), followed by a wash step using the MinElute PCR Purification Kit (Qiagen). After barcoding of the bisulfite treated samples two additional rounds of bead clean-up were performed. The final libraries were sequenced (single end 76 bp) with the Illumina Genome Analyzer II (Illumina, San Diego, USA) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 7
|
| Data processing |
Adapter and low quality sequences were trimmed from RRBS reads by trim_galore_v0.4.0 (parameters: --rrbs --stringency 1 -e 0.2 -a GATCGGAAGAGCA)
Curated reads were mapped in a directional manner using bismark_v0.14.5 with default parameters on the hg19 or the panTro4 genome respectively
CpG positions in the chimpanzee genome were transferred onto the human genome via liftover
Genome_build: hg19 and panTro 4
Supplementary_files_format_and_content: csv files contain chromosome name, coordinate, fraction of methylated nucleotides (percent), number of methylated nucleotides, number of unmethylated nucleotides
|
| |
|
| Submission date |
Jan 24, 2018 |
| Last update date |
Aug 14, 2018 |
| Contact name |
Christian W. Remmele |
| E-mail(s) |
christian.remmele@uni-wuerzburg.de
|
| Organization name |
University of Wuerzburg
|
| Department |
Department of Bioinformatics
|
| Street address |
Am Hubland
|
| City |
Würzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9378 |
| Series (1) |
| GSE109559 |
Cell type and species-specific methylation patterns in neuronal and non-neuronal cells of human and chimpanzee cortex |
|
| Relations |
| BioSample |
SAMN08390774 |
| SRA |
SRX3595195 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2946584_PTR1_N+.csv.gz |
8.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
