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| Status |
Public on Jun 11, 2024 |
| Title |
Str_Glast_154 pI [scNOME-seq] |
| Sample type |
SRA |
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| Source name |
striatum & ventricular-subventricular zone
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| Organism |
Mus musculus |
| Characteristics |
tissue: striatum & ventricular-subventricular zone
cell type: reactive astrocyte
genotype: TiCY
treatment: 2 days post ischemia
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| Treatment protocol |
Two months old TiCY mice were intraperitoneally injected with tamoxifen. In these mice, tamoxifen-induced Cre recombination takes place in neural stem cells in the vSVZ, which express Tlx (Nr2e1) and will stably activate the production of enhanced YFP, labeling NSCs and their progeny. Two weeks after injection, an injury by bilateral carotid artery occlusion (BCCAO) was performed as described (Llorens-Bobadilla et al., 2015). The animals were sacrificed for single cell sorting either 48 h or 3 weeks after ischemia. WT mice were not subjected to tamoxifen or ischemia.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022).The samples listed here represent the epigenomic portion of this multi-omic data set, i.e. DNA methylation and chromatin accessibility assessed with single-cell NOMe-seq.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
single-cell NOMe-seq
meth_mfrac_promoter.csv.gz
meth_shrunkResid_promoter.csv.gz
meth_mfrac_VMR.csv.gz
meth_shrunkResid_VMR.csv.gz
meth_coverage_VMR.csv.gz
acc_mfrac_promoter.csv.gz
acc_shrunkResid_promoter.csv.gz
acc_mfrac_VMR.csv.gz
acc_shrunkResid_VMR.csv.gz
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| Data processing |
read trimming and adapter removal
Bisulfite-aware read mapping
quantification of CpG and GpC methylation
Assembly: GRCm38 (mm10)
Supplementary files format and content: .csv.gz files: cell x region methylation matrices in gzip-compressed csv (comma-separated values) format. acc: chromatin accessibility (=GpC methylation). meth: DNA (=CpG) methylation. VMR: variably methylated regions identified with the ‘MethSCAn’ software. mfrac: fraction of methylated sites. shrunkResid: shrunken mean of residuals quantified with ‘MethSCAn’.
Supplementary files format and content: .cov.gz files: gzip-compressed tab-separated files produced by Bismark with the following columns: chromosome, start position, end position, methylation percentage, number of methylated cytosines, number of unmethylated cytosines.
Library strategy: Single-cell NOMe-seq
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| Submission date |
Jun 06, 2024 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Ana Martin-Villalba |
| Organization name |
German Cancer Research Center
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| Department |
Molecular Neurobiology
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69121 |
| Country |
Germany |
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| Platform ID |
GPL30172 |
| Series (2) |
| GSE210806 |
Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain |
| GSE211786 |
scNMT-seq of the adult NSC lineage - DNA methylation and chromatin accessibility |
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| Relations |
| BioSample |
SAMN41713481 |
| SRA |
SRX24826803 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8311211_AS-768994-LR-60487_R1R2_dedup.NOMe.CpG.cov.gz |
4.7 Mb |
(ftp)(http) |
COV |
| GSM8311211_AS-768994-LR-60487_R1R2_dedup.NOMe.GpC.cov.gz |
34.8 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
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