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| Status |
Public on Jul 07, 2022 |
| Title |
NeuN_Neg mouse brain nuclei |
| Sample type |
SRA |
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| Source name |
genomic DNA
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
nuclei subpopulation: NeuN_Neg
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| Treatment protocol |
N/A
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| Growth protocol |
Mouse brain nuclei are isolated and sorted into NeuN-High, NeuN-Low and NeuN_Neg subpopulation based on NeuN staining using fluorescence-activated nuclear sorting.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was purified from NeuN-High, NeuN-Low and NeuN-Neg mouse brain nuclei using DNeasy kit (Qiagen, Frederick, MD, USA #69504), according to the manufacturer’s instructions. TAB-seq libraries were constructed according to Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
library strategy: TAB–seq
Data were mapped to the Mus musculus GRCm38 reference genome
TAB-seq analysis were performed as described in Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text file
Column1: chromosome
Column2: cytosine position
Column3: strand
Column4: CNN (N = A, T, C, G)
Column5: methylated cytosines in this site
Column6: totally detected cytosines in this site
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| Submission date |
Aug 27, 2015 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE72432 |
Brain neuronal cell nuclei with exceptionally high levels of hydroxymethylcytosine |
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| Relations |
| BioSample |
SAMN04014365 |
| SRA |
SRX1165929 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1862590_Schmitzlab_allc_M_musculus_NeuN_negative_all.tsv.gz |
843.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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