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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 08, 2022 |
| Title |
hAstrocyte_SOX11 |
| Sample type |
SRA |
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| Source name |
Astrocyte
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| Organism |
Homo sapiens |
| Characteristics |
chip antibody: SOX11
cell line: Astrocyte
cell type: human astrocyte
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| Growth protocol |
hNSCs, MB002 and MB004 cells were cultured in complete NPC medium (Neurobasal medium containing B27 supplement, N2 supplement, 2 mM L-glutamine, 20 ng/ml EGF, 20 ng/ml bFGF, 2 mg/ml Heparin and 50 μg/ml BSA). hAstrocytes were cultured in DMEM with 10% FBS. Spheres were dissociated at a diameter of 100-200 μm and were changed with complete NPC medium every 3 days to maintain cell metabolic activity.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Bam files were calculated using Bowtie 2 and transform to Bigwig file using esATAC in R.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: Cut&run
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| Submission date |
Jul 11, 2022 |
| Last update date |
Oct 10, 2022 |
| Contact name |
Zaili Luo |
| Organization name |
CCHMC
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| Lab |
Richard Lu
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| Street address |
3333 Burnet Ave.
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE198565 |
Single cell transcriptional and chromatin accessibility profiling identify the cellular heterogeneity of human medulloblastoma |
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| Relations |
| BioSample |
SAMN29632308 |
| SRA |
SRX16116355 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6322945_hAstrocyte_SOX11.bw |
143.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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