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| Status |
Public on Feb 28, 2024 |
| Title |
K27 Scramble-2 |
| Sample type |
SRA |
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| Source name |
Flow cytometry sorted astrocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
Sex: Female
disease: induced EAE
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the ChIP-Seq protocol as described (Trombetta et al 2014).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
EAE_Scr_Chip-seq_K27_AS
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| Data processing |
The raw sequences are aligned to the GRCm38 reference genome, then duplicates are removed using Picard. After removing duplicates, the reads that are mapped to the blacklist region from UCSC are filtered. Then bedGraph was generated using the deepTools.
Assembly: GRCm38
Supplementary files format and content: gzipped bedGraph file from deepTools
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| Submission date |
Jul 17, 2023 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Zhaorong Li |
| E-mail(s) |
[email protected]
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| Organization name |
Brigham and Women's Hospital
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| Street address |
60 Fenwood Road
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| City |
Boston |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE237558 |
Disease-associated astrocyte epigenetic memory promotes CNS pathology [H3K27ac Chip-seq] |
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| Relations |
| BioSample |
SAMN36503498 |
| SRA |
SRX21050027 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7623814_ChIP_TGACCA.bedGraph.gz |
7.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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