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| Status |
Public on May 26, 2022 |
| Title |
SCI_WT-031221-2 |
| Sample type |
SRA |
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| Source name |
thoracic spinal cord
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
genotype: GfapCre:Ribotagfl/fl
treatment: Crush SCI at T10
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fourteen days after complete crush SCI, spinal cords of wild-type, Stat3-astro-cKO or Smarca4-astro-cKO mice were perfused with ice cold saline and spinal cords rapidly dissected and frozen on dry ice. For SCI samples, the central 3 mm of the lower thoracic lesion including the lesion core and 1 mm rostral and caudal were then rapidly removed and snap frozen in liquid nitrogen. Anatomically equivalent regions of spinal cord were taken from healthy controls. Frozen tissue samples were processed for immunoprecipitation of astrocyte nuclei for snATACseq. Astrocyte nuclei were isolated by antibody-binding and magnet-assisted nuclear immunoprecipitation (MAN-IP) using well characterized procedures. In breif, tissues were dissociated and single nuclei suspensions were incubated with Sox9 rabbit monoclonal antibody to positively select for astrocyt nuclei by MAN-IP.
Single nuclei partitioning, barcoding and library preparation was performed using the 10X Genomics Chromium Controller and Chromium™ Single Cell ATAC Solution, and sequenced using Novaseq S2 (illumina).
Libraries were prepared per the protocol for the 10x Genomics Single Cell ATAC Solution
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
SCI WT
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| Data processing |
genome alignment: cellranger-ATAC-v1.2
peak-calling: MACS2-v.2.27.1
data normalization and clustering: ArchR- v1.0.1
Assembly: mm10
Supplementary files format and content: .h5, ATAC peaks per cell
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| Submission date |
Mar 26, 2022 |
| Last update date |
Mar 29, 2024 |
| Contact name |
Joshua Evan Burda |
| E-mail(s) |
jburda1@gmail.com
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| Organization name |
Cedars Sinai Medical Center
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| Department |
Biomedical Sciences, Center for Neural Science and Medicine
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| Lab |
Burda Lab
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| Street address |
127 S San Vicente Blvd
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE199481 |
Divergent transcriptional regulation of astrocyte reactivity across disorders [TR_ATAC_SCI] |
| GSE199482 |
Divergent transcriptional regulation of astrocyte reactivity across disorders |
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| Relations |
| BioSample |
SAMN26992158 |
| SRA |
SRX14624702 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5973991_SCI_WT-031221-2_outs_barcodes.tsv.gz |
24.9 Kb |
(ftp)(http) |
TSV |
| GSM5973991_SCI_WT-031221-2_outs_filtered_peak_bc_matrix.h5 |
56.3 Mb |
(ftp)(http) |
H5 |
| GSM5973991_SCI_WT-031221-2_outs_matrix.mtx.gz |
113.9 Mb |
(ftp)(http) |
MTX |
| GSM5973991_SCI_WT-031221-2_outs_peaks.bed.gz |
493.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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