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| Status |
Public on Jul 30, 2024 |
| Title |
sham-1 |
| Sample type |
SRA |
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| Source name |
sham
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| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
treatment: sham
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)
snATAC-seq
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Fastq files was processed with CellrangerATAC 2.0.0 with refdata-cellranger-arc-mm10-2020-A-2.0.0
Assembly: mm10
Supplementary files format and content: a filtered barcode-peak matrix
Supplementary files format and content: a fragment file and an index file of a fragment file
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| Submission date |
Dec 27, 2023 |
| Last update date |
Jul 30, 2024 |
| Contact name |
Yoshiharu Muto |
| E-mail(s) |
y.muto@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Medicine / Nephrology
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| Lab |
Benjamin Humphreys Lab
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| Street address |
660. S Euclid Ave., CB 8118
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE252105 |
Single Cell Chromatin Accessibility Profiling on the mouse kidneys with ischemia-reperfusion injury |
| GSE252111 |
Mouse kidneys with ischemia-reperfusion injury; Human kidneys with acute kidney injury; RELA binding sites in primary human proximal tubular cells |
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| Relations |
| BioSample |
SAMN39144831 |
| SRA |
SRX23043853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7993680_sham-1_filtered_peak_bc_matrix.h5 |
76.0 Mb |
(ftp)(http) |
H5 |
| GSM7993680_sham-1_fragments.tsv.gz |
1.9 Gb |
(ftp)(http) |
TSV |
| GSM7993680_sham-1_fragments.tsv.gz.tbi.gz |
940.0 Kb |
(ftp)(http) |
TBI |
SRA Run Selector |
| Raw data are available in SRA |
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