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| Status |
Public on Feb 21, 2021 |
| Title |
Healthy2_snATACseq |
| Sample type |
SRA |
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| Source name |
Human Kidney
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| Organism |
Homo sapiens |
| Characteristics |
age: 62
gender: Male
race: HIS
egfr: 61
global glomerulosclerosis: None, < 10%
ifta: 1-10%
tissue: kidney
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche). 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 Buffer (10× Genomics, PN-2000153), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
snATAC-seq
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| Data processing |
Fastq files was processed with CellrangerATAC 1.2.0 by "count" function with refdata-cellranger-atac-GRCh38-1.2.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered barcode-peak matrix and fragment file
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| Submission date |
May 27, 2020 |
| Last update date |
Oct 14, 2021 |
| Contact name |
Yoshiharu Muto |
| E-mail(s) |
y.muto@wustl.edu
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| Organization name |
Washington University in St. Louis
|
| 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 |
GPL24676 |
| Series (1) |
| GSE151302 |
Single Cell Transcriptional and Chromatin Accessibility Profiling on the human adult kidneys |
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| Relations |
| Reanalyzed by |
GSM5627712 |
| BioSample |
SAMN15040603 |
| SRA |
SRX8408720 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4572188_Control2_filtered_peak_bc_matrix.h5 |
59.2 Mb |
(ftp)(http) |
H5 |
| GSM4572188_Control2_fragments.tsv.gz |
1.4 Gb |
(ftp)(http) |
TSV |
| GSM4572188_Control2_fragments.tsv.gz.tbi.gz |
891.1 Kb |
(ftp)(http) |
TBI |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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