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Sample GSM7993681 Query DataSets for GSM7993681
Status Public on Jul 30, 2024
Title 14day-2
Sample type SRA
 
Source name post IRI (14day)
Organism Mus musculus
Characteristics tissue: Kidney
treatment: IRI
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
 
Library strategy ATAC-seq
Library source genomic single cell
Library selection other
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Dec 27, 2023
Last update date Jul 30, 2024
Contact name Yoshiharu Muto
E-mail(s) y.muto@wustl.edu
Organization name Washington University in St. Louis
Department Medicine / Nephrology
Lab Benjamin Humphreys Lab
Street address 660. S Euclid Ave., CB 8118
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
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
Relations
BioSample SAMN39144830
SRA SRX23043854

Supplementary file Size Download File type/resource
GSM7993681_14day-2_filtered_peak_bc_matrix.h5 144.7 Mb (ftp)(http) H5
GSM7993681_14day-2_fragments.tsv.gz 3.2 Gb (ftp)(http) TSV
GSM7993681_14day-2_fragments.tsv.gz.tbi.gz 1.2 Mb (ftp)(http) TBI
SRA Run SelectorHelp
Raw data are available in SRA

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