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Sample GSM7429789 Query DataSets for GSM7429789
Status Public on Dec 01, 2023
Title Left kidney, ischemic reperfusion 2
Sample type SRA
 
Source name Kidney
Organism Mus musculus
Characteristics tissue: Kidney
Sex: M
age: 7-8 weeks
genotype: WT C57BL/6J
treatment: Ischemic reperfusion injury
slide serial_number: V11F09-115-A1
Treatment protocol All experiments were performed using experimental protocols approved by the Animal Care and Use Committee of Johns Hopkins University. An established model of bilateral renal ischemia-reperfusion in mice was used. Briefly, mice were anesthetized with an intraperitoneal injection of sodium pentobarbital (75 mg/kg). After an abdominal medial incision, both renal pedicles were dissected, and a microvascular clamp was placed on each renal pedicle for 30 minutes. Animals were kept well-hydrated with warm saline and at constant body temperature (37°C). After 30 minutes of ischemia, the clamps were removed and wounds were sutured. The animals were allowed to recover with free access to food and water. Serum creatinine levels were determined at baseline and 24 hours after renal ischemia to confirm the injury.
Extracted molecule total RNA
Extraction protocol 24 hours after ischemia, mice were anesthetized. Immediately after dissection and de-capsulation, kidneys were snap-frozen in liquid nitrogen and embedded in optimal cutting temperature (OCT) at -80°C. 10 µm thick sections were cut on a cryostat at -15°C.
Spatial transcriptomics was performed using 10X Visium Spatial Gene Expression Slide and Reagent Kit according to manufacturer’s instructions, with the following sample-specific parameters: tissue sections were permeabilized for 12 minutes at 37°C. cDNA was amplified using 14 cycles based on Cq values obtained using qPCR. Based on post-amplification cDNA yield, final libraries were amplified using 13 cycles during sample index PCR. Each sample was indexed with a unique well from the Dual Index Kit TT Set A. Libraries were sequenced on an Illumina NovaSeq with an SP200 flowcell, 4 samples per lane, in paired-end mode.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing 10X Visium data was preprocessed using the default settings. SpaceRanger was used for alignment and quantification with reference genome mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values barcode and feature files, matrix expression files, H&E png images, csv tissue position files, json scale factor files
Library strategy: Spatial Transcriptomics
 
Submission date May 25, 2023
Last update date Dec 01, 2023
Contact name Emily Lo
Organization name Johns Hopkins
Street address 733 N Broadway
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL24247
Series (2)
GSE233512 Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [spatial transcriptomics]
GSE233513 Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys
Relations
BioSample SAMN35370285
SRA SRX20520106

Supplementary file Size Download File type/resource
GSM7429789_IL2_barcodes.tsv.gz 14.8 Kb (ftp)(http) TSV
GSM7429789_IL2_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM7429789_IL2_matrix.mtx.gz 28.1 Mb (ftp)(http) MTX
GSM7429789_IL2_scalefactors_json.json.gz 169 b (ftp)(http) JSON
GSM7429789_IL2_tissue_hires_image.png.gz 5.2 Mb (ftp)(http) PNG
GSM7429789_IL2_tissue_lowres_image.png.gz 465.5 Kb (ftp)(http) PNG
GSM7429789_IL2_tissue_positions_list.csv.gz 69.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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