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Sample GSM7090410 Query DataSets for GSM7090410
Status Public on Jan 17, 2024
Title cartana_sham_male
Sample type RNA
 
Source name cartana_sham_male
Organism Mus musculus
Characteristics genotype: C57BL/6
Sex: male
surgery: sham
tissue: Kidney
Extracted molecule total RNA
Extraction protocol RNA hybridization-based in situ sequencing protocol: Fresh kidneys were incubated in 2-methylbutane (Millipore, Sigma) equilibrated in liquid nitrogen to maintain RNA integrity. Tissues were then stored at −80°C and embedded in cryomolds using OCT (Tissue-Tek 4583) on dry ice. For frozen sectioning, OCT blocks were equilibrated to −18°C, and 10 μm-thick sections were mounted onto the glass slides (1358W; Globe Scientific). Libraries were prepared using the high sensitivity (HS) library preparation kit provided by CARTANA (Sweden) per manufacturer’s instruction. In brief, slides were fixed in freshly prepared formaldehyde diluted in 0.01% DEPC treated PBS, followed by permeabilization in 0.1M HCl (DEPC treated). After dehydration and rehydration in series of alcohol gradients, slides were incubated in RM1-mix (provided by the library kit) overnight at 37°C. Kidney sections were incubated in WB4 (library kit) at 37°C for 30 min. Gene probes were ligated in ligases dissolved in RM2 (library kit) at 37°C for 2 hours. Transcripts were amplified in RM3-mix (library kit) at 30°C overnight. Slides were stained with DAPI for quality control imaging and shipped to 10x Genomics for in situ sequencing.
Label not applicable
Label protocol not applicable
 
Hybridization protocol not applicable
Scan protocol not applicable
Description ISS by Cartana
Data processing ISS data processing: ISS data was processed using our in-house pipeline called CellScopes https://github.com/TheHumphreysLab/CellScopes.jl.
Cell segmentation: Cell segmentation was performed using Baysor https://github.com/kharchenkolab/Baysor.
genome assembly: mm10
 
Submission date Mar 09, 2023
Last update date Jan 17, 2024
Contact name Haojia Wu
E-mail(s) haojiawu@wustl.edu
Organization name Washington University in St. Louis
Department Renal Division/Internal Medicine
Lab Humphreys Lab
Street address 600 S Euclid Ave
City St. Louis
State/province Missouri
ZIP/Postal code MO 63110
Country USA
 
Platform ID GPL33238
Series (2)
GSE227044 High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing [ISS, Cartana]
GSE227046 High resolution spatially resolved transcriptomic atlas of kidney injury and repair by RNA hybridization-based in situ sequencing

Supplementary file Size Download File type/resource
GSM7090410_cartana_sham_male_raw.tar.gz 1.3 Gb (ftp)(http) TAR
GSM7090410_cartana_sham_male_segmentation.tar.gz 390.7 Mb (ftp)(http) TAR
Processed data provided as supplementary file

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