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| Status |
Public on May 28, 2024 |
| Title |
Liver_ST_Adar1flox/flox 1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
strain: C57BL/6
genotype: Ifih1-/- Adar1flox/flox Alb-Cre+
Sex: female
age: 8 weeks
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Visium spatial gene expression kit (10x Genomics) was used. Briefly, immediately after mice were sacrificed, the livers were removed, cut into appropriately sized pieces, and embedded in OCT using an isopentane bath and liquid nitrogen. OCT sections were collected in a cryostat at 10µm per section. Three sections of each tissue were collected onto mRNA capture slides. Only samples with RIN quality more than 7 were used. Tissues were fixed in -20°C chilled methanol before H&E staining according to manufacturer’s protocol (CG000160 Rev B). Tissue optimization as performed according to manufacturer’s protocol to determine optimal permeabilization conditions (CG000238). Briefly, permeabilization enzyme was applied to H&E-stained tissues on optimization slide and a permeabilization time course was performed before fluorescent cDNA synthesis, tissue removal and slide imaging. All imaging was performed on EVOS M7000 imaging system (Thermo Fisher Scientific).
Tissue permeabilization was performed on Visium gene expression slides to release poly-adenylated mRNA from cells for capture by primers on ST spots underneath, followed by reverse transcription to generate barcoded full length cDNA. cDNA was amplified and cleanup performed using SPRIselect Reagent (Beckman Coulter, B23317). Library preparation was performed according to manufacturer’s protocol to generate libraries containing P5 and P7 Illumina primer sequences, Sample indexes i5 and i7 (10x, 3000431), TruSeq Read 1 and 2 sites, 10x Spatial Barcode, Unique Molecular Identifier (UMI), and inserts (CG000239 Rev D). 9 generated libraries were pooled and sequenced in one lane using Novaseq-6000 S4 for a depth of 2.5B total Paired end reads.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10X Visium platform
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| Data processing |
space ranger
seurat
R in-house scripts
Library strategy: Spatial transcriptomics sequencing
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| Submission date |
Mar 25, 2023 |
| Last update date |
May 28, 2024 |
| Contact name |
jinghe xie |
| E-mail(s) |
csihj@nus.edu.sg
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| Organization name |
nuh
|
| Street address |
21 Lower Kent Ridge Road
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| City |
Singapore |
| ZIP/Postal code |
119077 |
| Country |
Singapore |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE228195 |
Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -Spatial Transcriptomics |
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| Relations |
| BioSample |
SAMN33911916 |
| SRA |
SRX19769175 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7116327_55C2_filtered_feature_bc_matrix.h5 |
11.1 Mb |
(ftp)(http) |
H5 |
| GSM7116327_55C2_spatial.tar.gz |
8.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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