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| Status |
Public on Jan 29, 2023 |
| Title |
MouseBrain_20um_100barcodes_H3K27me3 |
| Sample type |
SRA |
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| Source name |
Mouse brain P22
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| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse brain
spatial resolution: 20 um
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| Extracted molecule |
total RNA |
| Extraction protocol |
The fresh frozen tissue section was fixed with formaldehyde. The adapters loaded Tn5/pA-Tn5 transposition containing a ligation linker was inserted into transposase accessible genomic DNA loci. The biotin decorated poly-T primer with a ligation linker was added to capture the mRNA for reverse transcription. In situ ligation was conducted by introducing distinct spatial barcode Ai (i = 1-50/100) to the adapters through an array of lateral microchannels. Then, distinct spatial barcode Bj (j = 1-50/100) were introduced through the longitudinal microchannels. Barcodes A and B with linkers were ligated to the 5’ end of the Tn5//pA-Tn5 oligo separately during each ligation. The tissue can be spatially barcoded with a distinct combination of barcodes Ai and Bj (i = 1-50/100, j = 1-50/100, n of barcoded pixels = 2,500/10,000). To correlate the spatially chromatin accessibility, transcriptome, and tissue morphology, the tissue was imaged after each ligation. Reverse crosslinking was then performed to collect barcoded cDNA and DNA fragments. The streptavidin beads were used to separate DNA and cDNA fragments. The cDNA fragments can be enriched with streptavidin beads and the DNA fragment was left in the supernatant. After separation, the DNA and cDNA libraries were constructed separately during PCR amplification. NGS sequencing was then performed using a NovaSeq 6000 sequencer with pair-end 150 bp mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 2, the Read 2 was refined to extract the Barcode A, Barcode B, and UMI. ST pipeline v1.7.2 was used to map the processed read 1 against the mouse genome (GRCm38), which created the gene matrix for downstream analysis. The gene expression matrix contains information of genes and spatial locations (barcode A x barcode B).
Assembly: mm10
Supplementary files format and content: *tsv: Tab-delimited text files include counts for each pixels for each Sample.
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| Submission date |
Nov 22, 2022 |
| Last update date |
Jan 31, 2023 |
| Contact name |
Di Zhang |
| E-mail(s) |
di.zhang@yale.edu
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| Organization name |
Yale University
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| Department |
Biomedical Engineering
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| Street address |
55 Prospect St
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE205055 |
Spatial epigenome-transcriptome co-profiling of mammalian tissues |
| GSE218593 |
Spatial epigenome-transcriptome co-profiling of mammalian tissues |
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| Relations |
| BioSample |
SAMN31841206 |
| SRA |
SRX18355553 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6753044_MouseBrain_20um_100barcodes_H3K27me3_matrix.tsv.gz |
21.9 Mb |
(ftp)(http) |
TSV |
| GSM6753044_MouseBrain_20um_100barcodes_H3K27me3_spatial.tar.gz |
20.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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