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| Status |
Public on May 20, 2022 |
| Title |
ME11_V2 |
| Sample type |
SRA |
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| Source name |
Mouse embryo E11
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| Organism |
Mus musculus |
| Characteristics |
tissue: E11 Embryo
spatial resolution: 50 um
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The fresh frozen tissue section on a standard aminated glass slide was first fixed with formaldehyde. Tn5 transposition was then performed, and adapters containing a ligation linker were inserted to transposase accessible genomic DNA. Afterwards, a set of DNA barcode A solutions were loaded via an array of microchannels 8 to the tissue section for in situ ligation of a distinct spatial barcode Ai (i = 1-50). Then, a second set of barcodes Bj (j = 1-50) were introduced on the tissue surface in microchannels perpendicularly to those in the first flow barcoding step. These barcodes were then ligated at the intersections, resulting in a mosaic of tissue pixels, each of which contains a distinct combination of barcodes Ai and Bj (i = 1-50, j = 1-50).
During each flow or afterward, the tissue slides were imaged under the microscope such that spatially barcoded accessible chromatin can be correlated with the tissue morphology. After forming a spatially barcoded tissue mosaic (n = 2500), reverse crosslinking was performed to release barcoded DNA fragments and library construction was completed during the PCR. NGS sequencing was then performed using a HiSeq sequencer with pair-end 150 bp mode with custom read 1 primer.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
ME11_V2_CKDL200159463-1A-N703_HC7VYBBXX_L8
This sample was used only for protocol validation. Images and associated files were not generated for this sample.
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| Data processing |
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 1, and the filtered sequences were transformed to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the new Read 1, barcodes A and barcodes B were included in new Read 2. Resulting fastq files were aligned to the mouse reference (mm10) or human reference (GRCh38), filtered to remove duplicates and counted using Cell Ranger ATAC v1.2. The BED like fragments file were generated for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).
Genome_build: mm10
Supplementary_files_format_and_content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).
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| Submission date |
May 10, 2021 |
| Last update date |
May 20, 2022 |
| Contact name |
Yanxiang Deng |
| E-mail(s) |
yanxiang.deng@yale.edu
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| Organization name |
Yale University
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| Department |
Biomedical Engineering
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| Lab |
Rong Fan Lab
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| Street address |
55 Prospect Street
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE171943 |
Spatial profiling of chromatin accessibility in mouse and human tissues |
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| Relations |
| BioSample |
SAMN19102986 |
| SRA |
SRX10839411 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5289490_ME11_V2.fragments.tsv.gz |
96.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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