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| Status |
Public on Feb 10, 2022 |
| Title |
ME11_20um_H3K27ac |
| Sample type |
SRA |
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| Source name |
Mouse embryo E11
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| Organism |
Mus musculus |
| Characteristics |
tissue: Embryo
spatial resolution: 20 um
antibody: H3K27ac (Abcam, ab177178)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
First, a tissue section on a standard aminated glass slide was lightly fixed with formaldehyde. Antibody binds to the target histone modification was added, followed by a secondary antibody binding to enhance the tethering of pA-Tn5 transposome. By adding Mg++ to activate the transposome in tissue, adapters containing a ligation linker were inserted to genomic DNA at the histone mark antibody recognition sites. Then, a set of DNA barcode A solutions were introduced to perform in situ ligation for appending a distinct spatial barcode Ai (i = 1-50). Afterwards, a second set of barcodes Bj (j = 1-50) were flowed 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). The tissue slide being processed could be imaged during each flow or afterward such that the tissue morphology can be correlated with spatial epigenomics map. After forming a spatially barcoded tissue mosaic, DNA fragments were collected by cross-link reversal and amplified by PCR to complete library construction. 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Read 1 was first filtered by two constant linker sequences (linker 1 and linker 2). Then filtered sequences were processed to cellranger atac format (10x Genomics), where the new Read 1 was genome sequences and the new Read 2 includes barcodes A and barcodes B. Resulting fastq files were aligned to the mouse genome (mm10), filtered for duplicates and counted using cellranger atac, which generated the BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome. We developed a preprocessing pipeline using Snakemake workflow management system, which is shared at https://github.com/dyxmvp/spatial-CUT-Tag
Genome_build: mm10
Supplementary_files_format_and_content: BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
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| Submission date |
Jan 20, 2021 |
| Last update date |
Feb 17, 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) |
| GSE165217 |
Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level |
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| Relations |
| BioSample |
SAMN17391738 |
| SRA |
SRX9904908 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5028440_ME11_H3K27ac_20um.fragments.tsv.gz |
292.8 Mb |
(ftp)(http) |
TSV |
| GSM5028440_spatial.tar.gz |
2.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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