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Sample GSM6671109 Query DataSets for GSM6671109
Status Public on Apr 14, 2024
Title SPATAC-seq with mouse organogenesis well-E17A
Sample type SRA
 
Source name mouse embryo
Organism Mus musculus
Characteristics tissue: mouse embryo
Extracted molecule genomic DNA
Extraction protocol Female mice were mated naturally, and the first day that the vaginal plug was observed was considered as E0.5. Dissections were performed as previously described (Cao J, et al. Nature. 2019) and all embryos were immediately snap-frozen in liquid nitrogen. Frozen embryos were stored at −80 °C. Embryo nuclei were extracted via previously described methods with some modifications (Corces MR, et al. Nat Methods. 2017; Cao J, et al. Nature. 2019). Briefly, each embryo was transferred into a pre-chilled 2 ml Dounce (D8938, Sigma) with 2 ml Homogenization Buffer (10 mM Tris-HCl pH 7.8, 5 mM CaCl2 (21115, Sigma), 3 mM Mg (Ac)2 (63052, Sigma), 0.1% NP-40 (11332473001, Sigma), 0.1mM EDTA (AM9260G, Thermo), 320 mM Sucrose (S8271-500G, Solarbio), 0.015mM PMSF (P7626, Sigma) and 0.15mM β-mercaptoethanol (M3148, Sigma)), and homogenized by pipetting 10 times with A pestle and B pestle, respectively. Homogenized embryos were filtered with a 40 μm filter. The filtered nuclei were then transferred to a new 15-ml tube containing 10ml nuclei wash buffer (NWB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl (AM9759, Thermo), 3 mM MgCl2 (AM9530G, Thermo), 1% BSA (130-091-376, Miltenyi Biotec) and 0.1% Tween-20 (11332465001, Sigma)) and pelleted by spinning 5 min at 4°C at 350 g and washed once with 10ml NWB. The nuclei were resuspended in 10ml NWB and fixed by adding 140 μl of 37% formaldehyde for exactly 10 min on ice. The fixation was stopped by adding 500 μl of 2.5M glycine (G8898, Sigma). The sample was incubated at room temperature for 5 minutes and then centrifuged at 500 g for 5 minutes to remove supernatant. The nuclei pellet was washed twice with 10 ml NWB and re-suspended in 2 ml NWB. Nuclei were then counted on a hemocytometer and diluted to 5,000 nuclei per 1 μl using NWB. Finally extracted nuclei from all samples were loaded into SPATAC-seq, a custom high-throughput single-cell ATAC-seq method, to capture the accessible regions during mouse organogenesis, which profiling more than 360,000 cells in one experiment.
Bulk ATAC-seq and SPATAC, a customized single-cell ATAC-seq library construction method, see description of our paper for details.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Raw Read1 Fastq files within genome DNA (position from 66-121 nucleotide) were extracted and renamed as new Read1 file. Similarly, raw Read2 Fastq files within genome DNA (position from 51-101 nucleotide) were extracted and renamed as new Read2 file of Cell Ranger ATAC format. Round 1, Round2 and Round3 barcodes are extracted from raw Read1 and Read2 Fastq files, are merged after correcting 1bp mismatch. Then merged barcodes were attached in the read name of new Read1 and Read2 fastq files by software sinto (https://timoast.github.io/sinto/index.html), which were aligned to the reference mouse (mm10) genome (https://cf.10xgenomics.com/supp/cell-atac/refdata-cellranger-atac-mm10-1.2.0.tar.gz) using BWA. The bam file of each sublibrary was converted to scATAC-seq fragment file by sinto according to standard procedure. Finnaly, the barcodes in fragment file of each sublibrary were tagged with Round4 barcodes (PCR wells).
Assembly: mm10
Supplementary files format and content: bed files, the fragment file of SPATAC-seq, the information of each unique fragment of SPATAC within each sublibrary, including the chromsome number, start site, end site and frequency.
Supplementary files format and content: CSV file, cell metadata information for the atlas of zebrafish development, including cell types, coordinate and quality metric of each cell
 
Submission date Oct 23, 2022
Last update date Apr 14, 2024
Contact name Keyong Sun
E-mail(s) keyongsuntsinghua@gmail.com
Organization name tsinghua university
Department School of Medicine
Street address Hai Dian street
City beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL24247
Series (1)
GSE216371 A single-cell atlas of chromatin accessibility in mouse organogenesis
Relations
BioSample SAMN31420851
SRA SRX17998852

Supplementary file Size Download File type/resource
GSM6671109_E17A.bed.gz 1.0 Gb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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