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| Status |
Public on Apr 30, 2024 |
| Title |
H3K36me3_heart_E16_EC_cell_17 |
| Sample type |
SRA |
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| Source name |
E16.5 heart
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: E16.5
tissue: heart
strain: C57BL/6
tissue preparation: Fixed by methanol
chip antibody: H3K36me3, Active motif, Cat. 61101
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| Treatment protocol |
Organs were digested with 0.06 Collagenase II at 37 °C. "Aged" animals are 17-19 months old.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following CoBATCH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Cells with less than 1,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file. These files contain single cell genome-wide coverage files after sorting and uniqing and removing duplicates. Since one cell only contains two copies of each genomic locus for assay, we usually use non-duplicated reads information to reflect peak information in one single cell (PMID: 31471188).
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| Submission date |
Apr 30, 2021 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Yaxi Liu |
| E-mail(s) |
yliu_1996@pku.edu.cn
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| Phone |
86-18813039296
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| Organization name |
Peking University
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| Street address |
5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE173679 |
Orchestrating endothelial cell fate regulation and function during multiple organs’ development, stress and aging at single cell resolution |
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| Relations |
| BioSample |
SAMN18943819 |
| SRA |
SRX10734380 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5273626_H3K36me3_heart_E16_EC_cell_17.bed.gz |
92.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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