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| Status |
Public on Jun 22, 2019 |
| Title |
flbioNkx2-5_E8.75_FHF_rep3 |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Mus musculus |
| Characteristics |
genotype/variation: NKX2.5fb/+::BirA/BirA
developmental stage: E8.75
tissue: Heart
heart field: First
chip antibody: Streptavidin beads (Invitrogen, cat#60210)
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| Growth protocol |
Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory take care.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed at 37°C before chromatin was fragmented, adaptor-ligated and released. For one bio-ChIP experiment, 10 μl streptavidin beads (Invitrogen, cat#60210) were used for incubation for 2 h at 4°C. Beads were briefly washed with 2% SDS/PBS once, and then washed with high salt buffer (1% Triton X-100, 2 mM EDTA, 50 mM HEPES pH 7.9, 500 mM NaCl, 0.1% sodium deoxycholate) for three times. Beads were re-suspended in 100 μl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After reverse crosslinking and proteinase K digestion, DNA was purified through phenol-chloroform extraction.
NEBNext Ultra II Master Mix was used for PCR enrichment, followed by size selection of 200-800 bp. The resulting libraries were subjected to 2 X 150 bp paired-end sequencing on NovaSeq 6000 systems.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ChIP_DNA
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| Data processing |
Basecalls performed using CASAVA version 1.8.2.
ChIP-seq reads were filtered by cutadapt (v1.11) with parameters to get high quality reads.
High-quality reads were aligned to mm10 mouse genome using bowtie2 (v2.3.1) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 30 were kept.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files that represented ChIP signals were generated using deeptools.
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| Submission date |
Mar 01, 2019 |
| Last update date |
Jun 22, 2019 |
| Contact name |
Haiqing Xiong |
| E-mail(s) |
haiqingxiong@pku.edu.cn
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| Organization name |
Peking University
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| Street address |
5 Yiheyuan Road, Haidian District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE108961 |
Single-cell transcriptomics reveals chemotaxis mediated intra-organ crosstalk during cardiogenesis [ChIP-seq] |
| GSE108963 |
Single-cell transcriptomic analysis reveals lineage hierarcies and communications for second heart lineage deployment |
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| Relations |
| BioSample |
SAMN11042486 |
| SRA |
SRX5453241 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3637962_flbioNkx2-5_E8.75_FHF_rep3.bw |
67.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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