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| Status |
Public on Apr 26, 2024 |
| Title |
PGC, H3K9me3, ChIP |
| Sample type |
SRA |
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| Source name |
primordial germ cells
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| Organism |
Gallus gallus |
| Characteristics |
cell type: primordial germ cells
antibody: H3K9me3 (Abcam, #ab8898)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 5 min at 37°C. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode).
Libraries were prepared from immunoprecipitated DNA using the NEBNext® UltraTM Library Prep Kit by Helixo (https://www.helixio.fr/)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalls were performed using bcl2fastq 2.0. Quality control was performed on fastq files using the FastQC v0.11.3 software.
Reads were aligned using Bowtie2 and multi-mapping reads were filtered out.
Reads were aligned using Bowtie2 and multi-mapping reads were filtered out.
SICER was used to identify the enriched regions in the immuno-precipitated samples compared to the input samples taken as control condition; MACS2 was used to confirm the outputs.
Assembly: Gallus_gallus-5.0
Supplementary files format and content: List of the genome coordinates of the validated H3K9me3 domains for each cell type (csv format)
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| Submission date |
Nov 28, 2023 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Clémence Kress |
| E-mail(s) |
clemence.kress@inserm.fr
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| Organization name |
INRAE, Inserm
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| Lab |
U1208
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| Street address |
18 avenue du Doyen Lépine
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| City |
Bron |
| ZIP/Postal code |
69500 |
| Country |
France |
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| Platform ID |
GPL19787 |
| Series (2) |
| GSE248766 |
Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [ChIP-Seq] |
| GSE248768 |
Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control |
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| Relations |
| BioSample |
SAMN38466832 |
| SRA |
SRX22659361 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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