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| Status |
Public on Feb 01, 2021 |
| Title |
ChIP-seq_H3K9Ac-HA-JICD |
| Sample type |
SRA |
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| Source name |
Ink4a-/- murine astrocyte
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| Organism |
Mus musculus |
| Characteristics |
cell type: Astrocyte
tissue: Brain
antibody: H3K9Ac (Millipore, 07-352)
genotype: Ink4a-/-
transfected with: pcDNA HA-JICD puro
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| Growth protocol |
Ink4a-/- astrocytes were cultured in DMEM with high glucose supplemented with 10% fetal bovine serum, 1% penicilin/streptomycin, 2mM L-glutamine and 50ug/mL gentamicin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin DNA was immunoprecipitated with anti-HA or anti-H3K9Ac and Protein A/G beads
DNA enrichment was performed using EpiMark® Methylated DNA Enrichment Kit (New England Biolabs, UK).
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.
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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 |
Illumina Casava1.8 software used for basecalling.
The reads were trimmed and aligned using Bowtie2 (Langmead and Salzberg, 2012).
We used MACS (Model-based Analysis of ChIP-Seq) to identify peaks from the alignment file.
Genome_build: mm10
Supplementary_files_format_and_content: 1) Transcription factor name, 2) DNA binding consensus, 3) P-value, 4) log P-pvalue, 5) q-value(Benjamini), 6) #Target sequences with motif, 7)% of Targets sequences with motif, 8) #Background sequences with motif, 9) % of Background sequences with motif
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| Submission date |
Feb 21, 2019 |
| Last update date |
Feb 02, 2021 |
| Contact name |
Eun-Jung Kim |
| E-mail(s) |
chunu84@hanmail.net
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| Phone |
010-4228-0530
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| Organization name |
Korea University
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| Street address |
Anamro 5ga
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| City |
Seoul |
| ZIP/Postal code |
02841 |
| Country |
South Korea |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE126854 |
ChIP sequencing analysis of HA-JICD overexpressed Ink4a-/- murine astrocytes |
| GSE126855 |
RNA-seq and ChIP-seq analysis of HA-JICD1 and NICD1 overexpressed Ink4a-/- murine astrocytes |
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| Relations |
| BioSample |
SAMN10983297 |
| SRA |
SRX5401834 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3615468_H3K9Ac-HA-JICD.bedGraph.gz |
53.0 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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