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| Status |
Public on Feb 28, 2022 |
| Title |
H3K4me3_ChIP_NPC_WT_rep2 |
| Sample type |
SRA |
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| Source name |
neural precursor cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: E14 mouse neural precursor cell
chip antibody: H3K4me3 (Millipore, 04-745)
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| Growth protocol |
Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP and input library preparation were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/)
ChIP-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 or HiSeq2500 protocols (Illumina, San Diego, CA).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
fastq: Illumina's HiSeq Control Software
Each fastq file was mapped to mouse genom (mm10) with BWA -aln (Li and Durbin, 2009) and PCR duplicates were removed using Picard MarkDuplicate. The bigWig files were created using deepTools (Ramírez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (bigWig) were created using deepTools (Ramírez et al., 2016).
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| Submission date |
Nov 05, 2020 |
| Last update date |
Feb 28, 2022 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
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| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE160890 |
KMT2C/KMT2D (MLL3/MLL4) Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell Differentiation [ChIP-seq] |
| GSE160892 |
Mll3/Mll4 catalytic activity is necessary for de novo enhancer-promoter contacts during embryonic stem cell differentiation |
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| Relations |
| BioSample |
SAMN16675192 |
| SRA |
SRX9443492 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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