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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 06, 2020 |
| Title |
Input_ChIP_CTCF-AID_NPC_d6_ctl_rep2 |
| Sample type |
SRA |
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| Source name |
neural precursor cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: F123 mouse neural precursor cell
chip antibody: none
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| Treatment protocol |
To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24 or 48 hours after stating auxin treatment. Neural cell differentiation treatment was performed with or without auxin treatment, and the neural precursor cells were harvested on day 4, 6 or 2 days after washing out auxin from the day 4, 6 sample.
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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 for histone modifications (H3K4me1, H3K4me3, H3K27ac) were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/), and ChIP and input library preparation for CTCF were also performed as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol for MicroChIP” 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 |
Mar 05, 2020 |
| Last update date |
Mar 06, 2020 |
| 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) |
| GSE94452 |
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation |
| GSE146451 |
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation III |
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| Relations |
| BioSample |
SAMN14307116 |
| SRA |
SRX7857002 |
| 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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