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| Status |
Public on Dec 08, 2015 |
| Title |
R-E2-Flag-rep3 |
| Sample type |
SRA |
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| Source name |
R-E2-Flag
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Foxd3 conditional knockout targeted with 3XFlag tag into endogenous Foxd3 allele
cell type: ESCs (R cells)
cell line of origin: embryonic stem cells: ESCs (R cells)
treatment: Lif 2i
chip antibody: M2 anti-Flag
chip antibody vendor: Sigma
chip antibody cat. #: F1804
chip antibody lot #: SLBJ4607V
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| Treatment protocol |
Tamoxifen was added at 1uM for 36 hours to induce Foxd3 KO
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| Growth protocol |
All cells were grown in Knockout DMEM with 15%FBS (excpet EpiSCs, that were grown in a 50:50 mix of DMEM:glutamax and Neurobasal with N2 and B27 supplements), Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using a standard ChIP protocol
Library was constructed using a standard Illumina protocol
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Fastq files were mapped to the genome using Bowtie2 with the following setting: -p 4 -q -D 15 -R 10 -L 22 -i S,1,1.15
ChromHMM was run on a subset of the data for identifying 6 chromatin states
MACS2 was used for peak finding using the following settings:
Dip-finding for nucleosome-free regions was performed as per: Wamstad, J. A., Alexander, J. M., Truty, R. M., Shrikumar, A., Li, F., Eilertson, K. E., et al. (2012). Cell, 151(1), 206–220. doi:10.1016/j.cell.2012.07.035
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format for all ChIP-seq files - duplicates for Foxd3 conditional knockout data have been consolidated into one bigwig file
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| Submission date |
Dec 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Raga Krishnakumar |
| E-mail(s) |
raga.krishnakumar@gmail.com
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| Organization name |
UCSF
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| Lab |
Blelloch
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| Street address |
912E RMB, 35 Medical Center Way
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE58407 |
Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [ChIP-seq] |
| GSE58408 |
Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation |
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| Relations |
| BioSample |
SAMN03272961 |
| SRA |
SRX823813 |
| 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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