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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 06, 2020 |
| Title |
CTCF-AID_rna_d6_auxin_rep1 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: F123 mouse ES cell
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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, 48 or 96 hours after stating auxin treatment. Neural progenitor cell differentiation treatment was performed with or without auxin treatment, and harvested on day 2, 4, 6 and 2 days after washing out auxin from day 4 and day 6 samples.
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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 |
total RNA |
| Extraction protocol |
RNA-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
fastq: Illumina's HiSeq Control Software
RNA-seq reads were aligned against the mouse mm10 genome assembly using STAR (Dobin et al., 2013). The processed data was created using HTseq (Anders et al., 2015) and used for differential expression analysis by edgeR (Robinson et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: The processed file include all sample data of the number of read counts in each gene that were calculated using HTseq (Anders et al., 2015).
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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 |
| GSE146454 |
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation IV |
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| Relations |
| BioSample |
SAMN14307272 |
| SRA |
SRX7857027 |
| 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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