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| Status |
Public on Feb 27, 2022 |
| Title |
-3xCTCF-TetO clone 1 |
| Sample type |
SRA |
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| Source name |
-3xCTCF-TetO clone 1
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| Organism |
Mus musculus |
| Characteristics |
clone: "-3xCTCF-TetO clone 1"
cell line: Embyonic stem cell (E14)
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| Growth protocol |
Cells were cultured on gelatin-coated culture plates in Glasgow Minimum Essential Medium (Sigma) supplemented with 15% foetal calf serum (Eurobio Abcys), 1% L-Glutamine (Thermo Fisher Scientific -25030024), 1% Sodium Pyruvate MEM (Thermo Fisher Scientific -11360039), 1% MEM Non-Essential Amino Acids (Thermo Fisher Scientific-11140035) 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade), 1 µM MEK inhibitor PDO35901 (Axon, 1408) and 3 µM GSK3 inhibitor CHIR 99021 (Axon, 1386) in 8% CO2 at 37°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (2 µg) was fragmented to an average of 500 bp by sonication (Covaris S220; duty cycle, 5%; peak power, 175 W; duration, 25 s). End-repair, A-tailing and ligation of full-length barcoded Illumina adapters were performed using the TruSeq DNA PCR-free kit (Illumina) according to the manufacturer’s guidelines, with the exception that large DNA fragments were not removed
In short, genomic DNA (2 µg) was fragmented to an average of 500 bp by sonication (Covaris) and ligation of full-length barcoded Illumina adapters was performed using the TruSeq DNA PCR-free kit (Illumina) according to the manufacturer’s guidelines, with the exception that large DNA fragments were not removed. Libraries were pooled together and capture of desired fragments was performed using biotinylated probes against the piggyBac inverted terminal repeats (ITRs) sequences using xGEN Hybridisation reagents (IDT). Following capture, libraries were amplified for 14 cycles (KAPA HiFi Hotstart)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Random integration of TetO arrays without 3xCTCF
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| Data processing |
Reads mapping to TetR and LacI were excluded. Reads are mapped to the integration cassettes treating paired end as single end reads where only one of the two reads are mappable to the cassette are kept and only the unmapped reads of the pair are kept Kept reads are mapped to the mouse genome
Genome_build: mm9
Supplementary_files_format_and_content: csv file containing integration site position, the relative position to the closest CTCF and which compartment it belongs to (A or B compartments)
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| Submission date |
Feb 22, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Luca Giorgetti |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Street address |
Fabrikstrasse 24
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| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE197237 |
Cohesin and CTCF control chromosomal contact dynamics in living cells [integration sites] |
| GSE197238 |
Cohesin and CTCF control chromosomal contact dynamics in living cells |
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| Relations |
| BioSample |
SAMN26177809 |
| SRA |
SRX14255696 |
| 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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