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Sample GSM5464957 Query DataSets for GSM5464957
Status Public on Apr 08, 2022
Title E100_vpGFP_LongTermNegative_rep2
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics genotype: E100
knock down: NA
hemin treatment: no_Hemin
facs: 6xGFP_negative
viewpoint: GFP
barcode: GGGGCACAAGCTGGAGTA
Treatment protocol For differentiation, culture medium was supplemented with porcine hemin (Sigma, 30 µM final concentration) one day after sorting. Hemin and medium were refreshed one day later.
Growth protocol Human erythroleukemia K562 cells were grown at 37°C at 5% CO2 in RPMI 1640 (Gibco) with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco). Density was kept between 1x105 and 5x105 cells per ml medium. Cells were routinely tested for mycoplasma. Prior to every experiment, cells were weekly bulk sorted for two consecutive weeks on Becton Dickinson SORP FACSAria FUSION Flow Cytometer. To obtain irreversibly silenced populations of cells, GFP negative cells where weekly sorted GFP-negative for six (E100) or nine (E407) consecutive weeks.
Extracted molecule genomic DNA
Extraction protocol 4C experiments were performed as described (Krijger et al., 2020). Eight to ten million cells were cross-linked with formaldehyde. DNA was digested in situ with Csp6I (first cutter) and NlaIII (second cutter).
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy as described in Krijger et al., 2020.
OTHER: 4C
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Reads were mapped and processed using pipe4C (Krijger et al., 2020) (github.com/deLaatLab/pipe4C) with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed
Genome_build: Modified versions of hg19 containing the sequences of the integrated regulatory elements at their respective integration site.
Supplementary_files_format_and_content: 4C: interaction coverage file (wig files generated using pipe4C)
 
Submission date Jul 21, 2021
Last update date Apr 08, 2022
Contact name Peter Krijger
E-mail(s) [email protected]
Organization name Hubrecht Institute
Lab Wouter de Laat
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platform ID GPL18573
Series (1)
GSE180566 Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes
Relations
BioSample SAMN20342537
SRA SRX11515355

Supplementary file Size Download File type/resource
GSM5464957_E100_vpGFP_LongTermNegative_rep2.wig.gz 458.2 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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