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Status |
Public on Jul 24, 2022 |
Title |
4C_St3gal6.TSS_Dox_Treated_rep1 [763] |
Sample type |
SRA |
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Source name |
Bone marrow leukemic cells
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Organism |
Mus musculus |
Characteristics |
cell type: Leukemic erythroid cells treatment: Dox_Treated
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Treatment protocol |
Cells were treated or not with doxycycline for 48h to induce the expression of an shRNA against Spi1. One biological replicate was generated for all conditions.
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Growth protocol |
Cells were maintained in culture with EPO, in exponential growth before treatment with Dox
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Extracted molecule |
genomic DNA |
Extraction protocol |
4C-seq experiments were performed as previously described (Krijger PHL, et al., Methods, 2019). For Alas2_enhancer the enzymes used were DpnII>EcoRI while for St3gal6_TSS DpnII>Csp6I. For library preparation purified circular fragments were amplified by PCR with View-Point specific primers. Resulting amplicons were purified with AMPure XP beads (0.8×) and amplified using standard indexed Illumina primers as previously described (Krijger PHL, et al., Methods, 2019). Second-round PCR products were purified with PCR purification columns (Qiagen) and quantified by 2100 Bioanalyzer (Agilent, DNA 7500 kit). 4C library was prepared by equimolar mix of the samples. The library was cleaned-up by AMPure XP beads (0.8x) to remove PCR dimers before sequencing through Illumina MiSeq with a 75bp Single-End reads setup.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Data processing |
library strategy: 4C-seq Fastq files have been demultiplexed by Cutadapt. 4C-seq reads were mapped on Mm10/GRCm38 genome assembly and signal normalized by pipe4C (v1.1) R-package (Krijger PHL, et al., Methods, 2019) in “cis” mode and with default parameters. Normalization between density files of different conditions (bigWig) was performed by using pipe4C (v1.1) R-package (Krijger PHL, et al., Methods, 2019). Assembly: mm10 Supplementary files format and content: Normalized bigWig files were generated using pipe4C (v1.1) R-package (Krijger PHL, et al., Methods, 2019).
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Submission date |
May 24, 2022 |
Last update date |
Jul 24, 2022 |
Contact name |
Christel GUILLOUF |
E-mail(s) |
christel.guillouf@gustaveroussy.fr
|
Organization name |
Gustave Roussy
|
Street address |
114 rue Edouard vaillant
|
City |
VILLEJUIF |
ZIP/Postal code |
94800 |
Country |
France |
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|
Platform ID |
GPL16417 |
Series (2) |
GSE172088 |
HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia. |
GSE203659 |
HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [763_4C-seq] |
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Relations |
BioSample |
SAMN28624607 |
SRA |
SRX15430202 |