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Sample GSM6181495 Query DataSets for GSM6181495
Status Public on Jul 24, 2022
Title 4C_St3gal6.TSS_Dox_Treated_rep1 [763]
Sample type SRA
 
Source name Bone marrow leukemic cells
Organism Mus musculus
Characteristics cell type: Leukemic erythroid cells
treatment: Dox_Treated
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.
Growth protocol Cells were maintained in culture with EPO, in exponential growth before treatment with Dox
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
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).
 
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
 
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]
Relations
BioSample SAMN28624607
SRA SRX15430202

Supplementary file Size Download File type/resource
GSM6181495_4C_St3gal6.TSS_Dox_Treated_rep1_WIN21.bw 2.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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