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| Status |
Public on Jul 24, 2023 |
| Title |
GFP_Sigma_MEL |
| Sample type |
SRA |
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| Source name |
MEL
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| Organism |
Mus musculus |
| Characteristics |
cell line: MEL
cell type: Mouse Erythroleukemia cells
cutnrun antibody: GFP ( Sigma, #SAB4301138)
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| Growth protocol |
DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were bound to BioMag Plus Concanavalin A-coated beads (Bangs Laboratories), permeabilized with digitonin and incubate with pA-Mnase, activated by CaCl2
Libraries were prepared with the MicroPlex Library Preparation kit v3 (Diagenode) and purified with Agencourt SPRIselect beads (Beckman Coulter)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw reads were subjected to quality control and adapter trimming using Trimgalore (version 0.6.6)
Trimmed reads were then aligned to the reference genome (mm9) using STAR aligner (version 2.7.9a)
Aligned reads were converted from SAM to BAM format, sorted, and indexed using Samtools (version 1.11)
Duplicate reads were removed using Picard tool (version 2.17.11)
Peak calling was performed using the HOMER (version 4.10.3)
bigWig files were generated using deepTools (version 3.4.2)
Assembly: mm9
Library strategy: CUT&RUN
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| Submission date |
Mar 28, 2023 |
| Last update date |
Jul 24, 2023 |
| Contact name |
Eric Soler |
| E-mail(s) |
eric.soler@igmm.cnrs.fr
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| Organization name |
IGMM
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| Street address |
1919 route de Mende
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| City |
Montpellier cedex 5 |
| ZIP/Postal code |
34293 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE228372 |
Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions |
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| Relations |
| BioSample |
SAMN33948732 |
| SRA |
SRX19793410 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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