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| Status |
Public on May 07, 2019 |
| Title |
MNK3-Tbet-IKZF3_IKZF3_2 |
| Sample type |
SRA |
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| Source name |
MNK3
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| Organism |
Mus musculus |
| Characteristics |
transfected with: pTbet+pIKZF3
chip target: Anti-IKZF3
replicate number: Rep2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cut and Run extracts were prepared as in published protocol (Skene, Henikoff, Henikoff - 2018, Nature Protocols). using 2 ug of antibody, 2 M cells per C&R. Briefly, MNK3 cells were permeabalized with 0.02% of DMSO-dissolved digitonin, bound to conA-beads, incubated with antibody, protein-A Mnase (a gift from Heinkoff), and finally chromatin was digested with ice-cold EDTA for 25 minutes. Antibodies were as follows: H3K27ac (abcam ab4729), IKZF3 (Biolegend 371002) and rabbit-anti-mouse IgG (invitrogen 31188). Antibody or pa-MN incubation, as well as washes, were done at room temperature for 5 minutes without rotation.
Nextera DNA Library Preparation Kit, Illuminia
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Cut and Run-seq
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| Data processing |
Library strategy: Cut and Run-seq
Cut and Run-seq reads were aligned ot the mm9 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
RPKM normalized Bigwigs for visulazation were created using bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: processed data is in bigwig format
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| Submission date |
May 06, 2019 |
| Last update date |
May 07, 2019 |
| Contact name |
Marco Colonna |
| E-mail(s) |
[email protected]
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| Organization name |
Washington University in St. Louis
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| Street address |
660 S. Euclid Ave.
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (2) |
| GSE130774 |
Genome Wide Chromatin Mapping of Aiolos accessability and H3K27ac histone modifications in transfected MNK3 cells |
| GSE130775 |
Expression profiling of ILC transitional populations and Aiolos accessability and H3K27ac histone modifications in transfected MNK3 cells |
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| Relations |
| BioSample |
SAMN11582869 |
| SRA |
SRX5797705 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3753418_12_anti-IKZF3_T-bet-and-Aiolos.bw |
61.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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