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| Status |
Public on Nov 03, 2015 |
| Title |
WT_DN3_Mi2beta |
| Sample type |
SRA |
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| Source name |
thymus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild-type
age: 4-5 weeks
cell type: FACS-sorted CD4-, CD8-, CD3-, B220-, CD11b-, Gr1-, NK1.1-, CD25+, CD44- thymocytes
chip antibody: anti-CHD4 (70469, Abcam)
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| Treatment protocol |
ILC87 cells were treated with 100 nM 4-hydroxytamoxifen (4OHT, Sigma) or vehicle (EtOH)
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| Growth protocol |
ILC87 cells were grown in RPMI medium w/25mM HEPES and 10% heat-inactivated FCS in standard humidified incubator at 5% CO2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP protocol was adapted from the Millipore ChIP Assay Kit (17-295). Cells were cross-linked with 1% formaldehyde at 37°C for 10min in PBS/0.5% BSA and lysed in 1% Triton X-100, 50 mM MgCl2, 100 mM Tris-HCl ([pH 7.1), 11% sucrose, 1x PIC buffer. Pelleted nuclei were then lysed in 1% SDS lysis buffer and sonicated to 200-500 bp fragments using a Bioruptor 200 (Diagenode). Chromatin samples were incubated with the appropriate antibodies. DNA was purified using the iPure Kit (Diagenode). Libraries were prepared according to standard Illumina protocols, and were validated with the Agilent Bioanalyzer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Image analysis and base calling was performed with the Illumina pipeline, and reads were aligned to the mm9 mouse genome with Bowtie
FASTQ files were generated by CASAVA
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated by extending the reads to 200 bp length, and the read densities in 25 bp bins were normalized to the library size. BedGraph tracks were generated after the quantile-normalization of read densities in 200 bp bins.
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| Submission date |
Sep 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Attila Oravecz |
| Organization name |
IGBMC
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| Street address |
1 rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE61148 |
Ikaros mediates gene silencing in T cells through Polycomb Repressive Complex 2 [ChIP-seq] |
| GSE61149 |
Ikaros mediates gene silencing in T cells through Polycomb Repressive Complex 2 |
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| Relations |
| BioSample |
SAMN04040909 |
| SRA |
SRX1205897 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1872306_WT_DN3_Mi2beta.wig.gz |
130.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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