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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 02, 2014 |
| Title |
Ikaros ChIP sample |
| Sample type |
SRA |
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| Source name |
T29 Ik1-ER cells treated with 4OHT
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| Organism |
Mus musculus |
| Characteristics |
cell type: T29 Ik1-ER cells treated with 4OHT
strain: mixed C57Bl/6/129sv
chip antibody: in house anti-Ikaros rabbit polyclonal antibody ; lot: A3
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| Treatment protocol |
T29-IKER cells were treated with 4OHT (100 nM) for 24h.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Illumina pipeline v1.3 to v1.6 are used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using GERALD. Only 2 mismatch reads were kept for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)
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| Submission date |
Apr 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Susan Chan |
| E-mail(s) |
scpk@igbmc.fr
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| Phone |
33 3 88 65 34 72
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| 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 |
GPL11002 |
| Series (1) |
| GSE46119 |
Mapping of Ikaros and RBPJ binding sites in the mouse T cell leukemia cell line T29 |
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| Relations |
| BioSample |
SAMN02046763 |
| SRA |
SRX266511 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1123946_wigs_for_T29_Ik1ER_IK-ChIP.wig.gz |
123.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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