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| Status |
Public on Jan 03, 2020 |
| Title |
ChIPSeq.HEK293_T1_mut_C |
| Sample type |
SRA |
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| Source name |
HEK293
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
treatment: Expressing Flag-tagged human ENL T1 mutant
antibody: Flag M2, Sigma F1804
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| Treatment protocol |
For generating Flag-tagged stable cell lines, 10 ug/ml blasticidin was used for stable cells selection. RNA-seq samples were collected 4 days after virus infection. ChIP-seq samples were crosslinked with 1% formaldehyde 9 days after virus infection. T1, T2 and T3 are three recurrent somatic ENL mutations originally identified in Wilms tumors (Ref: Perlman EJ, Nature communication 2015, DOI: 10.1038/ncomms10013). T1 is ENL117_118insNHL, T2 is ENL112_114PPV>L, and T3 is ENL111_113NPP>K.
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| Growth protocol |
HEK293 cells were maintained in alpha-MEM supplemented with 10% FBS, HK-2 cells were maintained in keratinocyte serum free medium. All cells were culture at 37C with 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. For RNA-seq, RNA was isolated using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD).
ChIP-seq libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer's protocol. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform. RNA-seq samples were prepared as instructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. Two biological replicates were prepared for each condition. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 3000 platform.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2+B102; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: RNA-seq read counts were calculated using HTSeq 0.6.1p1
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| Submission date |
Jan 16, 2019 |
| Last update date |
Jan 03, 2020 |
| Contact name |
Hong Wen |
| Organization name |
Van Andel Research Institute
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| Department |
Center for Epigenetics
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| Street address |
333 Bostwick Ave. N.E.
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| City |
Grand Rapids |
| State/province |
Michigan |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE125186 |
Impaired Cell Fate by Gain-of-function Mutations in a Chromatin Reader |
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| Relations |
| BioSample |
SAMN10755916 |
| SRA |
SRX5255101 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3564791_293_T1_C_treat.nsp.bw |
602.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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