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| Status |
Public on Jul 13, 2022 |
| Title |
TCF4_MC38 APC KO |
| Sample type |
SRA |
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| Source name |
MC38 with APC knockout
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| Organism |
Mus musculus |
| Characteristics |
antibody: TCF4
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| Growth protocol |
The CRC cell lines MC38 (RRID:CVCL_B288) and its isogenic cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% Tet System Approved FBS (Clontech) and 100 U/ml ampicillin/penicillin. All cells were confirmed to be mycoplasma-free and maintained at 37 °C and 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from PFA fixed cells were cross-linked with 1% PFA and then reactions were quenched using 0.125 M glycine. Cells were lysed with ChIP lysis buffer [10 mM Tris-HCl (pH 8.0), 140 mM NaCl, 1 mM EDTA (pH 8.0), 1% Triton X-100, 0.2% SDS and 0.1% deoxycholic acid] for 30 min on ice. Chromatin fragmentation was performed using a Diagenode BioruptorPico sonicator (30 s on and 30 s off, 45 cycles) and incubated with the appropriate mixture of antibody and Dynabeads (ThermoFisher Scientific, Cat# 10003D) overnight. Immune complexes were washed with RIPA buffer (three times), once with RIPA-500 (RIPA with 500 mM NaCl), and once with LiCl wash buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 250 mM LiCl, 0.5% NP-40 and 0.5% deoxycholic acid]. Elution and reverse-crosslinking were performed in direct elution buffer [10 mM Tris-Cl (pH 8.0), 5 mM EDTA, 300 mM NaCl, 0.5% SDS] containing proteinase K (20 mg/ml) at 65°C overnight.
Eluted DNA was purified using AMPure beads (Beckman-Coulter, Cat# 754 A63880), and then used to generate libraries using NEBNext Ultra DNA Library kit (New 755 England BioLabs Inc., Cat# E7370)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
binding peaks for TCF4 on the promoters of TDO2 gene in APC-KO MC38 cells.
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| Data processing |
Base-calling was performed with NextSeq RTA version 2.4.11.0; bcl2fastq version 2.20.0 was used to convert the bcl files into fastq files
ChIP-seq reads were aligned to the mm9/hg19 genome assembly using Bowtie version 1.2.2 with the following criteria: --best --chunkmbs 320
Peak-calling was performed using MACS version 1.4.2
Bigwig files were generated using deepTools version 2.7.15 by scaling the bam files to reads per kilobase per million (RPKM) using the following criteria: bamCoverage –b–normalizeUsing RPKM–smoothLength 300–binSize 30–extendReads 200 –o
Differential peaks were called using MACS2 with the following criteria: bdgdiff –g 60 –l 120
Assembly: mm9
Supplementary files format and content: bigwig
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| Submission date |
Apr 25, 2022 |
| Last update date |
Jul 13, 2022 |
| Contact name |
Chang-Jiun Wu |
| Organization name |
University of Texas, MD Anderson Cancer Center
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| Department |
Genomic Medicine
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| Lab |
DePinho Lab
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| Street address |
1515 Holcombe Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE200910 |
Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer |
| GSE201414 |
Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer [ChIP-Seq] |
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| Relations |
| BioSample |
SAMN27759124 |
| SRA |
SRX14986813 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6063106_TCF4_MC38_APC_KO.bw |
435.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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