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| Status |
Public on Oct 31, 2014 |
| Title |
Ade 3 |
| Sample type |
SRA |
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| Source name |
Apc Min small intestinal adenoma
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Apc min/+
tissue: small intestinal adenoma
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small intestinal crypts were isolated in PBS containing 3 mM EDTA, 0.5 mM DTT and protease inhibitor (Roche). Adenomas were dissected from the small intestine. RNA was extracted using RNaEasy kit (Qiagene).For ChIP-seq, crypts and adenoma in 1% formaldehyde for 10 Min at room temperature. Chromatin was sheared using the Covaris S2 system following the manufacturer’s instructions. ChIP was performed using a ChIP validated rabbit anti-Rad21 antibody (Ab992, Abcam) and Magna-ChIP A kit (Millipore).
Library preparations were performed using the TruSeq RNA Sample Preparation protocol (Illumina, San Diego, CA) and correct size established using the DNA 1000 kit (Agilent technologies, Santa Clara, CA). Libraries were quantified with qPCR, normalised and pooled to 2nM before sequencing with paired-end 50 bp reads using standard protocols on the HiSeq2000 (Illumina, San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
RNA-seq reads were mapped using bowtie version 0.12.8 & TopHat v1.4.1. Transcripts assembled using Cufflink. Reads count was performed with htseq-count (version 1.0.0)
ChIP-seq reads were mapped with BWA for Illumina (version 1.2.3).
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include limma-voom normalised log2 values for each Sample;
Supplementary_files_format_and_content: For ChIP-seq, peak calling was performed using MACS V3.1 with p value cutoff 1e-4 for peak detection and MFOLD 10 for enrichment ratio.
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| Submission date |
Jul 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Huiling Xu |
| E-mail(s) |
huiling.xu@petermac.org
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| Phone |
+61 3 9656 1274
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| Organization name |
Peter MacCallum Cancer Centre
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| Department |
Research Division
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| Lab |
Differentiation and transcription lab
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| Street address |
St Andrew Place
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| City |
East Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3002 |
| Country |
Australia |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE59283 |
Genome-wide mapping of Rad21 binding sites and gene expression profiling in wild type mouse small intestinal epithelial crypts and Apc Min adenomas |
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| Relations |
| BioSample |
SAMN02906708 |
| SRA |
SRX648708 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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