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| Status |
Public on Jun 07, 2014 |
| Title |
CR Colon DNase-seq Rep 2 |
| Sample type |
SRA |
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| Source name |
Intestinal Epithelial Cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Colon
condition: conventionally-raised (CR)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
IECs were isolated from the duodenum (anterior 5 cm of midgut), ileum (posterior 6 cm of midgut), and colon (6 cm of terminal hindgut) of 8 to 12-week old mice ; Nuclei were isolated by 0.1% NP-40 lysis for DNase digestions ; Total RNA extracted by cell lysis in TRIzol reagent (Invitrogen) and further purified using Qiagen RNeasy kit according to manufacturer's protocol
DNase-seq libraries were prepared as described (Song and Crawford 2010; PMID:20150147) with 5 µg of DNA pooled from nuclei digested for 2 min, 4 min, and 8 min at 37°C with no exogenous DNase I added ; RNA-seq libraries were prepared with 2 micrograms total RNA used for standard TruSeq library preparation (Illumina) with polyA selection and sequenced with 2 x 50bp paired-end reads
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA v1.8.2.
First 20bp of DNase-seq reads mapped to NCBI37/mm9 with BWA, RNA-seq mapped to NCBI37/mm9 with Tophat v2.0.8b; in both cases up to 2 mismatches and multireads that map up to 4 locations were allowed.
Putative PCR artifacts filtered from mapped DNase-seq.
DNase-seq peaks called with F-seq v1.84 with default parameters and -f set to zero.
RNA-seq FPKM transcript abundances estimated with Cufflinks and differential testing performed with Cuffdiff v2.0.2, both with -u and -b parameters specified.
Genome_build: mm9.
Supplementary_files_format_and_content: DNase-seq .bigWig files contain single base resolution summed cleavage events (5-prime end of mapped reads); DNase-seq .npf is narrow peak format (BED6+4) with chromosome, start, stop, name, score (for browser display), strand (N/A), signal value (test stat for enrichment), -log10(p-value), q-value (N/A), point-source for peak (0-based offset from start) for the top 100,000 DHS peaks detected by F-seq ; RNA-seq cufflinks files contain gene name, genomic loci, and FPKM abundances.
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| Submission date |
May 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher L Frank |
| E-mail(s) |
chris.frank21@gmail.com
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| Organization name |
Duke University
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| Lab |
Gregory Crawford
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| Street address |
101 Science Dr.
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE57919 |
Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape |
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| Relations |
| BioSample |
SAMN02798222 |
| SRA |
SRX551064 |
| Named Annotation |
GSM1397424_CR_Colon_Dnase_Rep2.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1397424_CR_Colon_Dnase_Rep2.bigWig |
958.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM1397424_CR_Colon_Dnase_Rep2_peaks.npf.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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