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SRX551055: GSM1397415: CR Ileum DNase-seq Rep 3; Mus musculus; DNase-Hypersensitivity
1 ILLUMINA (Illumina HiSeq 2000) run: 231.4M spots, 11.6G bases, 7.2Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape
show Abstracthide Abstract
We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin organization. Surprisingly, we discovered that microbiota modify host gene transcription in IECs without significantly impacting the accessible chromatin landscape. Instead, microbiota regulation of host gene transcription might be achieved by differential expression of specific TFs and enrichment of their binding sites in nucleosome depleted CRRs near target genes. Our results suggest that the chromatin landscape in IECs is pre-programmed by the host in a region-specific manner to permit responses to microbiota through binding of open CRRs by specific TFs. Overall design: mRNA and accessible chromatin (DNase-seq) profiles from colonic and ileal IECs were compared between conventionally-raised (CR), germ-free (GF), and conventionalized (CV) C57BL/6 mice.
Sample: CR Ileum DNase-seq Rep 3
SAMN02798212 • SRS618765 • All experiments • All runs
Organism: Mus musculus
Instrument: Illumina HiSeq 2000
Strategy: DNase-Hypersensitivity
Selection: DNase
Layout: SINGLE
Construction 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
Experiment attributes:
GEO Accession: GSM1397415
External link:
Runs: 1 run, 231.4M spots, 11.6G bases, 7.2Gb
Run# of Spots# of BasesSizePublished


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