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| Status |
Public on Nov 28, 2016 |
| Title |
CONVR.5 TCR γδ+ IEL |
| Sample type |
SRA |
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| Source name |
Intraepithelial lymphocyte
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| Organism |
Mus musculus |
| Characteristics |
microbial colonization state: conventionally-raised
cell type: Intraepithelial lymphocyte
strain: C57BL/6
tissue origin: Intestine
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| Treatment protocol |
C57BL/6 mice were maintained as sterile (germ-free), conventionally-raised, or colonized with the gut microbiota of a C57BL/6 donor mouse.
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| Growth protocol |
Mice were fed a sterilized low fat, plant polysaccharide rich chow (B&K Universal, Product 7378000, East Yorkshire, UK) that was provided ad lib.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral T cells and IELs were isolated by FACS, with a target maximum of 50,000 cells per transposition reaction. Nuclei were isolated and prepared as described in Buenrostro et al., Nature Methods, 2013.
Libraries were prepared using a modified version of the Illumina Nextera DNA Sample kit, based on the work of Buenrostro et al., Nature Methods, 2013 and outlined in the associated manuscript, Semenkovich et. al., 2016 (in submission).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Data were analyzed as described in the associated manuscript, Semenkovich et. al., 2016 (in submission).
In brief, Illumina reads were trimmed, then mapped to mm10 using bowtie2 with the parameters: --end-to-end --sensitive --no-unal --no-discordant.
Using samtools, low mapping quality reads were filtered (>=10), reads mapping to chrM were removed, and duplicates were then filtered.
Peaks were called using macs14 (with p = 1e-9), and overlapping peaks were used to generate merged .bed files.
Genome_build: mm10
Supplementary_files_format_and_content: .bed files: Per-sample .bed files identifying peaks identified from macs1.4, as described in the methods of the associated manuscript.
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| Submission date |
Nov 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey Gordon |
| Organization name |
Washington University
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| Department |
Center for Genome Sciences & Systems Biology
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| Street address |
4515 McKinley Research Building
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE89646 |
Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes |
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| Relations |
| BioSample |
SAMN05992175 |
| SRA |
SRX2336244 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2386016_CONVR_5_TCR_GD.bed.gz |
128.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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