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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 21, 2017 |
| Title |
ATAC-seq LPL Treg Ahr WT (rep2) |
| Sample type |
SRA |
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| Source name |
Lg. Int. Lamina Propria Treg
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| Organism |
Mus musculus |
| Characteristics |
tissue: Large Intestine
cell type: Treg
strain: C57BL/6
genotype: Ahrf/+ Foxp3Yfp-Cre
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
[RNA-seq] Lamina propria cells were isolated and sorted by flow cytometry. Sorted Tregs were lysed in Trizol (Invitrogen), and RNA was subsequently extracted with RNAeasy Mini Kit (Qiagen). [ATAC-seq] Lamina propria cells were isolated and Tregs were sorted by flow cytometry.
[RNA-seq] Total RNA was treated with Ribo-zero kit and RNAseq libraries were generated using kits from Illumina. Barcoded samples were pooled and sequenced over 2 lanes on an Illumina HiSeq 2500 instrument to produce 50 bp single-end reads. [ATAC-seq] Large intestinal CD4+TCRβ+YFP+ Tregs were sorted and subjected to ATAC-Seq according to a published protocol (Buenrostro et al., 2013) with a modification in the library purification step. Briefly, 5x10^4 sorted Tregs were washed once with 50 ul PBS, and then lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice. Pelleted nuclei were resuspended in transposition reaction mix with Tn5 transposase (Illumina) and incubated at 37℃ for 30 min with gentle shaking. The DNA was purified with MinElute PCR Purification Kit (Qiagen) and was used as a template of PCR with 10 cycles of amplification. The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter), to exclude the small fragments, before sequencing with Illumia HiSeq 2500.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
[ATAC-seq] ATAC-Seq reads were mapped to the mouse genome (mm9) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: [RNA-seq] Tab-delimited text file includes count values for each sample. [ATAC-seq] bedgraph files for each sample
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| Submission date |
Oct 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Liang Zhou |
| E-mail(s) |
liangzhou497@ufl.edu
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| Organization name |
University of Florida
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| Department |
Department of Infectious Diseases and Immunology
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| Street address |
2015 SW 16th AVE., V3-144
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32608 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE106083 |
Aryl Hydrocarbon Receptor Preferentially Marks and Promotes Gut Regulatory T Cells |
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| Relations |
| BioSample |
SAMN07832830 |
| SRA |
SRX3324098 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2830217_Treg_LI_AhrWT_R2_track.bedgraph.gz |
209.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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