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| Status |
Public on Jun 08, 2018 |
| Title |
TgN_03WO_Sp_rep1 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
age (weeks-old): 3
strain: C57BL/6
tissue: Spleen
cell type: CD4+FOXP3-ires-GFP+Treg
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
10,000 cells were sorted into collection buffer (PBS, 0.5% BSA, 2mM EDTA), pelleted and lysed in hypotonic buffer (10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% NP-40). Nuclei were pelleted by centrifugation for 30 min. at 500g, 4oC.
The ATAC-seq protocol was adapted from Buenrostro et al., 2013 and Lara-Astiaso et al., 2014. Nuclear pellets were re-suspended in 5uL of transposition mix (1uL Tagment DNA Enzyme, 2.5uL Tagment DNA Buffer from Nextera DNA Sample Prep Kit, 1.5uL H2O), and incubated at 37C for 60min. Two sequential PCR reactions were performed. After the first PCR, libraries were selected for small fragments (< 600bp) using SPRI beads followed by a second round of PCR with the same conditions, and a final SPRI bead purification to capture all fragments for the final library. Paired-end sequencing was performed on an Illumnina NextSeq 500 (50,10,0,31).
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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 |
Base calling was performed with Real-Time Analysis v2.4.11
ATAC-seq reads from two replicates per sample were filtered for quality using sickle v1.2 (default settings for PE reads), adapter-trimmed using cutadapt v1.8.3 (`-e 0.1, -m 20`), and mapped to mm9 using Bowtie v2.2.4, keeping only mate pairs that mapped to a single best location using samtools v1.3, and were non-duplicates using Picard v1.130.
To generate bigWig files, filtered and mapped reads were used to generate tag directories in HOMER v4.6 (`makeTagDirectory -tbp 1 -checkGC -illuminaPE`), followed by bedGraph files (HOMER `makeUCSCfile -fsize 1e50 -norm 1e6`), which were then used to generate bigWig files using UCSC-tools (`bedGraphToBigWig`).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
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| Submission date |
Apr 20, 2018 |
| Last update date |
Jun 08, 2018 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
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| Phone |
617-432-7747
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| Organization name |
Harvard Medical School
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| Department |
Microbiology and Immunobiology
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| Lab |
CBDM
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE113412 |
Tracking adipose-tissue Treg provenance, dependencies, and activities via T cell receptor transgenic mice |
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| Relations |
| BioSample |
SAMN08960479 |
| SRA |
SRX3978416 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3105230_TgN_03WO_Sp_rep1.bw |
109.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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