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| Status |
Public on Mar 28, 2017 |
| Title |
WT_rep1 |
| Sample type |
SRA |
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| Source name |
spleen + LN
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| Organism |
Mus musculus |
| Characteristics |
strain: NOD
genotype: Flicr WT
cell type: Treg
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were isolated form 8-10 week-old NOD mice and double sorted by flow cytometry for DAPI- CD4+ TCRb+ CD25hi (top 50%) Tregs
50,000 CD4+TCRβ+CD25hi (top 50%) Tregs were sorted and lysed. After transposition and PCR, a final bead purification and selection (100–600 bp) was performed twice using 0.6× and 1.6× SPRI beads. Libraries were paired-end sequenced using a 75-bp kit on an Illumina NextSeq high-throughput sequencing system.
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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 |
Filtered on quality using sickle1.2: sickle pe -f R1.fastq -r R2.fastq -o filtered_R1.fastq -p filtered_R2.fastq -t sanger -s filtered_singles.fastq
Mapping to the mouse mm9 genome: bowtie2 -p 2 -x mm9 -X 1000 –fr -1 clean_R1.fastq -2 clean_R2.fastq -S btout2.sam
Multiple location mapping filtering: sed ‘/XS:/d’ mapped.sam > mapped_1alignmentonly.sam
PCR duplicates removal using Picard tools 1.130: java -Xms1024m -jar /opt/picard-1.130/picard.jar MarkDuplicatesWithMateCigar INPUT = mapped_1align.sorted.bam OUTPUT=$prefix.sorted.uniq.bam METRICS_FILE = metrics.txt REMOVE_DUPLICATES = true ASSUME_SORTED = true SKIP_PAIRS_WITH_NO_MATE_CIGAR = true
Nucleosome-free fragments (<120 bp) isolation: samtools view -h $prefix.sorted.uniq.bam | awk ‘ ^/ @/ { print $0 >> “nuc120.sam” ; next } { if ($9 <120 && $9 > -120) {print $0 >> “nuc120.sam”} }’
Peak calling using Homer 4.6: findPeaks homer_tagdir_nuc120/ -o $prefix.nuc120.peaks_size250mindist500.txt -region -size 250 -minDist 500
Differential peak analysis was performed using DiffBind
Genome_build: mm9
Supplementary_files_format_and_content: bed: chromosome, start, end, name, score, strand, RPKM
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| Submission date |
Mar 27, 2017 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE97085 |
Flicr, a long noncoding RNA modulating Foxp3 expression and autoimmunity (ATAC-Seq) |
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| Relations |
| BioSample |
SAMN06645443 |
| SRA |
SRX2676232 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2551427_WT_rep1.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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