|
| Status |
Public on May 24, 2024 |
| Title |
Lane1_Sample_11 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Blood
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Whole Blood
lane.ordinal: 11
mouse: 40
infection.time.point.days: 14
age.days: 92
cage: 15
tb.status: infected
aerosol.run: Aerosol1
strain: Balb/c
lung.cfus: 108000
blood.source: Heart
sequencing.lane: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole blood was collected, mixed with EDTA, and mixed with Zymo Research DNA/RNA Shield. DNA was isolated using the Zymo Research Quick-DNA kit and Genomic DNA Clean & Concentrator kit.
Libraries were prepared using Reduced Representation Bisulfite Sequencing. 52 samples were pooled together using custom synthesized methylated adapters with unique dual indexes (Integrated DNA Technologies).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using bcl2fastq2 v.2.19
Adapter removal and quality trimming were performed by using Trim Galore! v.0.6.4
Alignment performed by BitMapperBS v.1.0.2.3 with default options: bitmapperBS --search ${REFERENCE} --seq1 ${R1} --seq2 ${R2} --bam -o Sample_${n}.bam
Methylation levels were determined using MethylDackel v.0.4.0 with default options: MethylDackel extract $DACKELREFERENCE $bam_file
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Processed files are MethylDackel bedGraph output files with 1. Chromosome name 2. Start coordinate 3. End coordinate 4. Methylation percentage 5. Number of alignments reporting methylated bases 6. Number of alignments reporting unmethylated bases
|
| |
|
| Submission date |
May 27, 2021 |
| Last update date |
May 24, 2024 |
| Contact name |
Russell Ault |
| Organization name |
The Ohio State University College of Medicine
|
| Street address |
370 W 9th Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE175661 |
Blood DNA methylation altered by Mycobacterium tuberculosis infection in mice |
|
| Relations |
| BioSample |
SAMN19369699 |
| SRA |
SRX11006562 |
