|
| Status |
Public on May 11, 2024 |
| Title |
Day_3_FSHD2_4_R2 [methylation] |
| Sample type |
SRA |
| |
|
| Source name |
Primary myoblasts from quadricep biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: FSHD2-4
cell type: Myoblasts
muscle group: quadricep
fshd status: FSHD2
day of differentiation: Day 3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was collected from a single 6 cm dish using the DNeasy Blood & Tissue kit (69504, Qiagen).
All DNA methylation data was generated using the TruSeq Methyl Capture EPIC kit (FC-151-1003, Illumina) according to manufacturer’s protocol.
Libraries were sequenced on the Illumina NextSeq500 with paired-end 75 bp reads to a depth of 20 to 82 million reads.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PerMeth.AllRegions.csv
|
| Data processing |
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Raw reads from TruSeq Methyl Capture EPIC libraries were mapped to canonical chromosomes from hg38 and the patch region of D4Z4 (chr4_KQ983257v1_fix) using bismark (version 0.19.0).
Sites were extracted from the bam file using bismark_methylation_extractor with paired end and no overlap specified. To remove bias from the ends of reads, 2 bp from the 5’ end of read 2 and 1 bp from the 3’ end of read 1 were ignored when extracting sites.
All CpG sites were read into methylKit (version 1.16.0). Sites within 200 bp were merged into one region using bumphunter (version 1.32.0). Methylation over those regions was summarized using regionCounts and filtered for at least three CpG sites.
Regions were then filtered for a coverage of at least 5. Regions were normalized using normalizeCoverage, and only regions with coverage in all samples were kept.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.bismark.cov: Coverage files are output from bismark and contain the 0-indexed site, percent methylation, number of methylated sites and number of unmethylated sites in that order.
Supplementary_files_format_and_content: PerMeth.AllRegions.csv: Percent methylation file contains the percent methylation for regions per sample normalized as described above.
|
| |
|
| Submission date |
May 12, 2021 |
| Last update date |
May 11, 2024 |
| Contact name |
Ali Mortazavi |
| E-mail(s) |
ali.mortazavi@uci.edu
|
| Organization name |
UC Irvine
|
| Street address |
2300E Biological Sciences 3
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE174369 |
Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD [methylation] |
| GSE174370 |
Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD |
|
| Relations |
| BioSample |
SAMN19132179 |
| SRA |
SRX10863193 |
