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| Status |
Public on Aug 31, 2013 |
| Title |
FSHD1 Replicate 2 |
| Sample type |
SRA |
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| Source name |
MB-FSHD-197
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| Organism |
Homo sapiens |
| Characteristics |
cell type: primary myoblast
disease state: FSHD2
Sex: Male
age (y): 42
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| Growth protocol |
Myoblasts grown at 37degC,5% CO2 in F-10 medium with 20% FBS, 1% Pen/strep, 10ng/ml bFGF, 1 uM dexamethasone
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Circular chromosome conformation capture (4C) was performed on 10e7 cells; inverse PCR with primers recognizing a HindIII-DpnII fragment containing the SSLP of the FSHD locus amplified prey fragments captured by this bait in the assay; inverse PCR products were prepared for Illumina sequencing using a custom library preparation method that involved Covaris fragmentation, adapter ligation and amplification to add attachment sequences; the library was subjected to paired-end sequecing, with the first read yielding the SSLP sequence and the second read yielding sequence from the bait fragment captured by each SSLP
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
With typical paired-end sequencing data, both reads map near each other in the genome within the distance expected by insert size; however, in my case the first read of a pair maps to a single position in the genome, while the second read of a pair maps elsewhere in the genome, even on a different chromosome from the first. Thus, insert size is not relevant.
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| Data processing |
Prey reads (read2) that passed the Illumina quality filter were scanned for the presence of DpnII sites; sequence after the DpnII site was trimmed and all reads of at least 20bp were kept
Trimmed prey reads were aligned to the reference human genome (hg19, standard chromosomes only) using BWA with default paramaters that allowed up to two mismatches in the seed region and retained only uniquely-aligning reads
Aligned prey reads and their paired SSLP reads were subsequently analyzed using a custom R script (v2.15) and the Bioconductor (v2.10) software packages
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files represent processed prey reads that were aligned to the hg19 reference genome; Columns indicate: chromosome (chr), alignment start (start), alignment end (end), strand, flowcell number and lane (flowcell), read name (readID), BWA mapping quality (mapq), genotype of paired bait read (SSLP)
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| Submission date |
Sep 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kyle Siebenthall |
| E-mail(s) |
ksiebent@fhcrc.org
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Human Biology
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| Street address |
1100 Fairview Ave N
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| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE40673 |
An allele-aware approach identifies altered nuclear associations of the contracted D4Z4 array at the FSHD locus |
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| Relations |
| SRA |
SRX183926 |
| BioSample |
SAMN01162435 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM999064_F1.2reads.txt.gz |
14.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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