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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 18, 2013 |
| Title |
SF3B1 mutant patient #1 |
| Sample type |
SRA |
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| Source name |
bone marrow mononuclear cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
genotype: SF3B1 somatic heterozygote, H666Q
disease: RARS-T, >15% ring sideroblasts
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| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated total RNA from bone marrow mononuclear cells
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
100-bp paired-end RNA-Seq reads were mapped to the hg19 RefSeq human transcriptome and spliceosome by DNAnexus (http://dnanexus.com) using a Bayesian method, in which a read was mapped when its posterior probability of mapping exceeded 0.9.
These filtered posterior probabilities were summed to generate fractional read counts per gene and per exon, with probabilities from splice-junction spanning reads counted for each relevant exon.
Genome_build: hg19
Supplementary_files_format_and_content: Mapped exon counts; Alternative Splicing format: type The type of element – either an exon or a junction; gene_id The unique identifier for the gene from the reference database; gene_name The reference gene name in the database; chromosome_name Chromosome name for the gene; strand Genomic strand for the gene; prev_exon_left If the element is a splice site, this represents the left boundary of the donor exon. If the element is an exon, this represents the left boundary; prev_exon_right If the element is a splice site, this represents the right boundary of the donor exon. If the element is an exon, this represents the right boundary; next_exon_left If the element is a splice site, this represents the left boundary of the acceptor exon. If the element is an exon, this field is not used; next_exon_right If the element is a splice site, this represents the right boundary of the acceptor exon. If the element is an exon, this field is not used; read_count The sum of the posterior probabilities for all confident reads that map to the element.
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| Submission date |
Jan 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
John Barnard |
| E-mail(s) |
barnarj@ccf.org
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| Phone |
2164445945
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| Organization name |
Cleveland Clinic Foundation
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| Department |
Quantitative Health Sciences
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| Street address |
9500 Euclid Ave.
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| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44195 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE43603 |
Differential gene expression and exon usage in bone marrow from RARS patients with SF3B1 somatic mutations compared to healthy patients. |
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| Relations |
| SRA |
SRX218318 |
| BioSample |
SAMN01889225 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1066119_RNA-Seq_Ot164_10032011_Alternative_Splicing.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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