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| Status |
Public on Apr 09, 2018 |
| Title |
MDS125_Normal_RNA-seq |
| Sample type |
SRA |
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| Source name |
Hematopoietic stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+ hematopoietic stem cells
disease status: Healthy
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA) from magnetic bead affinity-enriched CD34+ cells (>90%) obtained from marrow aspirates (Miltenyi Biotec, Auburn, CA). The samples were snap frozen in liquid nitrogen and stored at -80oC on the day of collection. Quality check was performed by Bioanalyzer2100 (Agilent Technologies, Palo Alto, CA) using High Sensitivity RNA Chips.
5-10ng of total RNA (RIN>7) was amplified by using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech Laboratories, Inc., Mountain View, CA) after testing for the fidelity of the protocol on HeLa cell derived RNA (Supplementary Methods, Suppl Figure 1 of publication). cDNA library synthesis and sequencing were performed as previously described (See Supplementary Methods of publication). The libraries were sequenced on the Illumina HiSeq 2000 platform at the Stanford Sequencing Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
MDS_58
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR or TopHat2.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C et al. Read Counts (cpm) were generated using EdgeR package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: MDS_isoform_fpkm.txt: Combined matrix of normalized abundance measurement - isoform expression (fpkm) using CuffDiff2.
Supplementary_files_format_and_content: MDS_genes_edgeR.txt: Combined matrix of normalized abundance measurement - gene expression (counts) using EdgeR.
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| Submission date |
Feb 25, 2018 |
| Last update date |
Apr 09, 2018 |
| Contact name |
Varsha Rao |
| E-mail(s) |
varshar@stanford.edu
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| Phone |
6507245777
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| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Snyder Lab
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE111085 |
Distinct Transcriptomic and Exomic Abnormalities within Myelodysplastic Syndrome Marrow Cells |
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| Relations |
| BioSample |
SAMN08605812 |
| SRA |
SRX3741189 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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