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Sample GSM3021873

Query DataSets for GSM3021873

Status

Public on Apr 09, 2018

Title

MDS1075_tMDS_RNA-seq

Sample type

SRA

Source name

Hematopoietic stem cells

Organism

Homo sapiens

Characteristics

cell type: CD34+ hematopoietic stem cells
disease status: Myelodysplastic syndrome
myelodysplastic syndrome stage: tMDS

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.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

MDS_12
processed data file: MDS_genes_edgeR.txt
processed data file: MDS_isoform_fpkm.txt

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.

Submission date

Feb 25, 2018

Last update date

Apr 09, 2018

Contact name

Varsha Rao

E-mail(s)

varshar@stanford.edu

Phone

6507245777

Organization name

Stanford University