NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3764720 Query DataSets for GSM3764720
Status Public on May 14, 2019
Title 73A-46B-183A
Sample type SRA
 
Source name Bone Marrow
Organism Mus musculus
Characteristics cell type: Leukemia
strain: C57Bl/6 x 129Sv/Jae F1
mutagen: MOL4070LTR
Treatment protocol Not applicable
Growth protocol Not applicable
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from the bone marrows of mice transplanted with IM-induced leukemias using TRIzol. Phenol-chloroform-isoamyl extraction and ethanol precipitation were performed. Total RNA (1 μg) was treated with DNase I at room temperature for 15 min. The integrity of the DNase I-treated RNA was analyzed on an Agilent 2100 Bioanalyzer before selection of poly(A) mRNA. Selection for poly(A) mRNA and subsequent cDNA synthesis and library preparation were carried out using the Illumina TruSeq RNA sample preparation kit according to the manufacturer's protocol. cDNA was fragmented (200-bp peak) with a Covaris E210 ultrasonicator prior to library preparation.
cDNA libraries were prepared for sequecing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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 mm10 using Bowtie v2
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values files including FPKM values for each sample.
 
Submission date May 13, 2019
Last update date May 15, 2019
Contact name Benjamin Huang
Organization name University of California San Francisco
Street address 1450 3rd Street Room 263
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL17021
Series (1)
GSE131151 Convergent Genetic Aberrations in Murine and Human T Lineage Acute Lymphoblastic Leukemias
Relations
BioSample SAMN11637388
SRA SRX5827217

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap