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Sample GSM3660020 Query DataSets for GSM3660020
Status Public on Sep 05, 2019
Title WT_LGMP_3
Sample type SRA
 
Source name WT Leukemic GMP cells
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wild type
cell type: Leukemic GMP cells
Treatment protocol L-GMP cells were isolated from AMPK WT and KO mice.
Extracted molecule total RNA
Extraction protocol Cell were sorted into Trizol and RNA were extracted using RNeasy MiniElute Cleanup kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions.
cDNA libraries were generated using the Smart-seq2 protocol. Sequencing libraries were generated from 250 pg of amplified cDNA using Nextera XT kit according to the manufacturer's instructions. Barcoded libraries were purified and sequenced on a NextSeq 500 platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were mapped to mm10 using STAR, version 2.5.3a, with settings: “alignSJoverhangMin” 8; “alignSJDBoverhangMin” 1; “outFilterMismatchNmax” 999; “alignIntronMin” 20; “alignIntronMax” 1000000; “alignMatesGapMax” 1000000; “twopassMode” Basic; “sjdbOverhang” 100.
FPKM and differential gene expression were calculated with DESeq2 (version 1.18.1) and Ensembl 84 as the reference.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited (TSV) file containing a matrix of FPKM values for all samples
 
Submission date Mar 07, 2019
Last update date Sep 05, 2019
Contact name Daisuke Nakada
E-mail(s) nakada@bcm.edu
Organization name Baylor College of Medicine
Department Molecular and Human Genetics
Street address One Baylor Plaza
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL19057
Series (2)
GSE127999 AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia: RNA-seq
GSE128001 AMPK links acetyl-coA homeostasis to BET recruitment in acute myeloid leukemia
Relations
BioSample SAMN11082567
SRA SRX5492048

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

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