NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2084859 Query DataSets for GSM2084859
Status Public on Mar 31, 2017
Title Leukemia cells IL4 rep1
Sample type SRA
 
Source name Leukemia cells IL4
Organism Mus musculus
Characteristics strain background: C57BL/6
variation: Actin-dsRed
tissue: Mouse leukemic bone marrow
cell type: c-Kit enriched MLL-AF9 leukemia cells
grown in: 20 ng/mL IL3 and IL4 for 18hrs
Extracted molecule total RNA
Extraction protocol Bone marrow of leukemic or healthy mice were crushed followed by CD117 selection (Miltenyi Biotec, Bergisch Gladbach, Germany). RNA was extracted using the QIAshredder and RNeasy Microkit (QIAgen, Hilden, Germany). Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description processed data file: MLL_IL4_TMM.txt
Data processing Bcl2FastQ software was used for basecalling.
Sequenced reads were mapped to the mm10 referece genome using Tophat 2.0.13 with parameters -p 2 --keep-fasta-order --bowtie1 --no-coverage-search
BAM files were imported to the Qlucore Omics Explorer 3.0 software and normalized using the TMM (Trimmed Mean of M-values) method.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt file of TMM values for all samples
 
Submission date Mar 10, 2016
Last update date May 15, 2019
Contact name Pablo Peña-Martínez
E-mail(s) pablo.pena@med.lu.se
Organization name Lund University
Department Clinical Genetics
Street address Klinikgatan 28
City Lund
ZIP/Postal code 22184
Country Sweden
 
Platform ID GPL19057
Series (1)
GSE79068 Interleukin 4 induces apoptosis of acute myeloid leukemia cells in a Stat6-dependent manner
Relations
BioSample SAMN04544512
SRA SRX1624435

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