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Sample GSM2084869 Query DataSets for GSM2084869
Status Public on Mar 31, 2017
Title NBM cells IL4 rep 4
Sample type SRA
Source name NBM cells IL4
Organism Mus musculus
Characteristics strain background: C57BL/6
tissue: Mouse normal bone marrow
cell type: c-Kit enriched normal bone marrow
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: NBM_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
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
BioSample SAMN04544522
SRA SRX1624445

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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