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Sample GSM1346216 Query DataSets for GSM1346216
Status Public on Mar 12, 2014
Title Mx1cre-JAK2V617F 6wks post-induction (n=3)
Sample type SRA
Source name Bone marrow nestin+ cells, Mx1-cre;JAK2-V617F
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: Nes-gfp;Mx1-cre;JAK2-V617F
cell type: bone marrow CD45- CD31- Ter119- Nes-GFP+ cells
developmental stage: adult
Treatment protocol pIpC
Extracted molecule total RNA
Extraction protocol RNA was obtained using Picopure RNA isolation kit (Arcturus).
cDNA Amplification: Amplified cDNAs were prepared from RNA samples (2-3 ng) using Ovation RNA-SeqSystem v2 (Nugen).
Library preparation: 1 ug of amplified cDNAs were fragmented by sonication to an average size of 300 pb aprox. Libraries for high-throughput sequencing were prepared from fragmented cDNAs using the Truseq DNA Sample Prep Kit (Illumina).
Sequencing: Libraries were sequenced in a Genome Analyzer IIx using standard procedures.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description Mx
Data processing Fastq files obtained and demultiplexed with CASAVA1.8.
Illumina adaptors were trimmed with cutadapt v1.2.1.
First 15 nucleotides were trimmed with fastx_timmer to remove signatures left by ovation protocol.
PolyGC stretches at the beginning of the reads were also removed.
Reads shorter than 30nt were discarded for posterior analysis.
Reads were mapped with tophat v2.0.7 and bowtie 2.0.6.
Gene FPKM were quantified using Cufflinks.
Gene build: Ensembl v70
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKMs
Submission date Mar 11, 2014
Last update date May 15, 2019
Contact name Simón Méndez-Ferrer
Organization name CNIC
Lab Stem cell niche pathophysiology
Street address Calle Melchor Fernández Almagro, 3
City Madrid
ZIP/Postal code 28029
Country Spain
Platform ID GPL11002
Series (2)
GSE55798 Neuropathy of the haematopoietic stem cell niche is essential for myeloproliferative neoplasms [RNA-seq]
GSE55802 Neuropathy of haematopoietic stem cell niche is essential for myeloproliferative neoplasms
BioSample SAMN02687925
SRA SRX484661

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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