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Sample GSM1688787 Query DataSets for GSM1688787
Status Public on Jan 04, 2016
Title WT_3
Sample type SRA
Source name Bone marrow Pre-Megakaryocyte/Erythroid progenitor, WT
Organism Mus musculus
Characteristics strain/background: C57BL/6
tissue: adult bone marrow
age: 12-16 weeks
cell type: PreMegE
genotype: wild type
Extracted molecule total RNA
Extraction protocol Mouse bone marrow (from 3 mice per sample) was flushed into DMEM supplemented with 10% Foetal Bovine Serum and stained with fluorescently conjugated antibodies. Pre-Megakaryocytic/Erythroid (PreMegE) progenitor cells were isolated by Fluorescence Activated Cell Sorting and RNA was harvested using the QIAGEN RNeasy Plus Micro Kit.
Indexed PolyA libraries were prepared using 50ng of total RNA and 16 cycles of amplification in the Agilent Sure Select Strand Specific RNA Library Prep kit for Illumina Sequencing (Agilent).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Basecall files generated from the NextSeq 500 sequencing run were converted to FASTQ format with Illumina’s bcl2fast v2.14. Lane-wise alignment was performed by bowtie2 v2.21 to GRCm38 reference genome with default parameters. Generated SAM files from bowtie2 alignment were converted to BAM files by samtools v0.1.19. Parameters for samtools SAM to BAM conversion: -q 10 -f 2 -F 268. Resulting lane-wise BAM files from the same sequence library were merged into one BAM file used for downstream analysis. Read counts from BAM files were extracted under the R environment (R v3.1.0) with the package Rsubread v1.16.1. Only genes with at least 1 count per million in at least three samples were retained for differential expression analysis. Count table was loaded to edgeR v3.8.5 and differentially expressed genes between groups were identified by exact test function.
Genome_build: GRCm38
Supplementary_files_format_and_content: PreMegE_Counts.txt: Tab-delimited text file includes raw counts for each Sample.
Submission date May 15, 2015
Last update date May 15, 2019
Contact name Georges Lacaud
Organization name University of Manchester
Department Cancer Research UK Manchester Institute
Lab Cancer Research UK Stem Cell Biology Group
Street address Wilmslow Road
City Manchester
ZIP/Postal code M20 4BX
Country United Kingdom
Platform ID GPL19057
Series (1)
GSE68958 RUNX1B expression distinguishes megakaryocytic and erythroid lineage fate in adult hematopoiesis
BioSample SAMN03659031
SRA SRX1029624

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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