|
| Status |
Public on Jan 04, 2016 |
| Title |
WT_1 |
| 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 |
|
| Relations |
| BioSample |
SAMN03659029 |
| SRA |
SRX1029622 |
