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Sample GSM3659314 Query DataSets for GSM3659314
Status Public on Mar 01, 2020
Title PaS cells – Ebf1+/+ Replicate 2
Sample type SRA
 
Source name Bone marrow CD45-CD31-Lin-PDGFRα+ Sca1+ cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone marrow
genotype: Ebf1+/+
Extracted molecule genomic DNA
Extraction protocol RNA-seq: Total RNA was isolated from the FACS sorted CAR and PaS cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. The total mRNA was enriched by using Oligo dT magnetic beads. ATAC-seq: minimum of 10.000 cells were resuspended in 50 µL of cold lysis buffer (10 mM Tris·Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% [v/v] Igepal CA-630) and incubated for 15 min on ice. The supernatant was discarded after centrifugation, and the nuclei were used for transposition reaction using NEB Nextera DNA sample preparation kit.
The RNA-seq libraries were prepared by using SMART-Seq v4 ultra-low input RNA library preparation protocol according to the manufacturer's instructions. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Description WTMerge_PaSSorted.bw
Data processing The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.17.1.14).
RNA-seq: The paired-end RNA-seq datasets were mapped to the mouse reference genome (mm10) using Tophat (v2.0.14).
RNA-seq: The mapped reads were further assembled by using Cufflinks (v2.2.1) and the expression level of the annotated genes (UCSC, mm10) was calculated by Cuffquant. The differential gene expression between the conditions was calculated by using Cuffdiff.
ATAC-seq: The paried-end sequencing reads were trimmed using trim galore (0.4.0), which is a wrapper for the Cutadapt (1.8.1) tools. The trimmed reads were mapped to the mouse genome (mm10) using bowtie2 (2.2.8) with the default settings.
ATAC-seq: The duplicated reads were removed using Picard tools (1.136). The reads mapping to blacklisted regions, mitochondrial genome and the reads with mapping below 30 were removed. The properly mapped reads were used for identifying peaks by MACS2 (2.1.1) with the extsize 125 and q-value cut off 0.01. Peaks were further filtered for a p-value cutoff 10-7.
ATAC-seq: The RPKM normalized tracks for each ATAC-seq replicates were generated using deeptools (version:2.4.1) with the bin size of 50.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: The normalized gene expression values (FPKM) calculated by Cuffnorm (v2.2.1) is provided in TXT format. ATAC-seq: The RPKM normalized ATAC-seq profile track is provided in bigWig format.
 
Submission date Mar 06, 2019
Last update date Mar 02, 2020
Contact name Senthilkumar Ramamoorthy
E-mail(s) senthilkumar@ie-freiburg.mpg.de
Phone 00497615108731
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Cellular & Molecular Immunology
Lab Laboratory Rudolf Grosschedl
Street address Stübeweg 51
City Freiburg
ZIP/Postal code D-79108
Country Germany
 
Platform ID GPL21493
Series (1)
GSE127970 EBF1-mutant bone marrow stroma confers long-term changes in hematopoietic stem cell potential
Relations
BioSample SAMN11079704
SRA SRX5487478

Supplementary file Size Download File type/resource
GSM3659314_WT3_PaSSorted.bw 71.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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