NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2861731 Query DataSets for GSM2861731
Status Public on Mar 13, 2020
Title Mof-/+ HSC MOF IP
Sample type SRA
 
Source name Bone Marrow
Organism Mus musculus
Characteristics tissue: HSCs
genotype: Mof -/+
strain: C57BL/6
Growth protocol Mouse bone marrow (BM) cells were isolated from pooled femora, tibiae, ilia and vertebrae by fluxing and crushing in cold PBS 2%FCS using a mortar and pistil. Lysis of erythrocytes was performed using ACK Lysing Buffer (Thermo Fisher Scientific). To deplete lineage-positive cells we used the MojoSort™ Mouse Hematopoietic Progenitor Cell Isolation Kit (Biolegend#48003). Total BM was incubated with biotin antibody cocktail followed by incubation with magnetic Streptavidin Nanobeads. Magnetically labeled fraction was retained using a magnetic separator and untouched hematopoietic stem/progenitor cells (HSPC) were collected by decanting the liquid in a clean tube. 15000 HSCs (LSK+CD34-Flt3-) and 30.000 MEPs (Linegae-Sca-1-cKit+CD34-IL7r-CD16/32-)were sorted by a FACS Fusion II (Becton Dickinson). HPC7 were cultured in Iscove Modified Medium supplemented with 10% FCS and 10 ng/mL of SCF.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The library was completed and amplified through a PCR following the DeepSeq using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina default instructions (NEB #E7645). ChIP libraries were sequenced using an Illumina HiSeq 3000.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Data processing Genome alignment (mm10) by Bowtie2 version 2.3.0.1 (Langmead and Salzberg, 2012) using default parameters
Quality control was assessed by deeptools
Calling Peaks by MACS2 software (Feng et al., 2012), in which we settled bandwidth was settled for 300, lower mfold bound as 5, upper mfold bound as 500. Peak detection was based on q-value (minimum FDR cutoff as 0.05). For build model we selected the shifting mode.
For normalization based on log 2 fold changes IP/Input deeptool Bamcompare (Galaxy Version 2.5.1.0.0) was used
Coverage files were generate with bamCoverage module (Galaxy version 2.5.1.0.0) normalized coverage to 1x and effective geno size for mm10
Genome_build: mm10
Supplementary_files_format_and_content: Score represent the log2/fold change, wig we generated with bamCoverage module from deeptools software, Heatmap was generated eith the plotHeatmap module from deeptools and summary plots were generated with plotProflie module from deeptoools
 
Submission date Nov 20, 2017
Last update date Mar 13, 2020
Contact name Asifa Akhtar
E-mail(s) akhtarlab_data@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Chromatin Regulation
Lab Akhtar Lab
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL21493
Series (2)
GSE107151 Genome-wide maps of chromatin state in HSC, HPC7 and lineage-committed cells
GSE107154 Decoding the regulatory circuit by epigenetic regulator MOF in haematopoiesis
Relations
BioSample SAMN08045393
SRA SRX3409003

Supplementary file Size Download File type/resource
GSM2861731_MUT_HSC_narrow_Peaks.bed.gz 9.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.