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Sample GSM1032609 Query DataSets for GSM1032609
Status Public on Jul 11, 2016
Title MK5D input
Sample type SRA
Source name Mature Megakaryocytes
Organism Mus musculus
Characteristics strain: CD1
age: E15
tissue: liver
cell type: Mature Megakaryocytes
genome/variation: wild-type
Extracted molecule genomic DNA
Extraction protocol Individual lineages were isolated by depleting other lineages using TER119, GR1, CD41, and CD11b (B-D Pharmingen) monoclonal antibodies (mAb) and immunomagnetic Dynabeads (Invitrogen) or by positive selection using GR1 or TER119 mAb for flow cytometry. MK isolations included additional passage over triple (4%, 3%, 1.5%) gradients of bovine serum albumin, with collection of the pellet. Cell isolations were monitored by viewing May-GrĂĽnwald-Giemsa stains of cytocentrifuged preparations with an Olympus BX41 microscope and by flow cytometry using the above-listed mAb. Transcription factors were pulled down with the respective antibodies after crosslinking + sonication of the cells.
At least 20 ng of precipitated or input DNA from pools of at least 3 replicates was processed for deep sequencing using different library preparation kits for cells (TruSeq, Illumina) and progenitors (TruPLEX-FD, Rubicon Genetics), following the manufacturers’ instructions. ChIP-seq libraries were sequenced using Illumina HiSeq2000 and tags were mapped to mouse genome build mm9.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with -m 1 and default parameters
Uniquely aligned reads were filtered using SICER v1.1 to keep 1 copies at each genomic location
Wiggle files were generated using MACS v1.4
Wiggle files were normalized to the same scale
Genome_build: mm9
Submission date Nov 07, 2012
Last update date May 15, 2019
Contact name Chongzhi Zang
Organization name University of Virginia
Street address P. O. Box 800717
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
Platform ID GPL13112
Series (1)
GSE42108 NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes
Alternative to GSM1032651
SRA SRX203229
BioSample SAMN01803715

Supplementary file Size Download File type/resource
GSM1032609_MK5D_input.bed.gz 145.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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