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| Status |
Public on Jul 11, 2016 |
| Title |
MK5D input |
| Sample type |
SRA |
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| Source name |
Mature Megakaryocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
age: E15
tissue: liver
cell type: Mature Megakaryocytes
genome/variation: wild-type
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Nov 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Chongzhi Zang |
| Organization name |
University of Virginia
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| Street address |
P. O. Box 800717
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE42108 |
NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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