|
| Status |
Public on Apr 19, 2016 |
| Title |
MxCre Jak2VF/+_H3K27me3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
LSK (Lin-Sca-1+c-kit+) cells sorted from MxCre Jak2VF/+ mouse bone marrow, 12 weeks after pI-pC injections
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: MxCre Jak2VF/+
tissue: bone marrow
cell type: LSK (Lin-Sca-1+c-kit+) cell
chip antibody: H3K27me3 (Millipore, 07-449, lot 2580679)
|
| Treatment protocol |
Harvested bone marrow cells were stained with antibodies against cell surface markers and LSK (Lin-Sca-1+c-kit+) cells were sorted with FACS AriaII (BD)
|
| Growth protocol |
Control, MxCre Jak2VF/+ and MxCre Jak2VF/+ EZH2-/- mice were injected with five doses of pI-pC (300μg/dose) at 4 weeks after birth. BM cells were harvested at 12 weeks after pI-pC injections.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiment was performed with EpiTect ChIP OneDay Kit (Qiagen) according to the manufacturer’s protocol and H3K27me3 antibody (07-449, Millipore)
Libraries were prepared using Illumina TruSeq ChIP Sample Prep Kit (Illumina) with immune-precipitated DNA for each sample. The sizes of the libraries were validated utilizing the DNA 1000 chip on the Agilent 2100 Bioanalyzer. The quantification of the libraries was done using the KAPA Library Quantification Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling performed using Illumina Real Time Analysis (RTA) v2. The RTA software is part of the NextSeq Control Software (NCS).
Reads were aligned to the mouse genome sequences (mm10) using Partek Flow, Version 3.0 (Partek Incorporated). Bowtie2 method was used in Partek Flow.
Peaks detection was performed using Strand NGS, Version 2.0 (Strand Genomics). MACS (Model-based Analysis for ChIP-Seq) method was selected for peak detection in Strand NGS software.
Genes had peaks within 5kb upstream to 0.5kb downstream of the transcription start sites (TSS) and p value less than 10-5 were determined as genes with significant H3K27me3 enrichment in Strand NGS.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using MACS in Galaxy. Peaks with p value less than 10-5 were selected.
|
| |
|
| Submission date |
Mar 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Golam Mohi |
| E-mail(s) |
mohim@upstate.edu
|
| Organization name |
SUNY Upstate Medical University
|
| Department |
Pharmacology
|
| Street address |
766 Irving Avenue
|
| City |
Syracuse |
| State/province |
New York |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE79319 |
H3K27me3 ChIP-sequencing on LSK (Lin-Sca-1+c-kit+) cells isolated from control, MxCre Jak2VF/+ and MxCre Jak2VF/+ EZH2-/- mice |
| GSE79472 |
Loss of Ezh2 cooperates with Jak2V617F in the development of myelofibrosis in a mouse model of myeloproliferative neoplasm |
|
| Relations |
| BioSample |
SAMN04562488 |
| SRA |
SRX1639063 |
