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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 25, 2016 |
| Title |
H3K4me3_ChIPSeq_Med12KO1 |
| Sample type |
SRA |
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| Source name |
HSPCs
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| Organism |
Mus musculus |
| Characteristics |
cell type: hematopoietic stem and progenitor cells
genotype/variation: KO
strain: 129Sv/B6
chip antibody 1: H3(abcam, ab1791-100ug, lot GR210023-1 )
chip antibody 2: H3K4me3 (abcam,ab8580, lot GR190102-2))
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| Treatment protocol |
Mice were injected every other day with pI:pC (10mg/Kg)
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| Growth protocol |
HSPCs (Lineage-, c-kit+, Sca1+) were sorted using Fluorescence Activated Cell Sorting 4 days after injection with pI:pC
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells from bone marrow were isolated from mice and eriched for c-Kit+ cells,crosslinked for 10 minutes with 1% formaldehyde and stained with Lineage antibodies (CD11b, Gr1, Ter119, B220, CD4, CD8), Sca1 and c-Kit and then sorted and snap frozen
Libraries were generated as previously published (Lara Astiaso et al, 2014) Briefly, sonicated chromatin was immunoprecipitated with H3 and libraries were generated on chromatin bound to beads. Libaries with multiplexed with NextFlex Barcoded primers from Bioo Scientific. ChIp with specific histone modifications were performed with barcoded chromatin and released DNA was amplified with ilumina standard primers
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
bowtie.K4me3KO.LSK.total.dd.sort.slop.bw
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| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.017
Processed reads were slopped by 250bp
Duplicates were removed with Picard tools and bedgraphs were normalized to reads per million.
MACS version 1.4.2 was used for ChIP-sequencing peak discovery.
Bedtools, GenomicTools version 2.7.2, Seqminer and deepTools weee used for performing genomic interval mathematical operations, genomic interval annotation, ChIP-seq heatmap generation and ChIP-seq profile construction.
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs of data normalized to reads per million
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| Submission date |
Dec 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Beatriz Aranda-Orgilles |
| Organization name |
NYU School of Medicine
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| Street address |
522 First Avenue
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| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE76052 |
Histone chromatin modifications in control and Med12-deficient mouse HSPCs |
| GSE76055 |
Regulation of enhancer dynamics by MED12 |
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| Relations |
| BioSample |
SAMN04338694 |
| SRA |
SRX1484869 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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