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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 01, 2022 |
| Title |
WTDN3_H3K4me3 |
| Sample type |
SRA |
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| Source name |
DN3 thymocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Lin(-)CD44-cKit-CD25+ DN3 thymocytes
genotype: WT
antibody: H3K4me3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Thymocytes were isolated by mechanical disruption. WTDP and WTDN3 cells were FACS sorted using cell surface markers (WTDN3; Lin-CD25+CD44-cKit-, WTDP; CD8+CD4+).
ChIP for histone modifications was performed from sorted DN3 and DP cells as described in Hu et al Gene Dev, 2016 (doi: 10.1101)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
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| Data processing |
Basecalls were performed using bcl2fastq v. 1.8.3
Read alignment was performed on the mm10 (mouse genome) assembly using the genome mappers STAR for RNAseq and ChIPseq.
For visualization of sequencing data, primary sequencing data were sorted, indexed, normalized with reads per kilobase per million mapped reads using DeepTools
Genome_build: mm10
Supplementary_files_format_and_content: fastq, bam, bigwig
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| Submission date |
Oct 28, 2021 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Katia Georgopoulos |
| E-mail(s) |
katia.georgopoulos@cbrc2.mgh.harvard.edu
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| Phone |
6177264445
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| Organization name |
Harvard Medical School
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| Department |
CBRC
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| Lab |
Georgopoulos
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| Street address |
13th street
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| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE186764 |
A double negative thymocyte specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and -selection. |
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| Relations |
| BioSample |
SAMN22657055 |
| SRA |
SRX12813770 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5660723_WTDN3_H3K4me3.SeqDepthNorm.bw |
257.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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