|
| Status |
Public on Mar 27, 2014 |
| Title |
Secondary_Th_Menin_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
KJ1+ transferred CD4 T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: BALB/c
genotype/variation: DO11.10 OVA-specific TCR transgenic
tissue: spleen
cell type: KJ1+ transferred CD4 T cells
chip antibody: Menin
chip antibody vendor: Bethyl Laboratories
chip antibody cat. #: A300-105A
chip antibody lot#: A300-105A-5
|
| Growth protocol |
KJ1+ naïve CD4 T cells from DO11.10 OVA-specific TCR TG mice were stimulated with plate bound anti-TCR-b mAb (3 μg/ml, H57-597, BioLegend) plus anti-CD28 mAb (1 μg/ml, 37.5, BioLegend) in the presence of IL-2 (2.5 ng/ml) for 2 days, and then cells were further expanded with IL-2 another 3 days in vitro. We termed these cells “primary effector CD4 T cells”. The primary effector CD4 T cells were transferred intravenously into syngeneic BALB/c nu/nu recipient mice to induce homeostatic expansion in vivo. Four weeks after transfer, KJ1+ transferred CD4 T cells were recovered from the spleen of recipient mice, and expanded same way as primary stimulation. The secondary expanded effecter CD4 T cells, we termed “secondary effector CD4 T cells”. Naïve CD4 T cells from Menin-WT and -KO mice were stimulated with immobilized anti-TCR-β mAb and an anti-CD28 mAb for 2 days with IL-2 (2.5 ng/ml). Next, cells were transferred to a new plate and cultured for 5 day in the presence of IL-2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and transcription factor- or histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP Sample Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
secondary effector CD4 T cells
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7
peaks were called using MACS 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: BED
|
| |
|
| Submission date |
Jan 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Junpei Suzuki |
| Organization name |
Ehime University
|
| Department |
Graduate School of Medicine
|
| Lab |
Immunology
|
| Street address |
Shitukawa
|
| City |
Toon |
| ZIP/Postal code |
791-0295 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE53831 |
The Menin–Bach2 axis is critical for regulating CD4 T cell senescence and homeostasis |
|
| Relations |
| BioSample |
SAMN02569757 |
| SRA |
SRX415268 |
