|
| Status |
Public on May 25, 2017 |
| Title |
Th2-3rd_WT_Menin_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Three-week cultured Th2 cells generated from primary splenic CD4_T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Th2 cells
strain: C57BL/6
chip antibody: Menin (bethyl: A300-105A)
genotype/variation: wild type
|
| Growth protocol |
Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro. The Th2 cells were further cultured in vitro for another 2 days in the absence of any exogenous cytokines. The cultured CD4 T cells were then restimulated with immobilized anti-TCR mAbs with IL-2 and anti-IL-4 mAbs for 5 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Antibody-specific immunoprecipitates and total input DNA samples were prepared using a NEBNext ChIP-Seq Library Prep Reagent Set for Illumina. Adaptor-ligated DNA was recovered using AMPure XP Beads. This DNA was then amplified by 15 cycles of PCR and again recovered using AMPure XP Beads. Fifty cycles of sequencing reaction were preformed on an Illumina HiSeq1500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina Casava software used for basecalling and making Fastq files.
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8).
Each aligned read sequence was extended to 120 bp in order to efficiently detect duplicate reads aligned to identical locations. These 120 bp tags were used for further analysis (Bed files)
Genome_build: mm10
Supplementary_files_format_and_content: Bed files
|
| |
|
| Submission date |
May 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Atsushi Onodera |
| Organization name |
Chiba University
|
| Department |
Immunology
|
| Street address |
Chuo-ku Inohana 1-8-1
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE99259 |
Menin controls the memory Th2 cell function by maintaining the epigenetic integrity of Th2 cells. [ChIP-Seq] |
| GSE99261 |
Menin controls the memory Th2 cell function by maintaining the epigenetic integrity of Th2 cells. |
|
| Relations |
| BioSample |
SAMN07163043 |
| SRA |
SRX2850805 |
