|
| Status |
Public on Oct 10, 2015 |
| Title |
Th1cell_Bmi1_exp1A |
| Sample type |
SRA |
| |
|
| Source name |
Five-day cultured Th1 cells generated from primary splenic CD4_T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Th1 cell
chip antibody: Bmi1 (Santa Cruz, catalog# sc-10745, lot# K1008)
|
| Growth protocol |
Splenic CD4_T cells were stimulated under Th1 culture conditions (15 ng/ml IL-2, 1 ng/ml IL-12) for 5 days in vitro.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
IP and input sample libraries were prepared using ChIP-Seq Sample Prep kit (Illumina). Adaptor-ligated DNA fragments were size fractionated by 12% acrylamide gel, and the 170- to 250-bp fraction was recovered. DNA thus obtained was amplified by 18 cycles of PCR. One nanogram of DNA was used for the sequencing reaction of the Illumina GAIIx or Illumina Hiseq 2500, according to the manufacturer’s instructions. A total of 250,000–370,000 clusters was generated per tile, and 36 cycles of the sequencing reactions were performed.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Th1_cells
|
| Data processing |
Illumina Casava software used for basecalling and making Fastq files.
Short-read sequences were aligned to the mouse genome sequences (mm9 from University of California, Santa Cruz Genome Browser; http://genome.ucsc.edu/) using the Eland program. Sequences with two or more mismatches per sequence were excluded from the analysis.
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: mm9
Supplementary_files_format_and_content: Bed files
|
| |
|
| Submission date |
Oct 07, 2015 |
| 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 |
GPL11002 |
| Series (2) |
| GSE73820 |
Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes [ChIP-Seq] |
| GSE73825 |
Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes |
|
| Relations |
| BioSample |
SAMN04155375 |
| SRA |
SRX1311000 |
