|
| Status |
Public on Dec 12, 2016 |
| Title |
Irf8 iChIP mTEC Hi |
| Sample type |
SRA |
| |
|
| Source name |
Mature mTECs from WT mice
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Thymic EpCAM+Ly51-MHCIIhi
mouse strain: C57BL/6
chip antibody: Irf8 (Bethyl A303-BL12058)
age: 6 weeks-old
|
| Growth protocol |
Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked and FACS sorted into MACS buffer and Chromatin was analysed using iChIP (Lara-Aatiaso et al.) with our new modification iChIP-IVT
protocol developed by (Lara-Astiaso et al.)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108). In case of paired end samples if single end protocol was used a short read in R2 was used as a UMI
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Nov 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jakub Abramson |
| E-mail(s) |
jakub.abramson@weizmann.ac.il
|
| Organization name |
Weizmann Institute
|
| Department |
Immunology
|
| Street address |
Herzl 234
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE90049 |
Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells [ChIP-Seq] |
| GSE90050 |
Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells |
|
| Relations |
| BioSample |
SAMN06039816 |
| SRA |
SRX2359705 |
