|
| Status |
Public on Jul 23, 2018 |
| Title |
mTEC-I_rep1_wce |
| Sample type |
SRA |
| |
|
| Source name |
whole_cell_extract_TEC-cluster-1-3-A
|
| Organism |
Mus musculus |
| Characteristics |
enrichment: CD45-Epcam+MHCIIlowItgb4+
tissue: Thymus
strain: C57BL/6
chip antibody: none
|
| Treatment protocol |
Mice were sacrified by CO2
|
| Growth protocol |
All mice were maintained under specific pathogen-free conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered, stained with Flow cytometry antibodies and cross linked with Formaldehyde.
High troughput ChIP, developed from the iChIP protocol (Lara-Astiaso, Weiner et al. Science 2014)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sorted cells enriched for mTEC-I from murine thymus
processed data file:
H3K4me2-TEC-cluster-1-3-Combined_peaks-top-set.txt
|
| 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).
findPeaks <input tag directory> -o <out file> -style histone -i <WCE tag directory>
IDR using from Qunhua Li and Anshul Kundaje method (Oct,2010)
Genome_build: mm9
Supplementary_files_format_and_content: merged peaks after IDR
Supplementary_files_format_and_content: Normalized read counts of merged peaks across all conditiones
|
| |
|
| Submission date |
Sep 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
ido.amit@weizmann.ac.il
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE103969 |
Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [ChIP-seq] |
| GSE103970 |
Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage |
|
| Relations |
| BioSample |
SAMN07664296 |
| SRA |
SRX3195895 |
