|
| Status |
Public on Dec 14, 2014 |
| Title |
moDC_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
07_ATAC_moDC_1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: moDC
tissue: Bone marrow
strain: C57BL/6
chip antibody: H3K4me1
|
| Growth protocol |
Bone marrows were extracted from femora and tibiae of C57BL/6J female mice (6 to 10 weeks old), growth in presence of GM-CSF (for moDC) or Flt3L (for pDC).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed and nuclei were treated with Tn5 transposase enzyme. Nuclei were clean up and treated with Proteinase K.
Tagmenteated DNA was isolated and undergoes two cycles of PCR amplification with indexing Nextra primers
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
ATAC-seq
|
| Data processing |
HISEQ split using cassava Y60,I10
alignment using bowtie 1.0.0. command (bowtie -a -m 1 --sam --best --strata -v 2 mm9)
tdf command( igvtools count -w 5 -e 200 )
Genome_build: mm9
|
| |
|
| Submission date |
Oct 24, 2014 |
| 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 |
GPL18480 |
| Series (1) |
| GSE62703 |
A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (ATAC-Seq) |
|
| Relations |
| BioSample |
SAMN03142940 |
| SRA |
SRX742900 |
