|
| Status |
Public on Nov 09, 2015 |
| Title |
BMDMs_HiC_biological_replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary bone marrow-derived macrophages (BMDM)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: BMDM cells (7th day of differentiation)
restriction enzyme: HindIII
|
| Growth protocol |
At day zero bone marrow cells were isolated from C57BL/6 mice and 1,5 × 10^6 cells/plate were seeded in 10 cm dishes in 10 ml of TET-free BM medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiment were conducted in biological replicates using HindIII, according to the protocol published by Belton JM. Et al. Methods 2012 (PMID: 22652625) except for using 2% formaldehyde.
DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Belton JM. Et al. Methods 2012 (PMID: 22652625).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: HiC-Seq
Reads were quality filtered according to the Illumina pipeline
The two ends of each paired-end sequenced fragment were separately aligned to the mm9 genome using NovoAlign (http://novocraft.com) (-s 2 -l 40)
Scripts provided with HOMER (PMID: 20513432) were used HiC data processing. As a first step, the makeTagDirectory script was run with the following parameters: restrictionSite AAGCTT -removeSelfLigation -removePEbg -genome mm9 -removeSpikes 10000 5. Then a background model considering a 40 kbps window was generated with the analyzeHiC script, using the following parameters: -res 40000 -bgonly
Locations of topologically associated domains (TADs) were computed using the scripts provided by Dixon et al. 2012 (PMID: 22495300)
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: The archive BMDMs_UT_HindIII.noSelfLigation.raw.tgz contains one file per chromosome showing the matrix of cis-interactions among all pairs of 40 kbps bins. BMDMs_UT_HindIII.noSelfLigation.raw.TADs.bed contains the coordinates of TADs.
|
| |
|
| Submission date |
Mar 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Iros Barozzi |
| E-mail(s) |
iros.barozzi@meduniwien.ac.at
|
| Organization name |
Medical University Vienna
|
| Street address |
Borschkegasse 8a
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE66952 |
Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [Hi-C] |
| GSE66955 |
Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination |
|
| Relations |
| BioSample |
SAMN03418560 |
| SRA |
SRX957610 |
