|
| Status |
Public on Sep 26, 2013 |
| Title |
Th1 ensemble Hi-C |
| Sample type |
SRA |
| |
|
| Source name |
T-helper cells (Th1)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
restriction enzyme: Bgl II
cell type: T-helper cells (Th1)
|
| Growth protocol |
CD4+ Th1 cells were prepared from spleens of male C57BL/6 mice by stimulating the single cell suspension from spleen with 1 µg/ml anti-CD3 (eBioscience) for 3 days in RPMI1640 medium with L-glutamine and 5% fetal calf serum, purified using magnetic beads coated with anti-CD4 (Miltenyi Biotec), and further expanded in the presence of 20 ng/ml IL-2 (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cells treated according to the modified Hi-C protocol were isolated in PBS and incubated at 65 degrees C for overnight.
The biotin-labelled DNA from each cell was bound to Dynabeads M-280 streptavidin magnetic beads (Life Technologies), digested with Alu I (New England Biolabs), A-tailed with Klenow Fragment (3'->5' exo-) (New England Biolabs) and dATP, ligated with customised Illumina adapter with T4 DNA ligase (New England Biolabs), then the library was amplified by PCR with library amplification primers, and size-selected between 300 and 700 bp on an agarose gel.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
ensemble Hi-C
|
| Data processing |
Paired-end reads of each multiplexed lane were paired-up and separated to single cell datasets based on the 3 bp unique identification tags prefixing each read. Read-pairs of each single cell were then processed independently. We mapped read ends separately to the Mus musculus genome (assembly mm9) using the Maq program with standard parameters and retained pairs of reads with unique hits of high quality (q ≥ 30) at both ends. The first RE1 (Bgl II or Dpn II) restriction site downstream of the read was identified and used as the fragment-end (fend) associated with the read. We retained read-pairs that reflect informative ligation events and with both ends mapped near the first RE2 (Alu I) site upstream of RE1 site. We discarded fend-pairs that were covered only once and used the list of unique fend-pairs, ignoring the coverage of each pair. Fend-pairs with problematic fragments (without a RE2 site or with a non-uniquely mapped start) were discarded. Samples that confidently originated from single cell, with substantial number of fend-pairs and with low noise levels were selected for the analysis.
Th1_bgl_pool.txt - Pool of 60 single-cell Hi-C samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include the list of unique fend-pairs of the sample (pair of genomic coordinates)
|
| |
|
| Submission date |
Jun 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yaniv Lubling |
| E-mail(s) |
yaniv.lubling@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
POB 26
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE48262 |
Single cell Hi-C reveals cell-to-cell variability in chromosome structure |
|
| Relations |
| BioSample |
SAMN02213057 |
| SRA |
SRX314798 |
