|
| Status |
Public on Jan 28, 2017 |
| Title |
Combinatorial scHi-C Library ML3 |
| Sample type |
SRA |
| |
|
| Source name |
Cultured Cell Lines
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell lines: Contains K562, GM12878, Patski, and primary MEF cells
|
| Treatment protocol |
Cells are fixed using 2% (HeLa, HAP1, GM12878, K562, MEF) or 2.5% (Patski) formaldehyde.
|
| Growth protocol |
Cells are grown under standard tissue culture conditions (10 - 15% FBS, 5% CO2, DMEM or RPMI media, and 1X Pen-Strep) as the Coriell culture practices demand)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells are lysed using 0.2% NP-40; 10 mM NaCl; 10 mM Tris pH 8.0 in ddH2O
Combinatorial single-cell Hi-C is carried out using a similar protocol to the insitu Hi-C and in situ DNase protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: Hi-C-seq
Reads were mapped to a combined Burrows-Wheeler reference of hg19 and mm10 using bowtie2. They were then filtered using custom Python scripts to generate validPairs files (see README file on series record).
|
| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vijay Ramani |
| Organization name |
UCSF
|
| Department |
Biochemistry & Biophysics
|
| Lab |
Ramani Lab
|
| Street address |
600 16th St, GH-S312B
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL22245 |
| Series (1) |
| GSE84920 |
Massively multiplex single-cell Hi-C |
|
| Relations |
| BioSample |
SAMN05449631 |
| SRA |
SRX1981064 |
