|
| Status |
Public on Feb 18, 2015 |
| Title |
4C-seq, MAN1C1 bait, H1 mesenchymal stem cells, replicate one |
| Sample type |
SRA |
| |
|
| Source name |
H1 mesenchymal stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: H1 embryonic stem cells
|
| Treatment protocol |
None
|
| Growth protocol |
Growth and differentiation of H1 hESCs was performed as previously described in Xie et al., 2013, Cell 153 (1134-1148)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
4C experiments were performed as described previously (van de Werken et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions, Nature Methods 9, 969-972 2012). Primer design for allelic 4C-seq was performed as previously described (Holwerda et al., Allelilc exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells. Nucleic Acids Research 41, 6905-6916 2013).
Sequencing libraries were constructed according to previous publication (van de Werken et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions, Nature Methods 9, 969-972 2012).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MAN1C1_rep1_read1.fastq.gz
MAN1C1_rep1_read2.fastq.gz
|
| Data processing |
fastq: Illumina's HiSeq Control Software
For 4C read alignment, sequences were aligned to an H1 variant masked version of the hg18 genome. Data was aligned and normalized using the 4cseqpipe software.
Normalized fragment level interactions were averaged over sliding windows with a 1kb step size surrounding the bait region of interest.
Genome_build: hg18
Supplementary_files_format_and_content: Normalized interaction frequency files are in bedGraph format.
|
| |
|
| Submission date |
Jun 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jesse R Dixon |
| E-mail(s) |
jedixon@salk.edu
|
| Organization name |
Salk Institute for Biological Studies
|
| Lab |
PBL-D
|
| Street address |
10010 N. Torrey Pines Rd.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE52457 |
Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation |
|
| Relations |
| BioSample |
SAMN02863140 |
| SRA |
SRX603269 |
