|
| Status |
Public on Jul 10, 2017 |
| Title |
Cab12: ES d7 input CHIRT-seq |
| Sample type |
SRA |
| |
|
| Source name |
PAR-TERRA CHIRT-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain background: CAST/Ei x 129/Sv/Jae
cell type: Embryonic stem cells
capture oligos: n/a
molecule subtype: input DNA
|
| Treatment protocol |
d7 ES cells were cultured without LIF for 4 days under non-adherent conditions and plated for an additional 3 days.
|
| Growth protocol |
Cells were cultured in regular ES medium (15% FBS) without LIF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CHIRT-seq: Nuclei were crosslinked in 1% glutaraldehyde and chromatin were sheared to 0.5~3kb. Chromatin was incubated with biotinylated capture oligonucleotides that were complementary to PAR-TERRA RNA, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion.
CHIRT-seq: Eluted genomic DNA or input samples were fragmented into a median size of 220 bp, and the sequencing libraries were constructed according to NEB ChIP-Seq library protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. CHIRT-seq: Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10
Supplementary_files_format_and_content: CHIRT-seq: The processed data are the coverage files (bigwig) generated using R software library SPP software with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Input files are wig files generated by MACS software.
|
| |
|
| Submission date |
Jun 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hsueh-Ping Chu |
| Organization name |
MGH, Harvard Medical School
|
| Department |
molecular biology
|
| Lab |
Jeannie T. Lee
|
| Street address |
185 Cambridge St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE69887 |
PAR-TERRA RNA directs homologous sex chromosome pairing |
|
| Relations |
| BioSample |
SAMN03775228 |
| SRA |
SRX1058768 |
