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| Status |
Public on Jul 10, 2017 |
| Title |
Cab10 ES d0 Sense CHIRT-seq |
| Sample type |
SRA |
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| Source name |
CHIRT-seq
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| Organism |
Mus musculus |
| Characteristics |
strain background: CAST/Ei x 129/Sv/Jae
cell type: Embryonic stem cells
capture oligos: TERRA-sense
molecule subtype: Sense control DNA
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| Growth protocol |
Cells were cultured in regular ES mediun (15% FBS) with LIF
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| 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, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion. 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Dec 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hsueh-Ping Chu |
| Organization name |
MGH, Harvard Medical School
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| Department |
molecular biology
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| Lab |
Jeannie T. Lee
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| Street address |
185 Cambridge St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE69887 |
PAR-TERRA RNA directs homologous sex chromosome pairing |
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| Relations |
| BioSample |
SAMN06143125 |
| SRA |
SRX2425130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2429691_ESd0_Sense_vs_Input.spp.bw |
255.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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