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| Status |
Public on Jul 10, 2017 |
| Title |
Cab11: MEF Sense CHIRT-seq |
| Sample type |
SRA |
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| Source name |
PAR-TERRA CHIRT-seq
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| Organism |
Mus musculus |
| Characteristics |
strain background: CAST/Ei x 129/Sv/Jae
cell type: Immortalized MEFs
capture oligos: TERRA-sense
molecule subtype: Sense control DNA
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| Growth protocol |
Cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS
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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 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
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.
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| Submission date |
Jun 15, 2015 |
| 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 |
SAMN03775222 |
| SRA |
SRX1058762 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1711921_MEF_Sense_vs_Input.spp.bw |
255.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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