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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 30, 2019 |
| Title |
An RNA binding region in CTCF regulates chromatin looping and CTCF nuclear organization |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
Expression profiling by high throughput sequencing
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| Summary |
The study investigates CTCF/cohesin binding and chromatin looping by ChIP-seq and Micro-C. By ChIP-seq, we determined the genome-wide binding profiles of CTCF and Smc1a cohesin subunit in a knock-in mouse ES cell line (wt-CTCF; clone C59) with endogenously tagged wild type CTCF (FLAG-Halo-mCTCF) and Rad21 (mRad21-SNAPf-V5), and compared them to the same ES line expressing a mutant CTCF (ΔRBR-CTCF; clone C59D2), where we replaced a previously described RNA binding region with a short linker (GDGAGLINS) followed by a 3xHA tag (N576_D611del::3xHA). By Micro-C, we compared nucleosome-resolution chromosome folding maps of the same ES cell lines C59 and C59D2 described above, to determine the effect of deleting CTCF RNA binding region on chromatin looping.
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| Overall design |
1) ChIP-Seq of CTCF and Smc1a cohesin subunit in mouse ES cells homozygous for FLAG-Halo-mCTCF and mRad21-SNAPf-V5 (C59: wt-CTCF) and in the same ES cell line where we deleted CTCF RNA binding region (C59D2: ΔRBR-CTCF). ChIP-Seq libraries were prepared independently from two ChIP biological replicates, using normal serum IgGs as a control, and including total inputs as reference datasets. 2) Three replicates of Micro-C data were generated in the same cell lines as ChIP-seq. Two replicates (named as “QC”) were initially generated for evaluating library quality and improving experimental protocol. These samples qualitatively and quantitatively reproduce the results by the optimized protocol, regardless a higher percentage of PCR duplicates. High quality and coverage of Micro-C data (named as “highCov”) were generated with an optimized protocol producing over 650M unique pairs per sample. 3) RNA-Seq of total RNA (ribosomal RNA depleted) in mouse ES cells homozygous for FLAG-Halo-mCTCF and mRad21-SNAPf-V5 (C59: wt-CTCF) and in the same ES cell line where we deleted CTCF RNA binding region (C59D2: ΔRBR-CTCF). RNA-Seq libraries were prepared from two biological replicates.
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| Contributor(s) |
Cattoglio C, Hsieh TS, Hansen AS, Tjian R, Darzacq X |
| Citation(s) |
31522987 |
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| Submission date |
Dec 11, 2018 |
| Last update date |
Sep 19, 2019 |
| Contact name |
Robert Tjian |
| E-mail(s) |
jmlim@berkeley.edu
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| Phone |
(510) 642-0884
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| Organization name |
UC Berkeley
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| Department |
MCB
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| Lab |
Tjian Lab
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| Street address |
University of California, Berkeley 450 Li Ka Shing #3370
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA509435 |
| SRA |
SRP173286 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123636_C59D2_1_2_RNAseq_coverage.bw |
24.0 Mb |
(ftp)(http) |
BW |
| GSE123636_C59D2_vs_C59_DeSeq2.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE123636_C59D2_vs_C59_edgeR.txt.gz |
675.3 Kb |
(ftp)(http) |
TXT |
| GSE123636_C59_1_2_RNAseq_coverage.bw |
22.1 Mb |
(ftp)(http) |
BW |
| GSE123636_RAW.tar |
34.3 Gb |
(http)(custom) |
TAR (of BW, HDF5, HIC, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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