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Series GSE123636 Query DataSets for GSE123636
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
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.
 
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.
 
Contributor(s) Cattoglio C, Hsieh TS, Hansen AS, Tjian R, Darzacq X
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Submission date Dec 11, 2018
Last update date Jun 02, 2019
Contact name Robert Tjian
E-mail(s) jmlim@berkeley.edu
Phone (510) 642-0884
Organization name UC Berkeley
Department MCB
Lab Tjian Lab
Street address University of California, Berkeley 450 Li Ka Shing #3370
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (18)
GSM3508475 C59_input (RTCC27A)
GSM3508476 C59_IgG_ChIPSeq (RTCC27B)
GSM3508477 C59_Smc1a_ChIPSeq (RTCC27C)
Relations
BioProject PRJNA509435
SRA SRP173286

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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