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| Status |
Public on Jun 13, 2023 |
| Title |
CTCF, SMS-CTR, rep2 |
| Sample type |
SRA |
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| Source name |
SMS-CTR
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SMS-CTR
antibody: CTCF
antibody vendor/catalog: Millipore, 07-729
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| Treatment protocol |
N/A
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| Growth protocol |
RH4, RH30, RD, SMS-CTR, and C2C12 were grown in DMEM supplemented with 10% FBS.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For spike-in normalized ChIP-seq, human RMS cells and mouse C2C12 cells were fixed in 1% formaldehyde for 10 minutes before quenching with 125 mM glycine. Cells were combined in a ratio of 3 human:1 mouse cell equivalents for each experiment prior to sonication. Sonicated chromatin was immunoprecipitated with antibodies against H3K27ac (Active Motif #39133), H3K9me3 (Active Motif #39062), MYOD1 (CST #13812), or CTCF (Millipore #07-729). Input and ChIP-enriched DNA was decrosslinked and purified using Qiagen MinElute PCR Purification columns prior to library preparation.
H3K27ac, MYOD1, and CTCF ChIP and Input DNA libraries were prepared by blunt end repair using the Lucigen End-It DNA End-Repair Kit, 3’ A-tailing by Klenow fragment (3’-5’ exo-) (NEB), adaptor ligation by T4 DNA ligase(NEB), and size selection on an E-Gel 2% EX agarose gel. Libraries were amplified with barcoded primers and isolated from unreacted primers by gel purification. Decrosslinked H3K9me3 ChIP and Input DNA was sonicated to enrich fragments 200-500-bp. Library prep was then performed without further size selection. Excess adapter and unused primers were removed with AmpureXP beads. Libraries were sequenced on the HiSeq4000 or NovaSeq6000 platform running in PEx150bp mode.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
All ChIP data were processed with ENCODE ChIP-seq pipeline (v2.1.2) with chip.xcor_exclusion_range_max set at 25
ENCODE ChIP-seq alignment: normalized paired-end fastqs were aligned with bowtie2 aligner to human genome UCSC hg38, with parameters bowtie2 -X2000 --mm
ENCODE ChIP-seq read filtering: black listed region, unmapped, mate unmapped, not primary alignment, multi-mapped, low mapping quality (MAPQ<30), duplicate reads and PCR duplicate were removed
ENCODE ChIP-seq peak calling: Peaks were called with MACS2, with parameters -p 1e-2 --nomodel --shift 0 --extsize ${FRAGLEN} --keep-dup all -B –SPMR. IDR analyses were performed on peaks from replicate samples, with threshold 0.05
Assembly: hg38
Supplementary files format and content: peak text files, BED format
Supplementary files format and content: bigwig files, signals represent fold change over Input
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| Submission date |
Oct 11, 2022 |
| Last update date |
Jun 13, 2023 |
| Contact name |
Benjamin Stanton |
| E-mail(s) |
Benjamin.Stanton@nationwidechildrens.org
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| Organization name |
Nationwide Children's Hospital
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| Department |
Center for Childhood Cancer
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| Street address |
700 Children's Drive
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| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43205 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE215202 |
The 3D chromatin landscape of rhabdomyosarcoma [ChIP-Seq] |
| GSE215203 |
The 3D chromatin landscape of rhabdomyosarcoma |
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| Relations |
| BioSample |
SAMN31236995 |
| SRA |
SRX17846515 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6626407_CTCF_SMS-CTR_rep2.bed.gz |
3.5 Mb |
(ftp)(http) |
BED |
| GSM6626407_CTCF_SMS-CTR_rep2.bigwig |
687.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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