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| Status |
Public on Feb 10, 2023 |
| Title |
Epigenetic data during proliferation and differentiation of C2C12 cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Hundreds of thousands or even millions active cis-regulatory elements like promoters and enhancers have been provide by different reasearches. But how to understanding the function of these cis-regulatory elements is a big challenge. Using C2C12 cell differentiation as a model, a number of regulatory elements that play an important role in myoblast differentiation were identified depend on ATAC-seq data. Then RNA-seq and Hi-C data was used to reveal how these regulatory elements regulate gene expression and affect the 3D structure of the genome.
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| Overall design |
High-throughput sequencing (RNA-seq, ATAC-seq and Hi-C) of different time point C2C12 cells during C2C12 differentiation
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| Contributor(s) |
Zhao Y, Hu M, Qi X, Zhao S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA916831 |
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| Submission date |
Feb 03, 2023 |
| Last update date |
Feb 10, 2023 |
| Contact name |
Mingyang Hu |
| E-mail(s) |
myhu@webmail.hzau.edu.cn
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| Phone |
18731237398
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| Organization name |
Huazhong Agricultural University
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| Street address |
No.1,Shizishan Street, Hongshan District
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platforms (1) |
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| Samples (28)
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| GSM7025048 |
C2C12, DM12h, RNA-seq, 1 |
| GSM7025049 |
C2C12, DM12h, RNA-seq, 2 |
| GSM7025050 |
C2C12, DM12h, RNA-seq, 3 |
| GSM7025051 |
C2C12, DM24h, RNA-seq, 1 |
| GSM7025052 |
C2C12, DM24h, RNA-seq, 2 |
| GSM7025053 |
C2C12, DM24h, RNA-seq, 3 |
| GSM7025054 |
C2C12, DM48h, RNA-seq, 1 |
| GSM7025055 |
C2C12, DM48h, RNA-seq, 2 |
| GSM7025056 |
C2C12, DM48h, RNA-seq, 3 |
| GSM7025057 |
C2C12, DM60h, RNA-seq, 1 |
| GSM7025058 |
C2C12, DM60h, RNA-seq, 2 |
| GSM7025059 |
C2C12, DM60h, RNA-seq, 3 |
| GSM7025060 |
C2C12, DM96h, RNA-seq, 1 |
| GSM7025061 |
C2C12, DM96h, RNA-seq, 2 |
| GSM7025062 |
C2C12, DM96h, RNA-seq, 3 |
| GSM7025063 |
C2C12, GM, ATAC-seq, 1 |
| GSM7025064 |
C2C12, GM, ATAC-seq, 2 |
| GSM7025065 |
C2C12, DM60h, ATAC-seq, 1 |
| GSM7025066 |
C2C12, DM60h, ATAC-seq, 2 |
| GSM7025067 |
C2C12, GM, HiC, 1 |
| GSM7025068 |
C2C12, GM, HiC, 2 |
| GSM7025069 |
C2C12, GM, HiC, 3 |
| GSM7025070 |
C2C12, DM60h, HiC, 1 |
| GSM7025071 |
C2C12, DM60h, HiC, 2 |
| GSM7025072 |
C2C12, DM60h, HiC, 3 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE224489_C2C12-DM60h-1_merge_2-ATAC.nodup.tn5.bigwig |
1.7 Gb |
(ftp)(http) |
BIGWIG |
| GSE224489_C2C12-GM-1_merge_2-ATAC.nodup.tn5.bigwig |
305.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE224489_C2C12_DM60h_40000_iced.tad.bed.gz |
32.5 Kb |
(ftp)(http) |
BED |
| GSE224489_C2C12_DM60h_40000_iced.tad.boundaries.bed.gz |
57.4 Kb |
(ftp)(http) |
BED |
| GSE224489_C2C12_DM60h_ATAC_peaks.broadPeak.gz |
4.7 Mb |
(ftp)(http) |
BROADPEAK |
| GSE224489_C2C12_DM60h_vs_GM_loop_juicebox.filter_50reads_filter_loop_ID.bedpe.gz |
605.5 Kb |
(ftp)(http) |
BEDPE |
| GSE224489_C2C12_GM_40000_iced.tad.bed.gz |
33.9 Kb |
(ftp)(http) |
BED |
| GSE224489_C2C12_GM_40000_iced.tad.boundaries.bed.gz |
58.6 Kb |
(ftp)(http) |
BED |
| GSE224489_C2C12_GM_ATAC_peaks.broadPeak.gz |
4.5 Mb |
(ftp)(http) |
BROADPEAK |
| GSE224489_C2C12_differentiation_all_samples_reads_count.txt.gz |
1022.1 Kb |
(ftp)(http) |
TXT |
| GSE224489_mmu_C2C12_DM12_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw |
228.8 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM12_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw |
236.8 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM24_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw |
235.1 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM24_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw |
244.2 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM48_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw |
230.1 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM48_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw |
238.3 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM60_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw |
196.5 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM60_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw |
203.0 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM96_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw |
208.5 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_DM96_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw |
215.0 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_GM_merge_sortBYchrSignal.UniqueMultiple.str1.out.sort.bw |
202.4 Mb |
(ftp)(http) |
BW |
| GSE224489_mmu_C2C12_GM_merge_sortBYchrSignal.UniqueMultiple.str2.out.sort.bw |
209.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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