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Series GSE241338 Query DataSets for GSE241338
Status Public on Jun 30, 2024
Title Genome-wide interference of chromatin architecture and Mediator in transcriptional bursting and gene network regulation
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Gene expression is a stochastic process that occurs in bursts of RNA synthesis. We applied a mathematical model to scRNA-Seq data to infer bursting dynamics transcriptome-wide under multiple perturbations in a wide range of cell types and identified possible molecular mechanisms. We find that mediator complex subunit MED26 primarily regulates frequency, MYC regulates burst size, while cohesin and super-enhancers can modulate both. Despite comparable effect sizes on RNA levels amongst these perturbations, we find that acute depletion of MED26 plays a larger role in perturbing gene regulatory networks. Furthermore, this perturbation acts downstream of both chromatin spatial architecture and preinitiation complex formation, indicating that later steps in the initiation of transcriptional bursts are primary nodes for integrating gene networks in single cells.
 
Overall design scRNAseq, ChIPseq. mRNAseq, PROseq
Web link https://github.com/PawelNIH/Bursting-project
 
Contributor(s) Trzaskoma P, Jung S, Pekowska A, Bohrer CH, Wang X, Naz F, Dell'Orso S, Dubois W, Olivera A, Vartak SV, Zhao Y, Nayak S, overmiller A, Morasso MI, Sartorelli V, Larson DR, Chow CC, Casellas RC, O'Shea JJ
Citation(s) 39121214
Submission date Aug 21, 2023
Last update date Oct 09, 2024
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (8)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (250)
GSM7727067 scRNA_ESCCTCFD_AUXIN
GSM7727068 scRNA_ESCCTCFD_DMSO
GSM7727070 scRNA_ESCRad21D_AUXIN
Relations
BioProject PRJNA1007704

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
GSE241338_ESCCTCFD_AUXIN_barcodes.tsv.gz 34.5 Kb (ftp)(http) TSV
GSE241338_ESCCTCFD_AUXIN_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_ESCCTCFD_AUXIN_matrix.mtx.gz 103.5 Mb (ftp)(http) MTX
GSE241338_ESCCTCFD_DMSO_barcodes.tsv.gz 40.6 Kb (ftp)(http) TSV
GSE241338_ESCCTCFD_DMSO_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_ESCCTCFD_DMSO_matrix.mtx.gz 110.8 Mb (ftp)(http) MTX
GSE241338_ESCRad21D_AUXIN_barcodes.tsv.gz 24.3 Kb (ftp)(http) TSV
GSE241338_ESCRad21D_AUXIN_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_ESCRad21D_AUXIN_matrix.mtx.gz 83.6 Mb (ftp)(http) MTX
GSE241338_ESCRad21D_DMSO_barcodes.tsv.gz 25.2 Kb (ftp)(http) TSV
GSE241338_ESCRad21D_DMSO_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_ESCRad21D_DMSO_matrix.mtx.gz 82.3 Mb (ftp)(http) MTX
GSE241338_HCTJQ1_ChIPseq_Brd4_DMSO_r1.bw 415.2 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_Brd4_DMSO_r2.bw 393.3 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_Brd4_JQ1_r1.bw 441.2 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_Brd4_JQ1_r2.bw 485.4 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_PolII_DMSO.bw 516.2 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_PolII_JQ1.bw 421.1 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_TBP_DMSO_r1.bw 159.9 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_TBP_DMSO_r2.bw 409.0 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_TBP_JQ1_r1.bw 141.9 Mb (ftp)(http) BW
GSE241338_HCTJQ1_ChIPseq_TBP_JQ1_r2.bw 386.8 Mb (ftp)(http) BW
GSE241338_HCTJQ1_DMSOr1_barcodes.tsv.gz 40.8 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_DMSOr1_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_DMSOr1_matrix.mtx.gz 192.7 Mb (ftp)(http) MTX
GSE241338_HCTJQ1_DMSOr2_barcodes.tsv.gz 55.4 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_DMSOr2_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_DMSOr2_matrix.mtx.gz 221.1 Mb (ftp)(http) MTX
GSE241338_HCTJQ1_JQ1r1_barcodes.tsv.gz 44.5 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_JQ1r1_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_JQ1r1_matrix.mtx.gz 206.1 Mb (ftp)(http) MTX
GSE241338_HCTJQ1_JQ1r2_barcodes.tsv.gz 39.7 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_JQ1r2_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTJQ1_JQ1r2_matrix.mtx.gz 181.9 Mb (ftp)(http) MTX
GSE241338_HCTJQ_mRNA_DMSO_r1.bw 105.4 Mb (ftp)(http) BW
GSE241338_HCTJQ_mRNA_DMSO_r2.bw 101.7 Mb (ftp)(http) BW
GSE241338_HCTJQ_mRNA_DMSO_r3.bw 114.7 Mb (ftp)(http) BW
GSE241338_HCTJQ_mRNA_JQ1_r1.bw 106.2 Mb (ftp)(http) BW
GSE241338_HCTJQ_mRNA_JQ1_r2.bw 103.8 Mb (ftp)(http) BW
GSE241338_HCTJQ_mRNA_JQ1_r3.bw 107.3 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Brd4_AUXIN_r1.bw 342.0 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Brd4_AUXIN_r2.bw 340.7 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Brd4_DMSO_r1.bw 320.8 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Brd4_DMSO_r2.bw 421.9 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Med26_AUXIN_r1.bw 103.8 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Med26_AUXIN_r2.bw 60.7 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Med26_DMSO_r1.bw 196.9 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Med26_DMSO_r2.bw 186.7 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_PolII_AUXIN_r1.bw 427.0 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_PolII_AUXIN_r2.bw 385.6 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_PolII_DMSO_r1.bw 424.0 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_PolII_DMSO_r2.bw 446.8 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Rad21_AUXIN_r1.bw 168.6 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Rad21_AUXIN_r2.bw 252.6 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Rad21_DMSO_r1.bw 188.9 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_Rad21_DMSO_r2.bw 221.2 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_TBP_AUXIN_r1.bw 237.4 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_TBP_AUXIN_r2.bw 288.6 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_TBP_DMSO_r1.bw 278.8 Mb (ftp)(http) BW
GSE241338_HCTMED26D_ChIPseq_TBP_DMSO_r2.bw 255.8 Mb (ftp)(http) BW
GSE241338_HCTMED26D_DMSOr1_barcodes.tsv.gz 39.6 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_DMSOr1_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_DMSOr1_matrix.mtx.gz 195.5 Mb (ftp)(http) MTX
GSE241338_HCTMED26D_DMSOr2_barcodes.tsv.gz 80.6 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_DMSOr2_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_DMSOr2_matrix.mtx.gz 232.0 Mb (ftp)(http) MTX
GSE241338_HCTMED26D_IAAr1_barcodes.tsv.gz 34.3 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_IAAr1_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_IAAr1_matrix.mtx.gz 125.6 Mb (ftp)(http) MTX
GSE241338_HCTMED26D_IAAr2_barcodes.tsv.gz 35.5 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_IAAr2_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCTMED26D_IAAr2_matrix.mtx.gz 184.4 Mb (ftp)(http) MTX
GSE241338_HCTMED26D_mRNA_AUXIN_r1.bw 150.1 Mb (ftp)(http) BW
GSE241338_HCTMED26D_mRNA_AUXIN_r2.bw 164.4 Mb (ftp)(http) BW
GSE241338_HCTMED26D_mRNA_AUXIN_r3.bw 168.5 Mb (ftp)(http) BW
GSE241338_HCTMED26D_mRNA_DMSO_r1.bw 158.6 Mb (ftp)(http) BW
GSE241338_HCTMED26D_mRNA_DMSO_r2.bw 170.9 Mb (ftp)(http) BW
GSE241338_HCTMED26D_mRNA_DMSO_r3.bw 146.0 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_ChIPseq_PolII_AUXIN.bw 874.5 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_ChIPseq_PolII_DMSO.bw 819.3 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_ChIPseq_TBP_AUXIN_r1.bw 366.7 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_ChIPseq_TBP_AUXIN_r2.bw 797.0 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_ChIPseq_TBP_DMSO_r1.bw 317.2 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_ChIPseq_TBP_DMSO_r2.bw 707.5 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_AUXIN0h_r1.bw 93.0 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_AUXIN0h_r2.bw 86.2 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_AUXIN2h_r1.bw 100.7 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_AUXIN2h_r2.bw 93.6 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_AUXIN30m_r1.bw 93.5 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_AUXIN30m_r2.bw 90.5 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_DMSO0h_r1.bw 94.5 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_DMSO0h_r2.bw 92.9 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_DMSO2h_r1.bw 92.0 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_DMSO2h_r2.bw 91.9 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_DMSO30m_r1.bw 90.4 Mb (ftp)(http) BW
GSE241338_HCTRAD21D_mRNA_DMSO30m_r2.bw 89.5 Mb (ftp)(http) BW
GSE241338_HCTRad21D_AUXIN_0h_barcodes.tsv.gz 22.4 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_AUXIN_0h_genes.tsv.gz 251.3 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_AUXIN_0h_matrix.mtx.gz 50.9 Mb (ftp)(http) MTX
GSE241338_HCTRad21D_AUXIN_2h_barcodes.tsv.gz 15.8 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_AUXIN_2h_genes.tsv.gz 251.3 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_AUXIN_2h_matrix.mtx.gz 50.5 Mb (ftp)(http) MTX
GSE241338_HCTRad21D_AUXIN_30m_barcodes.tsv.gz 23.6 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_AUXIN_30m_genes.tsv.gz 251.3 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_AUXIN_30m_matrix.mtx.gz 71.5 Mb (ftp)(http) MTX
GSE241338_HCTRad21D_DMSO_0h_barcodes.tsv.gz 24.4 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_DMSO_0h_genes.tsv.gz 251.3 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_DMSO_0h_matrix.mtx.gz 56.1 Mb (ftp)(http) MTX
GSE241338_HCTRad21D_DMSO_2h_barcodes.tsv.gz 16.6 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_DMSO_2h_genes.tsv.gz 251.3 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_DMSO_2h_matrix.mtx.gz 51.3 Mb (ftp)(http) MTX
GSE241338_HCTRad21D_DMSO_30m_barcodes.tsv.gz 26.5 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_DMSO_30m_genes.tsv.gz 251.3 Kb (ftp)(http) TSV
GSE241338_HCTRad21D_DMSO_30m_matrix.mtx.gz 73.9 Mb (ftp)(http) MTX
GSE241338_HCT_DMSO_halflife.csv.gz 303.4 Kb (ftp)(http) CSV
GSE241338_HCT_DMSOr1_barcodes.tsv.gz 69.8 Kb (ftp)(http) TSV
GSE241338_HCT_DMSOr1_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCT_DMSOr1_matrix.mtx.gz 189.6 Mb (ftp)(http) MTX
GSE241338_HCT_DMSOr2_barcodes.tsv.gz 51.7 Kb (ftp)(http) TSV
GSE241338_HCT_DMSOr2_features.tsv.gz 302.7 Kb (ftp)(http) TSV
GSE241338_HCT_DMSOr2_matrix.mtx.gz 188.6 Mb (ftp)(http) MTX
GSE241338_HCT_JQ1_halflife.csv.gz 253.1 Kb (ftp)(http) CSV
GSE241338_HCT_Med26Degron_DMSO_halflife.csv.gz 340.8 Kb (ftp)(http) CSV
GSE241338_HCT_Med26Degron_IAA_halflife.csv.gz 366.6 Kb (ftp)(http) CSV
GSE241338_HCT_Rad21Degron_IAA_halflife.csv.gz 312.5 Kb (ftp)(http) CSV
GSE241338_HCT_halflife.csv.gz 299.9 Kb (ftp)(http) CSV
GSE241338_HCT_nonstarved_halflife.csv.gz 384.2 Kb (ftp)(http) CSV
GSE241338_RAW.tar 867.0 Mb (http)(custom) TAR (of BEDGRAPH, MTX, TSV)
GSE241338_mBMB220_barcodes.tsv.gz 31.5 Kb (ftp)(http) TSV
GSE241338_mBMB220_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mBMB220_matrix.mtx.gz 43.7 Mb (ftp)(http) MTX
GSE241338_mCH12_r1_barcodes.tsv.gz 52.3 Kb (ftp)(http) TSV
GSE241338_mCH12_r1_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mCH12_r1_matrix.mtx.gz 147.5 Mb (ftp)(http) MTX
GSE241338_mCH12_r2_barcodes.tsv.gz 38.2 Kb (ftp)(http) TSV
GSE241338_mCH12_r2_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mCH12_r2_matrix.mtx.gz 80.3 Mb (ftp)(http) MTX
GSE241338_mLNK_barcodes.tsv.gz 66.7 Kb (ftp)(http) TSV
GSE241338_mLNK_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mLNK_matrix.mtx.gz 182.0 Mb (ftp)(http) MTX
GSE241338_mNK_halflife.csv.gz 281.4 Kb (ftp)(http) CSV
GSE241338_mSKIN_r1_barcodes.tsv.gz 18.6 Kb (ftp)(http) TSV
GSE241338_mSKIN_r1_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mSKIN_r1_matrix.mtx.gz 49.4 Mb (ftp)(http) MTX
GSE241338_mSKIN_r2_barcodes.tsv.gz 12.6 Kb (ftp)(http) TSV
GSE241338_mSKIN_r2_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mSKIN_r2_matrix.mtx.gz 35.6 Mb (ftp)(http) MTX
GSE241338_maBMYCKO_Mycmr1_barcodes.tsv.gz 23.6 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_Mycmr1_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_Mycmr1_matrix.mtx.gz 31.8 Mb (ftp)(http) MTX
GSE241338_maBMYCKO_Mycmr2_barcodes.tsv.gz 28.7 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_Mycmr2_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_Mycmr2_matrix.mtx.gz 41.9 Mb (ftp)(http) MTX
GSE241338_maBMYCKO_WTr1_barcodes.tsv.gz 28.7 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_WTr1_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_WTr1_matrix.mtx.gz 40.4 Mb (ftp)(http) MTX
GSE241338_maBMYCKO_WTr2_barcodes.tsv.gz 23.9 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_WTr2_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_maBMYCKO_WTr2_matrix.mtx.gz 32.1 Mb (ftp)(http) MTX
GSE241338_maB_72h_barcodes.tsv.gz 40.6 Kb (ftp)(http) TSV
GSE241338_maB_72h_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_maB_72h_matrix.mtx.gz 71.8 Mb (ftp)(http) MTX
GSE241338_maB_halflife.csv.gz 319.3 Kb (ftp)(http) CSV
GSE241338_mmast_barcodes.tsv.gz 40.0 Kb (ftp)(http) TSV
GSE241338_mmast_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mmast_halflife.csv.gz 372.0 Kb (ftp)(http) CSV
GSE241338_mmast_matrix.mtx.gz 61.4 Mb (ftp)(http) MTX
GSE241338_mrB_barcodes.tsv.gz 31.1 Kb (ftp)(http) TSV
GSE241338_mrB_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSE241338_mrB_matrix.mtx.gz 26.1 Mb (ftp)(http) MTX
GSE241338_mskin_halflife.csv.gz 449.3 Kb (ftp)(http) CSV
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