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Status |
Public on Aug 20, 2022 |
Title |
RNAseq Analysis of TP53+/+ and TP53-/- HCT116 colon carcinoma cell lines after treatment with p53 or ATF4-activating compounds |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
We examined the gene expression changes resulting from treatment of either "wild-type" or "p53-deficient" human cell lines with compounds known to activate either p53 (nutlin-3A,etoposide) or the integrated stress response (ISR) transcription factor ATF4 (histidinol,tunicamycin)
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Overall design |
Comparative gene expression profiling (polyA+ selected RNAseq) on three biological replicates
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Contributor(s) |
Sammons M |
Citation(s) |
36993734 |
NIH grant(s) |
Grant ID |
Grant title |
Affiliation |
Name |
R35 GM138120 |
Defining cis-regulatory networks controlling a core stress response |
UNIVERSITY AT ALBANY, SUNY |
Morgan Andrew Sammons |
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Submission date |
Aug 15, 2022 |
Last update date |
May 29, 2023 |
Contact name |
Morgan A Sammons |
E-mail(s) |
masammons@albany.edu
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Organization name |
University at Albany - SUNY
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Department |
Biological Sciences
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Lab |
Sammons
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Street address |
1400 Washington Ave, Life Sciences 2075
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City |
Albany |
State/province |
NY |
ZIP/Postal code |
12222 |
Country |
USA |
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Platforms (1) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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Samples (30)
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GSM6459601 |
WT_Nut_2_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep2 |
GSM6459602 |
WT_Nut_3_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep3 |
GSM6459603 |
WT_Etop_1_RNAseq_etoposide, 100 micromolar, 6hrs_rep1 |
GSM6459604 |
WT_Etop_2_RNAseq_etoposide, 100 micromolar, 6hrs_rep2 |
GSM6459605 |
WT_Etop_3_RNAseq_etoposide, 100 micromolar, 6hrs_rep3 |
GSM6459606 |
WT_His_1_RNAseq_histidinol, 2 millimolar, 6hrs_rep1 |
GSM6459607 |
WT_His_2_RNAseq_histidinol, 2 millimolar, 6hrs_rep2 |
GSM6459608 |
WT_His_3_RNAseq_histidinol, 2 millimolar, 6hrs_rep3 |
GSM6459609 |
WT_Tun_1_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep1 |
GSM6459610 |
WT_Tun_2_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep2 |
GSM6459611 |
WT_Tun_3_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep3 |
GSM6459612 |
PKO_DMSO_1_RNAseq_DMSO, 6hrs_rep1 |
GSM6459613 |
PKO_DMSO_2_RNAseq_DMSO, 6hrs_rep2 |
GSM6459614 |
PKO_DMSO_3_RNAseq_DMSO, 6hrs_rep3 |
GSM6459615 |
PKO_Nut_1_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep1 |
GSM6459616 |
PKO_Nut_2_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep2 |
GSM6459617 |
PKO_Nut_3_RNAseq_Nutlin 3A, 5 micromolar, 6hrs_rep3 |
GSM6459618 |
PKO_Etop_1_RNAseq_etoposide, 100 micromolar, 6hrs_rep1 |
GSM6459619 |
PKO_Etop_2_RNAseq_etoposide, 100 micromolar, 6hrs_rep2 |
GSM6459620 |
PKO_Etop_3_RNAseq_etoposide, 100 micromolar, 6hrs_rep3 |
GSM6459621 |
PKO_His_1_RNAseq_histidinol, 2 millimolar, 6hrs_rep1 |
GSM6459622 |
PKO_His_2_RNAseq_histidinol, 2 millimolar, 6hrs_rep2 |
GSM6459623 |
PKO_His_3_RNAseq_histidinol, 2 millimolar, 6hrs_rep3 |
GSM6459624 |
PKO_Tun_1_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep1 |
GSM6459625 |
PKO_Tun_2_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep2 |
GSM6459626 |
PKO_Tun_3_RNAseq_tunicamycin, 2 micromolar, 6hrs_rep3 |
GSM6459627 |
WT_DMSO_1_RNAseq_DMSO, 6hrs_rep1 |
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Relations |
BioProject |
PRJNA869674 |
Supplementary file |
Size |
Download |
File type/resource |
GSE211244_RAW.tar |
77.9 Mb |
(http)(custom) |
TAR (of TSV) |
GSE211244_deseq2_DMSO_vs_Etoposide_HCT116.tsv.gz |
2.0 Mb |
(ftp)(http) |
TSV |
GSE211244_deseq2_DMSO_vs_Etoposide_HCT116_p53KO.tsv.gz |
2.0 Mb |
(ftp)(http) |
TSV |
GSE211244_deseq2_DMSO_vs_Histidinol_HCT116.tsv.gz |
1.9 Mb |
(ftp)(http) |
TSV |
GSE211244_deseq2_DMSO_vs_Histidinol_HCT116_p53KO.tsv.gz |
1.9 Mb |
(ftp)(http) |
TSV |
GSE211244_deseq2_DMSO_vs_Nutlin_HCT116.tsv.gz |
1.9 Mb |
(ftp)(http) |
TSV |
GSE211244_deseq2_DMSO_vs_Nutlin_HCT116_p53KO.tsv.gz |
1.9 Mb |
(ftp)(http) |
TSV |
GSE211244_deseq2_DMSO_vs_Tunicamycin_HCT116.tsv.gz |
2.0 Mb |
(ftp)(http) |
TSV |
GSE211244_deseq2_DMSO_vs_Tunicamycin_HCT116_p53KO.tsv.gz |
2.0 Mb |
(ftp)(http) |
TSV |
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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