Basic Information

Dataset GSE164330
Status 2023-09-01
Species Homo sapiens
Source NCBI GEO
Subcellular Localization Cytosol|ER
PMID 37643813
Title Examining SRP pathway function in mRNA localization to the endoplasmic reticulum
Citation Child JR, Hofler AC, Chen Q, Yang BH et al. Examining SRP pathway function in mRNA localization to the endoplasmic reticulum. RNA 2023 Nov;29(11):1703-1724.
Experimental Design Parental HeLa/Cas9 cells (non-trasnsfected), parental HeLa/Cas9 cells transfected with a non-targeting siRNA, parental,HeLa/Cas9 cells transfected with siRNA targeting SRPRA, HeLa/Cas9 SRB knockout cells (non-transfected), HeLa/Cas9 SRB knockout cells transfected with a non-targeting siRNA, and HeLa/Cas9 SRB knockout cells transfected with siRNA targeting SRPRA, were cultured for 96 hrs in DMEM, 10% FCS, 5% CO2 and at the 96 hour time point fractionated by sequential detergent treatments to yield cytosol and ER fractions.

Sample Information

BioProject Sample Name Localization Treatment Source Label
PRJNA690012 GSM5724328 total RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_total (Sample 1)
PRJNA690012 GSM5724329 total RNA fraction parental HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_total (Sample 2)
PRJNA690012 GSM5724330 total RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_total (Sample 3)
PRJNA690012 GSM5724331 total RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_total (Sample 4)
PRJNA690012 GSM5724332 total RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRA_siRNA_total (Sample 5)
PRJNA690012 GSM5724333 total RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRA_siRNA_total (Sample 6)
PRJNA690012 GSM5724334 cytosol RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_Cyt l (Sample 7)
PRJNA690012 GSM5724335 cytosol RNA fraction Total cytosolic RNA from HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_Cyt l (Sample 8)
PRJNA690012 GSM5724336 cytosol RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_Cyt l (Sample 9)
PRJNA690012 GSM5724337 cytosol RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_Cyt l (Sample 10)
PRJNA690012 GSM5724338 cytosol RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRA_siRNA_Cyt l (Sample 11)
PRJNA690012 GSM5724339 cytosol RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRA_siRNA_Cyt l (Sample 12)
PRJNA690012 GSM5724340 endoplasmic reticulum RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_ER l (Sample 13)
PRJNA690012 GSM5724341 endoplasmic reticulum RNA fraction parental HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_ER l (Sample 14)
PRJNA690012 GSM5724342 endoplasmic reticulum RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_ER l (Sample 15)
PRJNA690012 GSM5724343 endoplasmic reticulum RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_ER l (Sample 16)
PRJNA690012 GSM5724344 endoplasmic reticulum RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRA_siRNA_ER l (Sample 17)
PRJNA690012 GSM5724345 endoplasmic reticulum RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRa_siRNA_ER l (Sample 18)
PRJNA690012 GSM5724346 total RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_total (Sample 19)
PRJNA690012 GSM5724347 total RNA fraction parental HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_total (Sample 20)
PRJNA690012 GSM5724348 total RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_total (Sample 21)
PRJNA690012 GSM5724349 total RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_total (Sample 22)
PRJNA690012 GSM5724350 total RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRA_siRNA_total (Sample 23)
PRJNA690012 GSM5724351 total RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRa_siRNA_total (Sample 24)
PRJNA690012 GSM5724352 cytosol RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_Cyt l (Sample 25)
PRJNA690012 GSM5724353 cytosol RNA fraction Total cytosolic RNA from HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_Cyt l (Sample 26)
PRJNA690012 GSM5724354 cytosol RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_Cyt l (Sample 27)
PRJNA690012 GSM5724355 cytosol RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_Cyt l (Sample 28)
PRJNA690012 GSM5724356 cytosol RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRa_siRNA_Cyt l (Sample 29)
PRJNA690012 GSM5724357 cytosol RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRa_siRNA_Cyt l (Sample 30)
PRJNA690012 GSM5724358 endoplasmic reticulum RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_ER l (Sample 31)
PRJNA690012 GSM5724359 endoplasmic reticulum RNA fraction parental HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_ER l (Sample 32)
PRJNA690012 GSM5724360 endoplasmic reticulum RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_ER l (Sample 33)
PRJNA690012 GSM5724361 endoplasmic reticulum RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_ER l (Sample 34)
PRJNA690012 GSM5724362 endoplasmic reticulum RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRa_siRNA_ER l (Sample 35)
PRJNA690012 GSM5724363 endoplasmic reticulum RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRa_siRNA_ER l (Sample 36)
PRJNA690012 GSM5724364 total RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_total l (Sample 37)
PRJNA690012 GSM5724365 total RNA fraction parental HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_total l (Sample 38)
PRJNA690012 GSM5724366 total RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_total l (Sample 39)
PRJNA690012 GSM5724367 total RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_total l (Sample 40)
PRJNA690012 GSM5724368 total RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRa_siRNA_total l (Sample 41)
PRJNA690012 GSM5724369 total RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRa_siRNA_total l (Sample 42)
PRJNA690012 GSM5724370 cytosol RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_Cyt l (Sample 43)
PRJNA690012 GSM5724371 cytosol RNA fraction Total cytosolic RNA from HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_Cyt l (Sample 44)
PRJNA690012 GSM5724372 cytosol RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_Cyt l (Sample 45)
PRJNA690012 GSM5724373 cytosol RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_Cyt l (Sample 46)
PRJNA690012 GSM5724374 cytosol RNA fraction parental Cas9 cells & transfected with SRA targeting siRNA HeLa cells HeLa Cas9 WT SRa_siRNA_Cyt l (Sample 47)
PRJNA690012 GSM5724375 cytosol RNA fraction Cas9 SRB KO cells & transfected with a SRA-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 SRa_siRNA_Cyt l (Sample 48)
PRJNA690012 GSM5724376 endoplasmic reticulum RNA fraction parental HeLa Cas9 cells & untransfected HeLa cells HeLa Cas9 WT untransfected_ER l (Sample 49)
PRJNA690012 GSM5724377 endoplasmic reticulum RNA fraction parental HeLa Cas9 SRB KO cells & untransfected HeLa cells HeLa Cas9 SRB-3-12 untransfected_ER l (Sample 50)
PRJNA690012 GSM5724378 endoplasmic reticulum RNA fraction parental HeLa Cas9 cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 WT non-targeting siRNA_ER l (Sample 51)
PRJNA690012 GSM5724379 endoplasmic reticulum RNA fraction Cas9 SRB KO cells & transfected with a non-targeting siRNA HeLa cells HeLa Cas9 SRB-3-12 non-targeting siRNA_ER l (Sample 52)

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Localization Differential Analysis

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Dynamic RNA Localization

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Specific RNA Ratio

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