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GSE117291

GSE GEO
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Large-scale tethered function assays identify factors that regulate mRNA stability and translation (polysome profiling)

Organism: Homo sapiens
Platform: GPL20301
Samples: 12
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jul 18 2018
Last Updated: Jul 02 2021
Status: Public on Aug 18 2020
Contact: En-Ching,,Luo (UCSD)

Relations

SubSeries of: GSE117294 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA482134 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP154579

Summary

Performed polysome profiling in cell lysates from two independent UBAP2L knockout clonal isolates and from two control samples.

Overall Design

RNAseq

Analysis (5 steps)

View Data Processing
Processing steps for GSE117291
  1. RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i).
  2. Reads did not map to repetitive elements were then mapped to the human genome (hg19).
  3. Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
  4. Differential expression was calculated using DESeq2 version 1.10.1
  5. The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.

Supplementary Files (1)

GSE117291_293T_KO_UBAP2L.polysome_RPKM.csv.gz Download
GEO Samples (12)
GSM3290512 GSM3290513 GSM3290514 GSM3290515 GSM3290516 GSM3290517 GSM3290518 GSM3290519 GSM3290520 GSM3290521 GSM3290522 GSM3290523

Dataset Citations (1)

Large-scale tethered function assays identify factors that regulate mRNA stability and translation.
PMID 32807991 · 2020 · Nature structural & molecular biology
En-Ching Luo, Jason L Nathanson, Frederick E Tan, Joshua L Schwartz, Jonathan C Schmok, Archana Shankar, Sebastian Markmiller, Brian A Yee, Shashank Sathe, Gabriel A Pratt, Duy B Scaletta, Yuanchi Ha, David E Hill, Stefan Aigner, Gene W Yeo

SRA Experiments (12) and Runs (12)

Total: 9794 MB
SRX4413967 SRP154579 RNA-Seq SINGLE
GSM3290512: EC_Input_293T_1; Homo sapiens; RNA-Seq
Sample: SRS3567287
BioProject: PRJNA482134
BioSample: SAMN09698139
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547726 62932679 4719950925 1603.17 EC_Input_293T_1_S1_L001_R1_001.fastq.gz, SRR7547726, SRR7547726.srali… SRA
SRX4413968 SRP154579 RNA-Seq SINGLE
GSM3290513: EC_Input_293T_2; Homo sapiens; RNA-Seq
Sample: SRS3567302
BioProject: PRJNA482134
BioSample: SAMN09698138
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547727 67238053 5042853975 1713.36 EC_Input_293T_2_S2_L001_R1_001.fastq.gz, SRR7547727, SRR7547727.srali… SRA
SRX4413969 SRP154579 RNA-Seq SINGLE
GSM3290514: EC_Input_KO1_1; Homo sapiens; RNA-Seq
Sample: SRS3567293
BioProject: PRJNA482134
BioSample: SAMN09698137
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547728 34170278 2562770850 873.79 EC_Input_KO1_1_S3_L001_R1_001.fastq.gz, SRR7547728, SRR7547728.sralite SRA
SRX4413970 SRP154579 RNA-Seq SINGLE
GSM3290515: EC_Input_KO1_2; Homo sapiens; RNA-Seq
Sample: SRS3567308
BioProject: PRJNA482134
BioSample: SAMN09698136
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547729 19971270 1497845250 527.92 EC_Input_KO1_2_S4_L001_R1_001.fastq.gz, SRR7547729, SRR7547729.sralite SRA
SRX4413971 SRP154579 RNA-Seq SINGLE
GSM3290516: EC_Input_KO9_1; Homo sapiens; RNA-Seq
Sample: SRS3567286
BioProject: PRJNA482134
BioSample: SAMN09698135
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547730 39378615 2953396125 1016.53 EC_Input_KO9_1_S5_L001_R1_001.fastq.gz, SRR7547730, SRR7547730.sralite SRA
SRX4413972 SRP154579 RNA-Seq SINGLE
GSM3290517: EC_Input_KO9_2; Homo sapiens; RNA-Seq
Sample: SRS3567296
BioProject: PRJNA482134
BioSample: SAMN09698134
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547731 28421516 2131613700 723.27 EC_Input_KO9_2_S6_L001_R1_001.fastq.gz, SRR7547731, SRR7547731.sralite SRA
SRX4413973 SRP154579 RNA-Seq SINGLE
GSM3290518: EC_Poly_293T_1; Homo sapiens; RNA-Seq
Sample: SRS3567298
BioProject: PRJNA482134
BioSample: SAMN09698133
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547732 35036864 2627764800 893.3 EC_Poly_293T_1_S7_L001_R1_001.fastq.gz, SRR7547732, SRR7547732.sralite SRA
SRX4413974 SRP154579 RNA-Seq SINGLE
GSM3290519: EC_Poly_293T_2; Homo sapiens; RNA-Seq
Sample: SRS3567311
BioProject: PRJNA482134
BioSample: SAMN09698132
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547733 21170367 1587777525 534.59 EC_Poly_293T_2_S8_L001_R1_001.fastq.gz, SRR7547733, SRR7547733.sralite SRA
SRX4413975 SRP154579 RNA-Seq SINGLE
GSM3290520: EC_Poly_KO1_1; Homo sapiens; RNA-Seq
Sample: SRS3567299
BioProject: PRJNA482134
BioSample: SAMN09698129
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547734 26192425 1964431875 665.64 EC_Poly_KO1_1_S9_L001_R1_001.fastq.gz, SRR7547734, SRR7547734.sralite SRA
SRX4413976 SRP154579 RNA-Seq SINGLE
GSM3290521: EC_Poly_KO1_2; Homo sapiens; RNA-Seq
Sample: SRS3567288
BioProject: PRJNA482134
BioSample: SAMN09698128
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547735 24139297 1810447275 624.67 EC_Poly_KO1_2_S10_L001_R1_001.fastq.gz, SRR7547735, SRR7547735.sralite SRA
SRX4413977 SRP154579 RNA-Seq SINGLE
GSM3290522: EC_Poly_KO9_1; Homo sapiens; RNA-Seq
Sample: SRS3567289
BioProject: PRJNA482134
BioSample: SAMN09698127
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547736 8632102 647407650 222.77 EC_Poly_KO9_1_S11_L001_R1_001.fastq.gz, SRR7547736, SRR7547736.sralite SRA
SRX4413978 SRP154579 RNA-Seq SINGLE
GSM3290523: EC_Poly_KO9_2; Homo sapiens; RNA-Seq
Sample: SRS3567379
BioProject: PRJNA482134
BioSample: SAMN09698126
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
tissue: HEK293T cells
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR7547737 15570200 1167765000 394.96 EC_Poly_KO9_2_S12_L001_R1_001.fastq.gz, SRR7547737, SRR7547737.sralite SRA

Linked Publications (1)

Large-scale tethered function assays identify factors that regulate mRNA stability and translation.
Nature structural & molecular biology · 2020

Data Files (24)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— EC_Input_293T_1_S1_L001_R1_001.fastq.gz RNA-Seq 1.6 GB link
— EC_Input_293T_2_S2_L001_R1_001.fastq.gz RNA-Seq 1.7 GB link
— EC_Input_KO1_1_S3_L001_R1_001.fastq.gz RNA-Seq 873.8 MB link
— EC_Input_KO1_2_S4_L001_R1_001.fastq.gz RNA-Seq 527.9 MB link
— EC_Input_KO9_1_S5_L001_R1_001.fastq.gz RNA-Seq 1016.5 MB link
— EC_Input_KO9_2_S6_L001_R1_001.fastq.gz RNA-Seq 723.3 MB link
— EC_Poly_293T_1_S7_L001_R1_001.fastq.gz RNA-Seq 893.3 MB link
— EC_Poly_293T_2_S8_L001_R1_001.fastq.gz RNA-Seq 534.6 MB link
— EC_Poly_KO1_1_S9_L001_R1_001.fastq.gz RNA-Seq 665.6 MB link
— EC_Poly_KO1_2_S10_L001_R1_001.fastq.gz RNA-Seq 624.7 MB link
— EC_Poly_KO9_1_S11_L001_R1_001.fastq.gz RNA-Seq 222.8 MB link
— EC_Poly_KO9_2_S12_L001_R1_001.fastq.gz RNA-Seq 395.0 MB link
— SRR7547726_GSM3290512 RNA-Seq 1.6 GB link
— SRR7547727_GSM3290513 RNA-Seq 1.7 GB link
— SRR7547728_GSM3290514 RNA-Seq 873.0 MB link
— SRR7547729_GSM3290515 RNA-Seq 527.0 MB link
— SRR7547730_GSM3290516 RNA-Seq 1016.0 MB link
— SRR7547731_GSM3290517 RNA-Seq 723.0 MB link
— SRR7547732_GSM3290518 RNA-Seq 893.0 MB link
— SRR7547733_GSM3290519 RNA-Seq 534.0 MB link
— SRR7547734_GSM3290520 RNA-Seq 665.0 MB link
— SRR7547735_GSM3290521 RNA-Seq 624.0 MB link
— SRR7547736_GSM3290522 RNA-Seq 222.0 MB link
— SRR7547737_GSM3290523 RNA-Seq 394.0 MB link