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GSE112353

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Active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells

Organism: Homo sapiens
Platform: GPL16791
Samples: 4
Experiment Types:
Other
Submitted: Mar 26 2018
Last Updated: Mar 27 2019
Status: Public on Oct 09 2018
Contact: Toma,,Tebaldi (University of Trento)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA445733 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP136497

Summary

We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to enhance Ribo-Seq, obtaining a global snapshot on active ribosome footprints at single nucleotide resolution from eukaryotic in vitro and in vivo systems. Keywords: ribosome profiling, translation, RiboLace, Ribo-Seq, active translation

Overall Design

We performed active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells. Experiments were performed in biological duplicate.

Analysis (5 steps)

View Data Processing
Processing steps for GSE112353
  1. Raw reads were processed by removing 5’ adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide (using Trimmomatic v0.36).
  2. Reads mapping on rRNAs and tRNAs (downloaded from the SILVA rRNA and the Genomic tRNA databases respectively) were removed.
  3. The remaining reads were aligned to the human transcriptome (Ensembl v85, corresponding to GENCODE 25) with Bowtie2 (v2.2.6) employing the default settings.
  4. All reads aligning to the very same region were collapsed to avoid potential PCR duplicates, and only strand-specific reads were kept.
  5. The number of ribosome protected fragments was determined with samtools idxstats.

Supplementary Files (1)

GSE112353_HEK_count_table.txt.gz Download
GEO Samples (4)
GSM3068264 GSM3068265 GSM3068266 GSM3068267

Dataset Citations (1)

PubMed citation (PMID 30355487)

SRA Experiments (4) and Runs (4)

Total: 6263 MB
SRX3849510 SRP136497 OTHER SINGLE
GSM3068264: HEK-293 cells, RiboLace RIBOseq, rep 1; Homo sapiens; OTHER
Sample: SRS3094037
BioProject: PRJNA445733
BioSample: SAMN08797678
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: HEK-293 cells, active ribosome profiling with RiboLace, biological replicate 1
cells: HEK-293
rna fraction: RiboLace-RIBOseq
replicate: #1
Original files (1)
HEK-293 cells, active ribosome profiling with RiboLace, biological replicate 1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6900519 76688954 3834447700 1606.85 ribolace_HEK_1.fastq.gz, SRR6900519, SRR6900519.sralite SRA
SRX3849511 SRP136497 OTHER SINGLE
GSM3068265: HEK-293 cells, RiboLace RIBOseq, rep 2; Homo sapiens; OTHER
Sample: SRS3094038
BioProject: PRJNA445733
BioSample: SAMN08797690
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: HEK-293 cells, active ribosome profiling with RiboLace, biological replicate 2
cells: HEK-293
rna fraction: RiboLace-RIBOseq
replicate: #2
Original files (1)
HEK-293 cells, active ribosome profiling with RiboLace, biological replicate 2
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6900520 76513705 3825685250 1596.12 ribolace_HEK_2.fastq.gz, SRR6900520, SRR6900520.sralite SRA
SRX3849512 SRP136497 OTHER SINGLE
GSM3068266: HEK-293 cells, standard RIBOseq, rep 1; Homo sapiens; OTHER
Sample: SRS3094040
BioProject: PRJNA445733
BioSample: SAMN08797689
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: HEK-293 cells, standard ribosome profiling, biological replicate 1
cells: HEK-293
rna fraction: standard-RIBOseq
replicate: #1
Original files (1)
HEK-293 cells, standard ribosome profiling, biological replicate 1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6900521 71668291 3583414550 1500.09 riboseq_HEK_1.fastq.gz, SRR6900521, SRR6900521.sralite SRA
SRX3849513 SRP136497 OTHER SINGLE
GSM3068267: HEK-293 cells, standard RIBOseq, rep 2; Homo sapiens; OTHER
Sample: SRS3094039
BioProject: PRJNA445733
BioSample: SAMN08797688
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: HEK-293 cells, standard ribosome profiling, biological replicate 2
cells: HEK-293
rna fraction: standard-RIBOseq
replicate: #2
Original files (1)
HEK-293 cells, standard ribosome profiling, biological replicate 2
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR6900522 74606273 3730313650 1559.65 riboseq_HEK_2.fastq.gz, SRR6900522, SRR6900522.sralite SRA

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Nature methods · 2021

Data Files (4)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— ribolace_HEK_1.fastq.gz OTHER 1.6 GB link
— ribolace_HEK_2.fastq.gz OTHER 1.6 GB link
— riboseq_HEK_1.fastq.gz OTHER 1.5 GB link
— riboseq_HEK_2.fastq.gz OTHER 1.5 GB link