Chothani et al. 2022 (PRJNA756018)
General Details
| Title | smORF atlas (part 1-RiboSeq) |
|---|---|
| Organism | |
| Number of Samples | 79 |
| Release Date | 2021/08/18 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
|---|---|
Repository Details
| SRA | SRP333128 |
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| ENA | SRP333128 |
| GEO | GSE182371 |
| BioProject | PRJNA756018 |
Publication
| Title | |
|---|---|
| Authors | Chothani SP,Adami E,Widjaja AA,Langley SR,Viswanathan S,Pua CJ,Zhihao NT,Harmston N,D'Agostino G,Whiffin N,Mao W,Ouyang JF,Lim WW,Lim S,Lee CQE,Grubman A,Chen J,Kovalik JP,Tryggvason K,Polo JM,Ho L,Cook SA,Rackham OJL,Schafer S |
| Journal | Molecular cell |
| Publication Date | 2022 Aug 4 |
| Abstract | Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome. Copyright © 2022 Elsevier Inc. All rights reserved. |
| PMC | |
| PMID | 35841888 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR15513148 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated |  |
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| SRR15513149 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513150 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513151 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513152 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513153 | PRJNA756018 | Homo sapiens | ES | Ribo-Seq | untreated | |
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| SRR15513154 | PRJNA756018 | Homo sapiens | ES | Ribo-Seq | untreated | |
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| SRR15513155 | PRJNA756018 | Homo sapiens | ES | Ribo-Seq | untreated | |
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| SRR15513156 | PRJNA756018 | Homo sapiens | ES | Ribo-Seq | untreated | |
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| SRR15513157 | PRJNA756018 | Homo sapiens | ES | Ribo-Seq | untreated | |
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| SRR15513158 | PRJNA756018 | Homo sapiens | ES | Ribo-Seq | untreated | |
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| SRR15513159 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513160 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513161 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513162 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513163 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513164 | PRJNA756018 | Homo sapiens | Ribo-Seq | untreated | |
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| SRR15513165 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513166 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513167 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513168 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513169 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513170 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513171 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513172 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513173 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513174 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513175 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513176 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513177 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513178 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513179 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513180 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513181 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513182 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513183 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513184 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513185 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513186 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513187 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513188 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513189 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513190 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513191 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513192 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513193 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513194 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513195 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | untreated | |
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| SRR15513196 | PRJNA756018 | Homo sapiens | Fibroblast | Ribo-Seq | |
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| SRR15513197 | PRJNA756018 | Homo sapiens | HA_EC | Ribo-Seq | untreated | |
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| SRR15513198 | PRJNA756018 | Homo sapiens | HA_EC | Ribo-Seq | untreated | |
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| SRR15513199 | PRJNA756018 | Homo sapiens | HA_EC | Ribo-Seq | untreated | |
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| SRR15513200 | PRJNA756018 | Homo sapiens | HA_EC | Ribo-Seq | untreated | |
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| SRR15513201 | PRJNA756018 | Homo sapiens | HA_EC | Ribo-Seq | untreated | |
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| SRR15513202 | PRJNA756018 | Homo sapiens | HA_EC | Ribo-Seq | untreated | |
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| SRR15513203 | PRJNA756018 | Homo sapiens | HCAEC | Ribo-Seq | untreated | |
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| SRR15513204 | PRJNA756018 | Homo sapiens | HCAEC | Ribo-Seq | untreated | |
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| SRR15513205 | PRJNA756018 | Homo sapiens | HCAEC | Ribo-Seq | untreated | |
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| SRR15513206 | PRJNA756018 | Homo sapiens | HCAEC | Ribo-Seq | untreated | |
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| SRR15513207 | PRJNA756018 | Homo sapiens | HCAEC | Ribo-Seq | untreated | |
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| SRR15513208 | PRJNA756018 | Homo sapiens | Hepatocytes | Ribo-Seq | untreated | |
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| SRR15513209 | PRJNA756018 | Homo sapiens | Hepatocytes | Ribo-Seq | untreated | |
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| SRR15513210 | PRJNA756018 | Homo sapiens | Hepatocytes | Ribo-Seq | untreated | |
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| SRR15513211 | PRJNA756018 | Homo sapiens | Hepatocytes | Ribo-Seq | untreated | |
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| SRR15513212 | PRJNA756018 | Homo sapiens | Hepatocytes | Ribo-Seq | untreated | |
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| SRR15513213 | PRJNA756018 | Homo sapiens | HUVEC | Ribo-Seq | untreated | |
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| SRR15513214 | PRJNA756018 | Homo sapiens | HUVEC | Ribo-Seq | untreated | |
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| SRR15513215 | PRJNA756018 | Homo sapiens | HUVEC | Ribo-Seq | untreated | |
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| SRR15513216 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513217 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513218 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513219 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513220 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513221 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513222 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513223 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513224 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513225 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| SRR15513226 | PRJNA756018 | Homo sapiens | VSMC | Ribo-Seq | untreated | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
ⓘ For more Information on the columns shown here see: About