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Status |
Public on Aug 25, 2023 |
Title |
Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes |
Organisms |
Homo sapiens; Mus musculus |
Experiment type |
Other Expression profiling by high throughput sequencing
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Summary |
Investigation of translation in rare cell types or subcellular contexts is challenging due to large input requirements for standard approaches. Here, we present “nanoRibo-seq” an optimized approach using 102- to 103-fold less input material than bulk approaches. nanoRibo-seq exhibits rigorous quality control features consistent with quantification of ribosome protected fragments with as few as 1,000 cells. We compare translatomes of two closely related cortical neuron subtypes, callosal projection neurons (CPN) and subcerebral projection neurons (SCPN), during their early postnatal development. We find that, while translational efficiency is highly correlated between CPN and SCPN, several dozen mRNAs are differentially translated. We further examine upstream open reading frame (uORF) translation and identify that mRNAs involved in synapse organization and axon development are highly enriched for uORF translation in both subtypes. nanoRibo-seq enables investigation of translational regulation of rare cell types in vivo and offers a flexible approach for globally quantifying translation from limited input material.
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Overall design |
nanoRibo-seq: low input ribosome profiling
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Web link |
https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01006-9
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Contributor(s) |
Froberg JE |
Citation(s) |
37624698 |
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Submission date |
Feb 20, 2022 |
Last update date |
Nov 13, 2023 |
Contact name |
John Edward Froberg |
E-mail(s) |
jfroberg@fas.harvard.edu
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Phone |
8479770174
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Organization name |
Harvard University
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Department |
Stem Cell & Regenerative Biology
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Lab |
Macklis Lab
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Street address |
7 Divinity Avenue
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02138 |
Country |
USA |
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Platforms (3) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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Samples (45)
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GSM5907718 |
forebrain, 2.5U/mL_RP |
GSM5907719 |
forebrain, 12.5U/mL_RP |
GSM5907720 |
forebrain, 62.5U/mL_RP |
GSM5907721 |
forebrain, 312.5U/mL_RP |
GSM5907722 |
forebrain, in_vitro_R>G |
GSM5907723 |
cortex, AlkFrag_test |
GSM5907724 |
cortex, 50kCPN_12.5U_RP |
GSM5907725 |
cortex, 50kCPN_2.5U_RP |
GSM5907726 |
cortex, 17kCPN_12.5U_RP |
GSM5907727 |
cortex, 50kSCPN_12.5U_RP |
GSM5907728 |
cortex, CPN_hemi1_RP |
GSM5907729 |
cortex, CPN_hemi2_RP |
GSM5907730 |
cortex, CPN_hemi3_RP |
GSM5907731 |
cortex, CPN_hemi4_RP |
GSM5907732 |
cortex, CPN_hemi5_RP |
GSM5907733 |
cortex, CPN_hemi1_AF |
GSM5907734 |
cortex, CPN_hemi2_AF |
GSM5907735 |
cortex, CPN_hemi3_AF |
GSM5907736 |
cortex, CPN_hemi4_AF |
GSM5907737 |
cortex, CPN_hemi5_AF |
GSM7453771 |
nanoRibo-seq_A_1000 |
GSM7453772 |
nanoRibo-seq_A_10000 |
GSM7453773 |
nanoRibo-seq_A_50000 |
GSM7453774 |
nanoRibo-seq_B_1000 |
GSM7453775 |
nanoRibo-seq_B_10000 |
GSM7453776 |
nanoRibo-seq_B_50000 |
GSM7453777 |
RP_CPN_15000 |
GSM7453778 |
RP_CPN_13900 |
GSM7453779 |
RP_SCPN_13000 |
GSM7453780 |
RP_SCPN_13200 |
GSM7453781 |
AF_CPN_5000 |
GSM7453782 |
AF_CPN_4600 |
GSM7453783 |
AF_SCPN_3100 |
GSM7453784 |
AF_SCPN_3300 |
GSM7453785 |
RP_CPN_22500-1 |
GSM7453786 |
RP_CPN_22500-2 |
GSM7453787 |
RP_SCPN_14400 |
GSM7453788 |
RP_SCPN_15800 |
GSM7453789 |
AF_CPN_7500-1 |
GSM7453790 |
AF_CPN_7500-2 |
GSM7453791 |
AF_SCPN_3600 |
GSM7453792 |
AF_SCPN_5200 |
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Relations |
BioProject |
PRJNA808741 |
Supplementary file |
Size |
Download |
File type/resource |
GSE197060_BulkVs30ng_CDS_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_BulkVs30ng_five_utr_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_BulkVs30ng_lengthDistro.csv.gz |
14.5 Kb |
(ftp)(http) |
CSV |
GSE197060_BulkVs30ng_three_utr_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_CPN_RiboCode_ORFs_collapsed.bed.gz |
1.7 Mb |
(ftp)(http) |
BED |
GSE197060_CPN_RiboCode_ORFs_collapsed.txt.gz |
6.5 Mb |
(ftp)(http) |
TXT |
GSE197060_CPN_SCN_FC_3pUTR_summary.txt.gz |
957.5 Kb |
(ftp)(http) |
TXT |
GSE197060_CPN_SCN_FC_5pUTR_summary.txt.gz |
882.1 Kb |
(ftp)(http) |
TXT |
GSE197060_CPN_SCN_FC_CDS_summary.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
GSE197060_CPN_SCPN_DESeq2_counts_matrix.csv.gz |
206.1 Kb |
(ftp)(http) |
CSV |
GSE197060_CPN_SCPN_lengthDistroTidy.txt.gz |
16.9 Kb |
(ftp)(http) |
TXT |
GSE197060_CPN_hemispheres_CDS_FC_matrix.csv.gz |
2.2 Mb |
(ftp)(http) |
CSV |
GSE197060_CPN_hemispheres_five_utr_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_CPN_hemispheres_lengthDistro.csv.gz |
29.3 Kb |
(ftp)(http) |
CSV |
GSE197060_CPN_hemispheres_three_utr_FC_matrix.csv.gz |
2.2 Mb |
(ftp)(http) |
CSV |
GSE197060_HEK_TPMs.csv.gz |
1013.6 Kb |
(ftp)(http) |
CSV |
GSE197060_RiboCode_ORFs_collapsed.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
GSE197060_RiboCode_ORFs_collapsed.txt.gz |
6.3 Mb |
(ftp)(http) |
TXT |
GSE197060_RnaseTitration_CDS_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_RnaseTitration_five_utr_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_RnaseTitration_lengthDistro.csv.gz |
25.4 Kb |
(ftp)(http) |
CSV |
GSE197060_RnaseTitration_three_utr_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_SCPN_RiboCode_ORFs_collapsed.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
GSE197060_SCPN_RiboCode_ORFs_collapsed.txt.gz |
6.9 Mb |
(ftp)(http) |
TXT |
GSE197060_sorted_neurons_CDS_FC_matrix.csv.gz |
2.2 Mb |
(ftp)(http) |
CSV |
GSE197060_sorted_neurons_five_utr_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
GSE197060_sorted_neurons_lengthDistro.csv.gz |
16.5 Kb |
(ftp)(http) |
CSV |
GSE197060_sorted_neurons_three_utr_FC_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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