← Back to search

Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.

Pratibha Jagannatha, Alexandra T Tankka, Daniel A Lorenz, Tao Yu, Brian A Yee, Kristopher W Brannan, Cathy J Zhou, Jason G Underwood, Gene W Yeo

Genome research · 2024 · Vol. 34 (11) · pp. 2012-2024

PubMed ↗ DOI ↗ PMC full text ↗

Abstract

Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed an integrated computational and experimental framework called long-read Ribo-STAMP (LR-Ribo-STAMP) that capitalizes on advancements in long-read sequencing and RNA-base editing-mediated technologies to simultaneously profile translation and transcription at both the gene and mRNA isoform levels. We also developed the EditsC metric to quantify editing and leverage the single-molecule, full-length transcript information provided by long-read sequencing. Here, we report concordance between gene-level translation profiles obtained with long-read and short-read Ribo-STAMP. We show that LR-Ribo-STAMP successfully profiles translation of mRNA isoforms and links regulatory features, such as upstream open reading frames (uORFs), to translation measurements. We apply LR-Ribo-STAMP to discovering translational differences at both the gene and isoform levels in a triple-negative breast cancer cell line under normoxia and hypoxia and find that LR-Ribo-STAMP effectively delineates orthogonal transcriptional and translation shifts between conditions. We also discover regulatory elements that distinguish translational differences at the isoform level. We highlight <i>GRK6</i>, in which hypoxia is observed to increase expression and translation of a shorter mRNA isoform, giving rise to a truncated protein without the AGC Kinase domain. Overall, LR-Ribo-STAMP is an important advance in our repertoire of methods that measures mRNA translation with isoform sensitivity.

Linked datasets 8

GSE155726 GSE · via ncbi_elink
GEO ↗

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

Homo sapiens

10 data files
FileTypeSize
control_STAMP_possorted_genome_bam.bam RNA-Seq 12.0 GB
NPC_HEK_control_STAMP_possorted_genome_bam.bam RNA-Seq 8.6 GB
NPC_HEK_RBFOX2_STAMP_possorted_genome_bam.bam RNA-Seq 8.6 GB
RBP_STAMP_possorted_genome_bam.bam RNA-Seq 18.6 GB
RPS2_STAMP_possorted_genome_bam.bam RNA-Seq 12.3 GB
SRR12391497_GSM4711280 RNA-Seq 8.6 GB
SRR12391498_GSM4711281 RNA-Seq 8.6 GB
SRR12391499_GSM4711282 RNA-Seq 18.6 GB
SRR12391500_GSM4711283 RNA-Seq 12.0 GB
SRR12391501_GSM4711284 RNA-Seq 12.3 GB
GSE155728 GSE · via ncbi_elink
GEO ↗

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

Homo sapiens

6 data files
FileTypeSize
SRR12391632_GSM4711321 RIP-Seq 291.0 MB
SRR12391633_GSM4711322 RIP-Seq 178.0 MB
SRR12391634_GSM4711323 RIP-Seq 460.0 MB
TIA_293T.rep1_clip.r1.reformatted.fq.gz RIP-Seq 291.5 MB
TIA_293T.rep1_input.NIL.r1.fq.gz RIP-Seq 460.5 MB
TIA_293T.rep2_clip.r1.reformatted.fq.gz RIP-Seq 178.8 MB
GSE166402 GSE · via ncbi_elink
GEO ↗

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]

Homo sapiens

17 data files
FileTypeSize
NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB
NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB
NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB
NTIA_2_S2_L001_R1_001.fastq.gz RIP-Seq 333.4 MB
PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB
PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB
PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB
PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB
SRR13663711_GSM5070681 RIP-Seq 636.0 MB
SRR13663712_GSM5070682 RIP-Seq 333.0 MB
SRR13663712.lite RIP-Seq 333.4 MB
SRR13663713_GSM5070683 RIP-Seq 597.0 MB
SRR13663714_GSM5070684 RIP-Seq 878.0 MB
SRR13663715_GSM5070685 RIP-Seq 567.0 MB
SRR13663716_GSM5070686 RIP-Seq 583.0 MB
SRR13663717_GSM5070687 RIP-Seq 1.0 GB
SRR13663718_GSM5070688 RIP-Seq 888.0 MB
GSE155649 GSE · via ncbi_elink
GEO ↗

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]

Homo sapiens

154 data files
FileTypeSize
Apobec_plusT_1_S30_L003_R1_001.fastq.gz OTHER 564.3 MB
Apobec_plusT_2_S31_L003_R1_001.fastq.gz OTHER 631.7 MB
Apobec-T_1_S28_L003_R1_001.fastq.gz OTHER 614.7 MB
Apobec-T_2_S29_L003_R1_001.fastq.gz OTHER 814.8 MB
ApoControl-0_S7_L001_R1_001.fastq.gz OTHER 1.5 GB
ApoControl-1000_S21_L002_R1_001.fastq.gz OTHER 1.5 GB
ApoControl-50_S14_L002_R1_001.fastq.gz OTHER 1.3 GB
RBFOX2-0_S6_L001_R1_001.fastq.gz OTHER 1.4 GB
RBFOX2-1000_S20_L002_R1_001.fastq.gz OTHER 1.6 GB
RBFOX2-50_S13_L002_R1_001.fastq.gz OTHER 1.4 GB
RPS2-0_S4_L001_R1_001.fastq.gz OTHER 1.1 GB
RPS2-1000_S18_L002_R1_001.fastq.gz OTHER 1.4 GB
RPS2-50_S11_L001_R1_001.fastq.gz OTHER 1.5 GB
RPS3-0_S5_L001_R1_001.fastq.gz OTHER 1.8 GB
RPS3-1000_S19_L002_R1_001.fastq.gz OTHER 1.8 GB
Sample_10_S60_L006_R1_001.fastq.gz OTHER 925.3 MB
Sample11_S29_merged.fastq.gz OTHER 133.9 MB
Sample12_S30_merged.fastq.gz OTHER 131.5 MB
Sample13_S31_merged.fastq.gz OTHER 148.9 MB
Sample14_S13_merged.fastq.gz OTHER 457.9 MB
Sample15_S14_merged.fastq.gz OTHER 349.1 MB
Sample16_S32_merged.fastq.gz OTHER 92.0 MB
Sample17_S15_merged.fastq.gz OTHER 357.1 MB
Sample18_S16_merged.fastq.gz OTHER 271.3 MB
Sample19_S17_merged.fastq.gz OTHER 422.5 MB
Sample1_S23_merged.fastq.gz OTHER 225.8 MB
Sample20_S18_merged.fastq.gz OTHER 302.1 MB
Sample21_S33_merged.fastq.gz OTHER 154.6 MB
Sample22_S34_merged.fastq.gz OTHER 125.2 MB
Sample23_S35_merged.fastq.gz OTHER 260.5 MB
Sample24_S36_merged.fastq.gz OTHER 132.1 MB
Sample25_S19_merged.fastq.gz OTHER 273.1 MB
Sample26_S20_merged.fastq.gz OTHER 241.7 MB
Sample27_S37_merged.fastq.gz OTHER 146.2 MB
Sample28_S21_merged.fastq.gz OTHER 344.7 MB
Sample29_S38_merged.fastq.gz OTHER 265.3 MB
Sample2_S24_merged.fastq.gz OTHER 172.2 MB
Sample30_S39_merged.fastq.gz OTHER 138.2 MB
Sample31_S40_merged.fastq.gz OTHER 139.6 MB
Sample32_S22_merged.fastq.gz OTHER 237.7 MB
Sample_33_S61_L006_R1_001.fastq.gz OTHER 440.1 MB
Sample_34_S62_L006_R1_001.fastq.gz OTHER 556.8 MB
Sample_35_S63_L006_R1_001.fastq.gz OTHER 882.0 MB
Sample_36_S64_L006_R1_001.fastq.gz OTHER 538.0 MB
Sample_37_S65_L006_R1_001.fastq.gz OTHER 664.4 MB
Sample_38_S66_L006_R1_001.fastq.gz OTHER 963.6 MB
Sample_39_S67_L006_R1_001.fastq.gz OTHER 715.0 MB
Sample_3_S57_L006_R1_001.fastq.gz OTHER 980.1 MB
Sample_40_S68_L006_R1_001.fastq.gz OTHER 730.7 MB
Sample41_S41_merged.fastq.gz OTHER 63.0 MB
Sample42_S42_merged.fastq.gz OTHER 124.1 MB
Sample4_S25_merged.fastq.gz OTHER 211.6 MB
Sample5_S26_merged.fastq.gz OTHER 205.2 MB
Sample_6_S58_L006_R1_001.fastq.gz OTHER 587.0 MB
Sample7_S27_merged.fastq.gz OTHER 209.6 MB
Sample8_S28_merged.fastq.gz OTHER 226.2 MB
Sample_9_S59_L006_R1_001.fastq.gz OTHER 720.2 MB
SLBP_0_48hr_A_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_48hr_B_merged_R1.fastq.gz OTHER 1.5 GB
SLBP_0_48hr_C_merged_R1.fastq.gz OTHER 1.7 GB
SLBP_0_72hr_A_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_72hr_B_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_0_72hr_C_merged_R1.fastq.gz OTHER 1.1 GB
SLBP_1000_72hr_A_merged_R1.fastq.gz OTHER 937.1 MB
SLBP_1000_72hr_B_merged_R1.fastq.gz OTHER 1.2 GB
SLBP_1000_72hr_C_merged_R1.fastq.gz OTHER 1.1 GB
SRR12382153_GSM4709474 OTHER 1.5 GB
SRR12382154_GSM4709475 OTHER 1.3 GB
SRR12382155_GSM4709476 OTHER 1.5 GB
SRR12382156_GSM4709477 OTHER 225.0 MB
SRR12382157_GSM4709478 OTHER 172.0 MB
SRR12382158_GSM4709479 OTHER 980.0 MB
SRR12382159_GSM4709480 OTHER 211.0 MB
SRR12382160_GSM4709481 OTHER 205.0 MB
SRR12382161_GSM4709482 OTHER 586.0 MB
SRR12382162_GSM4709483 OTHER 209.0 MB
SRR12382163_GSM4709484 OTHER 226.0 MB
SRR12382164_GSM4709485 OTHER 720.0 MB
SRR12382165_GSM4709486 OTHER 925.0 MB
SRR12382166_GSM4709487 OTHER 133.0 MB
SRR12382167_GSM4709488 OTHER 131.0 MB
SRR12382168_GSM4709489 OTHER 148.0 MB
SRR12382169_GSM4709490 OTHER 457.0 MB
SRR12382170_GSM4709491 OTHER 564.0 MB
SRR12382171_GSM4709492 OTHER 631.0 MB
SRR12382172_GSM4709493 OTHER 614.0 MB
SRR12382173_GSM4709494 OTHER 814.0 MB
SRR12382174_GSM4709495 OTHER 1.4 GB
SRR12382175_GSM4709496 OTHER 1.4 GB
SRR12382176_GSM4709497 OTHER 1.6 GB
SRR12382177_GSM4709498 OTHER 349.0 MB
SRR12382178_GSM4709499 OTHER 92.0 MB
SRR12382179_GSM4709500 OTHER 357.0 MB
SRR12382180_GSM4709501 OTHER 271.0 MB
SRR12382181_GSM4709502 OTHER 422.0 MB
SRR12382182_GSM4709503 OTHER 302.0 MB
SRR12382183_GSM4709504 OTHER 154.0 MB
SRR12382184_GSM4709505 OTHER 125.0 MB
SRR12382185_GSM4709506 OTHER 260.0 MB
SRR12382186_GSM4709507 OTHER 132.0 MB
SRR12382187_GSM4709508 OTHER 273.0 MB
SRR12382188_GSM4709509 OTHER 241.0 MB
SRR12382189_GSM4709510 OTHER 146.0 MB
SRR12382190_GSM4709511 OTHER 344.0 MB
SRR12382191_GSM4709512 OTHER 1.2 GB
SRR12382192_GSM4709513 OTHER 1.2 GB
SRR12382193_GSM4709514 OTHER 1.1 GB
SRR12382194_GSM4709515 OTHER 937.0 MB
SRR12382195_GSM4709516 OTHER 1.2 GB
SRR12382196_GSM4709517 OTHER 1.1 GB
SRR12382197_GSM4709518 OTHER 1.2 GB
SRR12382198_GSM4709519 OTHER 1.5 GB
SRR12382199_GSM4709520 OTHER 1.7 GB
SRR12382200_GSM4709521 OTHER 951.0 MB
SRR12382201_GSM4709522 OTHER 708.0 MB
SRR12382202_GSM4709523 OTHER 722.0 MB
SRR12382203_GSM4709524 OTHER 792.0 MB
SRR12382204_GSM4709525 OTHER 486.0 MB
SRR12382205_GSM4709526 OTHER 581.0 MB
SRR12382206_GSM4709527 OTHER 1.1 GB
SRR12382207_GSM4709528 OTHER 1.5 GB
SRR12382208_GSM4709529 OTHER 1.4 GB
SRR12382209_GSM4709530 OTHER 265.0 MB
SRR12382210_GSM4709531 OTHER 138.0 MB
SRR12382211_GSM4709532 OTHER 139.0 MB
SRR12382212_GSM4709533 OTHER 237.0 MB
SRR12382213_GSM4709534 OTHER 440.0 MB
SRR12382214_GSM4709535 OTHER 556.0 MB
SRR12382215_GSM4709536 OTHER 881.0 MB
SRR12382216_GSM4709537 OTHER 538.0 MB
SRR12382217_GSM4709538 OTHER 664.0 MB
SRR12382218_GSM4709539 OTHER 963.0 MB
SRR12382219_GSM4709540 OTHER 714.0 MB
SRR12382220_GSM4709541 OTHER 730.0 MB
SRR12382221_GSM4709542 OTHER 63.0 MB
SRR12382222_GSM4709543 OTHER 124.0 MB
SRR12382223_GSM4709544 OTHER 1.8 GB
SRR12382225_GSM4709545 OTHER 1.8 GB
SRR12382226_GSM4709546 OTHER 883.0 MB
SRR12382227_GSM4709547 OTHER 241.0 MB
SRR12382228_GSM4709548 OTHER 262.0 MB
SRR12382229_GSM4709549 OTHER 718.0 MB
SRR12774694_GSM4818032 RNA-Seq 958.0 MB
TI_55_S13_L001_R1_001.fastq.gz OTHER 883.8 MB
TI_56_S14_L001_R1_001.fastq.gz OTHER 241.8 MB
TI_58_S15_L001_R1_001.fastq.gz OTHER 262.8 MB
TI_59_S16_L001_R1_001.fastq.gz OTHER 718.1 MB
TI_8_S6_L001_R1_001.fastq.gz RNA-Seq 958.8 MB
Tia1_0ng_1_S40_L003_R1_001.fastq.gz OTHER 951.1 MB
Tia1_0ng_2_S41_L003_R1_001.fastq.gz OTHER 708.4 MB
Tia1_1000ng_1_S14_L001_R1_001.fastq.gz OTHER 486.1 MB
Tia1_1000ng_2_S27_L002_R1_001.fastq.gz OTHER 581.7 MB
Tia1_50ng_1_S42_L003_R1_001.fastq.gz OTHER 722.9 MB
Tia1_50ng_2_S13_L001_R1_001.fastq.gz OTHER 792.6 MB
GSE155729 GSE · via ncbi_elink
GEO ↗

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Homo sapiens

GSE255844 GSE · via ncbi_elink
GEO ↗

Long-read Ribo-STAMP simultaneously measures transcription and translation at full length isoform resolution

Homo sapiens

22 data files
FileTypeSize
APOBEC1_only_HEK293T_rep1_ccs.bam RNA-Seq 493.9 MB
APOBEC1_only_HEK293T_rep2_ccs.bam RNA-Seq 474.4 MB
APOBEC1_only_HEK293T_rep3_ccs.bam RNA-Seq 361.6 MB
Ribo_STAMP_HEK293T_rep1_ccs.bam RNA-Seq 763.2 MB
Ribo_STAMP_HEK293T_rep2_ccs.bam RNA-Seq 498.9 MB
Ribo_STAMP_HEK293T_rep3_ccs.bam RNA-Seq 477.0 MB
Ribo_STAMP_MDA_MB_231_CoCl2_rep1_ccs.bam RNA-Seq 1.7 GB
Ribo_STAMP_MDA_MB_231_CoCl2_rep2_ccs.bam RNA-Seq 1.6 GB
Ribo_STAMP_MDA_MB_231_NT_rep1_ccs.bam RNA-Seq 2.2 GB
Ribo_STAMP_MDA_MB_231_NT_rep2_ccs.bam RNA-Seq 1.9 GB
SRR27982876_GSM8081595 RNA-Seq 1.6 GB
SRR27982877_GSM8081594 RNA-Seq 1.7 GB
SRR27982878_GSM8081593 RNA-Seq 1.9 GB
SRR27982879_GSM8081592 RNA-Seq 2.2 GB
SRR27982880_GSM8081591 RNA-Seq 476.0 MB
SRR27982881_GSM8081590 RNA-Seq 498.0 MB
SRR27982882_GSM8081589 RNA-Seq 763.0 MB
SRR27982883 RNA-Seq 361.6 MB
SRR27982883_GSM8081588 RNA-Seq 361.0 MB
SRR27982884 RNA-Seq 474.4 MB
SRR27982884_GSM8081587 RNA-Seq 474.0 MB
SRR27982885_GSM8081586 RNA-Seq 493.0 MB
GSE166404 GSE · via ncbi_elink
GEO ↗

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

Homo sapiens

60 data files
FileTypeSize
CCS_Demux_5759_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 32.0 MB
CCS_Demux_5759_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 29.7 MB
CCS_Demux_5759_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 20.7 MB
CCS_Demux_5759_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 12.6 MB
CCS_Demux_5759_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 19.5 MB
CCS_Demux_5759_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 28.2 MB
CCS_Demux_5779_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 327.6 MB
CCS_Demux_5779_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 291.7 MB
CCS_Demux_5779_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 228.5 MB
CCS_Demux_5779_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 141.2 MB
CCS_Demux_5779_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 208.6 MB
CCS_Demux_5779_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 293.3 MB
CCS_Demux_5896_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 52.7 MB
CCS_Demux_5896_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 63.0 MB
CCS_Demux_5896_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 46.5 MB
CCS_Demux_5896_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 39.6 MB
CCS_Demux_5896_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 55.5 MB
CCS_Demux_5896_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 60.4 MB
CCS_Demux_6465_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 37.6 MB
CCS_Demux_6465_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 55.7 MB
CCS_Demux_6465_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 37.0 MB
CCS_Demux_6465_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 38.8 MB
CCS_Demux_6465_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 49.2 MB
CCS_Demux_6465_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 52.9 MB
CCS_Demux_6499_APO1_1_demultiplex.bc1001_BAK8A_OA__bc1001_B… OTHER 43.8 MB
CCS_Demux_6499_APO1_2_demultiplex.bc1015_BAK8B_OA__bc1015_B… OTHER 34.3 MB
CCS_Demux_6499_APO1_3_demultiplex.bc1016_BAK8B_OA__bc1016_B… OTHER 28.8 MB
CCS_Demux_6499_RBFOX_1_demultiplex.bc1020_BAK8B_OA__bc1020_… OTHER 17.3 MB
CCS_Demux_6499_RBFOX_2_demultiplex.bc1021_BAK8B_OA__bc1021_… OTHER 27.2 MB
CCS_Demux_6499_RBFOX_3_demultiplex.bc1022_BAK8B_OA__bc1022_… OTHER 39.1 MB
SRR13663731_GSM5070701 OTHER 12.0 MB
SRR13663732_GSM5070701 OTHER 38.0 MB
SRR13663733_GSM5070701 OTHER 49.0 MB
SRR13663734_GSM5070701 OTHER 52.0 MB
SRR13663735_GSM5070701 OTHER 17.0 MB
SRR13663736_GSM5070701 OTHER 27.0 MB
SRR13663737_GSM5070701 OTHER 39.0 MB
SRR13663738_GSM5070701 OTHER 19.0 MB
SRR13663739_GSM5070701 OTHER 28.0 MB
SRR13663740_GSM5070701 OTHER 141.0 MB
SRR13663741_GSM5070701 OTHER 208.0 MB
SRR13663742_GSM5070701 OTHER 293.0 MB
SRR13663743_GSM5070701 OTHER 39.0 MB
SRR13663744_GSM5070701 OTHER 55.0 MB
SRR13663745_GSM5070701 OTHER 60.0 MB
SRR13663746_GSM5070702 OTHER 32.0 MB
SRR13663747_GSM5070702 OTHER 37.0 MB
SRR13663748_GSM5070702 OTHER 55.0 MB
SRR13663749_GSM5070702 OTHER 37.0 MB
SRR13663750_GSM5070702 OTHER 43.0 MB
SRR13663751_GSM5070702 OTHER 34.0 MB
SRR13663752_GSM5070702 OTHER 28.0 MB
SRR13663753_GSM5070702 OTHER 29.0 MB
SRR13663754_GSM5070702 OTHER 20.0 MB
SRR13663755_GSM5070702 OTHER 327.0 MB
SRR13663756_GSM5070702 OTHER 291.0 MB
SRR13663757_GSM5070702 OTHER 228.0 MB
SRR13663758_GSM5070702 OTHER 52.0 MB
SRR13663759_GSM5070702 OTHER 63.0 MB
SRR13663760_GSM5070702 OTHER 46.0 MB
GSE155708 GSE · via ncbi_elink
GEO ↗

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Homo sapiens

10 data files
FileTypeSize
APOBEC_cDNA_all_pass.fastq.gz RNA-Seq 7.7 GB
APOBEC_dRNA.fastq.gz RNA-Seq 545.2 MB
RBFOX2_cDNA_all_pass.fastq.gz RNA-Seq 21.1 GB
RBFOX2_dRNA.fastq.gz RNA-Seq 1.2 GB
SRR12389273_GSM4711012 RNA-Seq 545.0 MB
SRR12389274 RNA-Seq 7.7 GB
SRR12389274_GSM4711013 RNA-Seq 7.7 GB
SRR12389275_GSM4711014 RNA-Seq 1.2 GB
SRR12389276_GSM4711015 RNA-Seq 21.1 GB
SRR12389276.lite RNA-Seq 21.1 GB

Potentially related datasets 3

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

Accession Source Title
PXD020630 PXD · PRIDE No title in the index
GSE155729 GSE · GEO GEO ↗ Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes
GSE255844 GSE · GEO GEO ↗ Long-read Ribo-STAMP simultaneously measures transcription and translation at full length isoform resolution

Analysis pipelines 1

Pipeline Assay Steps Dataset
GSE255844 PacBio sequencing Data Processing geo_data_processing PacBio sequencing 5 GSE255844
Funding 9 grants
Grant Funder
U24 HG009889 NHGRI NIH HHS (United States)
R01 HG004659 NHGRI NIH HHS (United States)
RF1 MH126719 NIMH NIH HHS (United States)
R01 HG011864 NHGRI NIH HHS (United States)
T32 CA067754 NCI NIH HHS (United States)
U41 HG009889 NHGRI NIH HHS (United States)
R01 CA284315 NCI NIH HHS (United States)
T32 GM145427 NIGMS NIH HHS (United States)
K22 NS112678 NINDS NIH HHS (United States)