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GSE166402

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

Organism: Homo sapiens
Platform: GPL20301
Samples: 8
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Feb 08 2021
Last Updated: Jan 24 2025
Status: Public on May 09 2021
Contact: Gene,,Yeo (UCSD)

Relations

SubSeries of: GSE155729 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA700720 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP305416

Summary

RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP RNA interactions. STAMP does not rely on UV crosslinking or immunoprecipitation and, when coupled with single cell capture, can identify RBP and cell type specific RNA protein interactions for multiple RBPs and cell types in single pooled experiments. Pairing STAMP with long read sequencing also yields RBP target sites for full length isoforms. Finally, conducting STAMP using small ribosomal subunits (RiboSTAMP) allows analysis of transcriptome wide ribosome association in single cells. STAMP enables the study of RBP RNA interactomes and translational landscapes with unprecedented cellular resolution.

Overall Design

Crosslinking and immunoprecipitation of APOBEC, SLBP, TIA1, and RBFOX2 bound RNA and sequencing from 2 technical replicates.

Analysis (18 steps)

View Data Processing
Processing steps for GSE166402
  1. Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0).
  2. Args: --random-seed 1 --bc-pattern NNNNNNNNNN
  3. Reads were then trimmed with cutadapt (1.14).
  4. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
  5. Reads were then trimmed once more with cutadapt (1.14) to remove double-ligation events.
  6. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
  7. Trimmed reads were then mapped with STAR (2.4.0i) against a human-specific repeat element database (RepBase 18.05).
  8. Args: --runThreadN 16 \ --genomeDir human_repbase \ --readFilesIn path/to/read1 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd
Showing first 8 steps.

Supplementary Files (3)

GSE166402_PRBF_1.vs.PRBF_2.bed.gz Download
GSE166402_PTIA_1.vs.PTIA_2.bed.gz Download
GSE166402_RAW.tar Download
GEO Samples (8)
GSM5070681 GSM5070682 GSM5070683 GSM5070684 GSM5070685 GSM5070686 GSM5070687 GSM5070688

Dataset Citations (3)

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
PMID 33963355 · 2021 · Nature methods
Kristopher W Brannan, Isaac A Chaim, Ryan J Marina, Brian A Yee, Eric R Kofman, Daniel A Lorenz, Pratibha Jagannatha, Kevin D Dong, Assael A Madrigal, Jason G Underwood, Gene W Yeo
FLARE: a fast and flexible workflow for identifying RNA editing foci.
PMID 37784060 · 2023 · BMC bioinformatics
Eric Kofman, Brian Yee, Hugo C Medina-Munoz, Gene W Yeo
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
PMID 38906680 · 2024 · Genome research
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

SRA Experiments (8) and Runs (8)

Total: 5510 MB
SRX10055396 SRP305416 RIP-Seq SINGLE
GSM5070681: HEK293T, TIA1 rep1 input; Homo sapiens; RIP-Seq
Sample: SRS8217982
BioProject: PRJNA700720
BioSample: SAMN17838292
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: none
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663711 24838508 1887726608 636.0 NTIA_1_S1_L001_R1_001.fastq.gz, SRR13663711, SRR13663711.lite SRA
SRX10055397 SRP305416 RIP-Seq SINGLE
GSM5070682: HEK293T, TIA1 rep2 input; Homo sapiens; RIP-Seq
Sample: SRS8217983
BioProject: PRJNA700720
BioSample: SAMN17838291
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: none
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663712 13070476 993356176 333.36 NTIA_2_S2_L001_R1_001.fastq.gz, SRR13663712, SRR13663712.lite SRA
SRX10055398 SRP305416 RIP-Seq SINGLE
GSM5070683: HEK293T, TIA1 rep1 clip; Homo sapiens; RIP-Seq
Sample: SRS8217984
BioProject: PRJNA700720
BioSample: SAMN17838290
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: anti-HA tag antibody
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663713 23232509 1765670684 597.65 PTIA_1_S7_L001_R1_001.fastq.gz, SRR13663713, SRR13663713.lite SRA
SRX10055399 SRP305416 RIP-Seq SINGLE
GSM5070684: HEK293T, TIA1 rep2 clip; Homo sapiens; RIP-Seq
Sample: SRS8217985
BioProject: PRJNA700720
BioSample: SAMN17838289
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: anti-HA tag antibody
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663714 33888797 2575548572 878.54 PTIA_2_S8_L001_R1_001.fastq.gz, SRR13663714, SRR13663714.lite SRA
SRX10055400 SRP305416 RIP-Seq SINGLE
GSM5070685: HEK293T, RBFOX2 rep1 input; Homo sapiens; RIP-Seq
Sample: SRS8217986
BioProject: PRJNA700720
BioSample: SAMN17838288
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: none
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663715 22164085 1684470460 567.88 NRBF_1_S3_L001_R1_001.fastq.gz, SRR13663715, SRR13663715.lite SRA
SRX10055401 SRP305416 RIP-Seq SINGLE
GSM5070686: HEK293T, RBFOX2 rep2 input; Homo sapiens; RIP-Seq
Sample: SRS8217987
BioProject: PRJNA700720
BioSample: SAMN17838287
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: none
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663716 22351436 1698709136 583.59 NRBF_2_S4_L001_R1_001.fastq.gz, SRR13663716, SRR13663716.lite SRA
SRX10055402 SRP305416 RIP-Seq SINGLE
GSM5070687: HEK293T, RBFOX2 rep1 clip; Homo sapiens; RIP-Seq
Sample: SRS8217988
BioProject: PRJNA700720
BioSample: SAMN17838286
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: anti-HA tag antibody
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663717 39761648 3021885248 1024.92 PRBF_1_S9_L001_R1_001.fastq.gz, SRR13663717, SRR13663717.lite SRA
SRX10055403 SRP305416 RIP-Seq SINGLE
GSM5070688: HEK293T, RBFOX2 rep2 clip; Homo sapiens; RIP-Seq
Sample: SRS8217989
BioProject: PRJNA700720
BioSample: SAMN17838285
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: anti-HA tag antibody
antibody manufacturer: Abcam
adapter: InvRNA3
Original files (1)
HEK293T
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR13663718 33444662 2541794312 888.12 PRBF_2_S10_L001_R1_001.fastq.gz, SRR13663718, SRR13663718.lite SRA

Linked Publications (4)

Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research · 2024
FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics · 2023
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Nature methods · 2021
FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics · 2023

Data Files (48)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB link
— NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB link
— NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB link
— NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB link
— NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB link
— NRBF_1_S3_L001_R1_001.fastq.gz RIP-Seq 567.9 MB link
— NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB link
— NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB link
— NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB link
— NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB link
— NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB link
— NRBF_2_S4_L001_R1_001.fastq.gz RIP-Seq 583.6 MB link
— NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB link
— NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB link
— NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB link
— NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB link
— NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB link
— NTIA_1_S1_L001_R1_001.fastq.gz RIP-Seq 636.0 MB link
— NTIA_2_S2_L001_R1_001.fastq.gz RIP-Seq 333.4 MB link
— NTIA_2_S2_L001_R1_001.fastq.gz RIP-Seq 333.4 MB link
— NTIA_2_S2_L001_R1_001.fastq.gz RIP-Seq 333.4 MB link
— PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB link
— PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB link
— PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB link
— PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB link
— PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB link
— PRBF_1_S9_L001_R1_001.fastq.gz RIP-Seq 1.0 GB link
— PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB link
— PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB link
— PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB link
— PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB link
— PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB link
— PRBF_2_S10_L001_R1_001.fastq.gz RIP-Seq 888.1 MB link
— PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB link
— PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB link
— PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB link
— PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB link
— PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB link
— PTIA_1_S7_L001_R1_001.fastq.gz RIP-Seq 597.6 MB link
— PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB link
— PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB link
— PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB link
— PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB link
— PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB link
— PTIA_2_S8_L001_R1_001.fastq.gz RIP-Seq 878.5 MB link
— SRR13663712.lite RIP-Seq 333.4 MB link
— SRR13663712.lite RIP-Seq 333.4 MB link
— SRR13663712.lite RIP-Seq 333.4 MB link