GSE155728
GSE GEORobust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]
Organism:
Homo sapiens
Platform:
GPL16791
Samples:
3
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Aug 05 2020
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/PRJNA655419
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP276058
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 TIA1 bound RNA and sequencing from 2 technical replicates.
Analysis (21 steps)
View Data Processing
Processing steps for GSE155728
- Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1).
- Args: --length 10
- Reads were then trimmed with cutadapt (1.14).
- Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
- Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events.
- Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
- Trimmed reads were then mapped with STAR (2.4.0i) against a human-specific repeat element database (RepBase 18.05).
- Args: --runThreadN 16 '--genomeDir human_repbase '--readFilesIn path/to/read1 path/to/read2 '--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 (2)
GEO Samples (3)
Dataset Citations (2)
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
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 (3) and Runs (3)
Total: 931 MBGSM4711321: TIA1 rep1 clip; Homo sapiens; RIP-Seq
Sample: SRS7149483
BioProject: PRJNA655419
BioSample: SAMN15734832
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: anti-TIA1
antibody manufacturer: MBL
inline barcode1: A01 (AAGCAAT)
inline barcode2: B06 (GGCTTGT)
Original files (1)
HEK293T
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR12391632 | 10693694 | 868070947 | 291.49 | TIA_293T.rep1_clip.r1.reformatted.fq.gz, TIA_293T.rep1_clip.r2.reform… | SRA |
GSM4711322: TIA1 rep2 clip; Homo sapiens; RIP-Seq
Sample: SRS7149484
BioProject: PRJNA655419
BioSample: SAMN15734824
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: anti-TIA1
antibody manufacturer: MBL
inline barcode1: C01 (ACAAGTT)
inline barcode2: D8f (TGGTCCT)
Original files (1)
HEK293T
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR12391633 | 4249735 | 379146196 | 178.81 | TIA_293T.rep2_clip.r1.reformatted.fq.gz, TIA_293T.rep2_clip.r2.reform… | SRA |
GSM4711323: TIA1 input; Homo sapiens; RIP-Seq
Sample: SRS7149485
BioProject: PRJNA655419
BioSample: SAMN15734823
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
rip antibody: none
inline barcode1: None (NIL)
inline barcode2: None (NIL)
Original files (1)
HEK293T
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR12391634 | 20254358 | 938014391 | 460.52 | TIA_293T.rep1_input.NIL.r1.fq.gz, TIA_293T.rep1_input.NIL.r2.fq.gz.ad… | SRA |
Linked Publications (3)
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research · 2024
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