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GSE171553

GSE GEO
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Mapping cell structure across scales by fusing protein images and interactions

Organism: Homo sapiens
Platform: GPL20301
Samples: 4
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Apr 06 2021
Last Updated: Nov 28 2021
Status: Public on Aug 23 2021
Contact: Yue,,Qin (University of California San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA720057 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP313651

Summary

Enhanced crosslinking and immunoprecipitation assay (eCLIP) for C-terminally FLAG-HA-tagged RPS3A in HEK293T cells.

Overall Design

eCLIP-seq; 2 replicates

Analysis (2 steps)

View Data Processing
Processing steps for GSE171553
  1. After sequencing, raw reads were aligned to GRCh38 and analyzed following the detailed instructions in ENCODE eCLIP-seq Processing Pipeline v2.2 (https://www.encodeproject.org/pipelines/ENCPL357ADL/).
  2. Consistent with the ENCODE standard, reads aligning to artifact-enriched or repetitive genomic regions were removed.

Supplementary Files (1)

GSE171553_RPS3A_eCLIP_peaks.tsv.gz Download
GEO Samples (4)
GSM5227081 GSM5227082 GSM5227083 GSM5227084

Dataset Citations (1)

A multi-scale map of cell structure fusing protein images and interactions.
PMID 34819669 · 2021 · Nature
Yue Qin, Edward L Huttlin, Casper F Winsnes, Maya L Gosztyla, Ludivine Wacheul, Marcus R Kelly, Steven M Blue, Fan Zheng, Michael Chen, Leah V Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John J Lee, Wei Ouyang, Sophie N Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F Kreisberg, Steven P Gygi, Jianzhu Ma, J Wade Harper, Gene W Yeo, Denis L J Lafontaine, Emma Lundberg, Trey Ideker

SRA Experiments (4) and Runs (4)

Total: 1605 MB
SRX10519906 SRP313651 RIP-Seq SINGLE
GSM5227081: RPS3A_rep1_Input; Homo sapiens; RIP-Seq
Sample: SRS8643704
BioProject: PRJNA720057
BioSample: SAMN18631389
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Embryonic kidney cells
cell line: HEK293T
experimental: input
Original files (1)
Embryonic kidney cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14150910 14026243 1065994468 379.62 RPS3A_rep1_input_S5_L008_R1_001.fastq.gz, SRR14150910, SRR14150910.li… SRA
SRX10519907 SRP313651 RIP-Seq SINGLE
GSM5227082: RPS3A_rep1_IP; Homo sapiens; RIP-Seq
Sample: SRS8643705
BioProject: PRJNA720057
BioSample: SAMN18631388
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Embryonic kidney cells
cell line: HEK293T
experimental: IP
Original files (1)
Embryonic kidney cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14150911 16411027 1247238052 444.63 RPS3A_rep1_IP_S15_L008_R1_001.fastq.gz, SRR14150911, SRR14150911.lite SRA
SRX10519908 SRP313651 RIP-Seq SINGLE
GSM5227083: RPS3A_rep2_Input; Homo sapiens; RIP-Seq
Sample: SRS8643707
BioProject: PRJNA720057
BioSample: SAMN18631387
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Embryonic kidney cells
cell line: HEK293T
experimental: input
Original files (1)
Embryonic kidney cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14150912 15684024 1191985824 423.19 RPS3A_rep2_input_S6_L008_R1_001.fastq.gz, SRR14150912, SRR14150912.li… SRA
SRX10519909 SRP313651 RIP-Seq SINGLE
GSM5227084: RPS3A_rep2_IP; Homo sapiens; RIP-Seq
Sample: SRS8643706
BioProject: PRJNA720057
BioSample: SAMN18631386
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Embryonic kidney cells
cell line: HEK293T
experimental: IP
Original files (1)
Embryonic kidney cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR14150913 13217661 1004542236 357.22 RPS3A_rep2_IP_S16_L008_R1_001.fastq.gz, SRR14150913, SRR14150913.lite SRA

Linked Publications (1)

A multi-scale map of cell structure fusing protein images and interactions.
Nature · 2021

Data Files (4)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— RPS3A_rep1_input_S5_L008_R1_001.fastq.gz RIP-Seq 379.6 MB link
— RPS3A_rep1_IP_S15_L008_R1_001.fastq.gz RIP-Seq 444.6 MB link
— RPS3A_rep2_input_S6_L008_R1_001.fastq.gz RIP-Seq 423.2 MB link
— RPS3A_rep2_IP_S16_L008_R1_001.fastq.gz RIP-Seq 357.2 MB link