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GSE224998

GSE GEO
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RPS19 binding with and without Diamond-Blackfan anemia variants

Organism: Homo sapiens
Platform: GPL24676
Samples: 11
Experiment Types:
Other
Submitted: Feb 10 2023
Last Updated: Sep 11 2023
Status: Public on Feb 14 2023
Contact: Gene,W,Yeo (University of California San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA933532

Summary

We found that endogenously expressed RPS19 binds evolutionarily constrained intronic elements. By assessing overexpression of WT RPS19 and RPS19 harboring the most common Diamond-Blackfan anemia missense mutations, we confirmed that disease-relevant mutations alter RPS19 binding preferences in human cells.

Overall Design

eCLIP of WT and mutant overexpressed RPS19 in HEK Please note that processed data generated from all replicates is linked to the corresponding *rep1 sample records.

Analysis (6 steps)

View Data Processing
Processing steps for GSE224998
  1. library strategy: eCLIP
  2. Data was processed using Skipper, available at: http://github.com/yeolab/skipper
  3. Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
  4. Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
  5. Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
  6. Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper

Supplementary Files (1)

GSE224998_RAW.tar Download
GEO Samples (11)
GSM7036818 GSM7036819 GSM7036820 GSM7036821 GSM7036822 GSM7036823 GSM7036824 GSM7036825 GSM7036826 GSM7036827 GSM7036828

Dataset Citations (1)

Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
PMID 37388912 · 2023 · Cell genomics
Evan A Boyle, Hsuan-Lin Her, Jasmine R Mueller, Jack T Naritomi, Grady G Nguyen, Gene W Yeo

SRA Experiments (11) and Runs (22)

Total: 28096 MB
SRX19329746 SRP421822 RIP-Seq SINGLE
GSM7036818: Crosslinked HEK293T, RPS19 size-matched IN, rep1; Homo sapiens; RIP-Seq
Sample: SRS16726690
BioProject: PRJNA933532
BioSample: SAMN33238804
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: control
antibody: none (input)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391964 42818503 4281850300 1294.36 RPS19-IN-1_S1_L001_R1_001.fastq.gz, SRR23391964, SRR23391964.lite SRA
SRR23391965 40949175 4094917500 1255.4 RPS19-IN-1_S1_L002_R1_001.fastq.gz, SRR23391965, SRR23391965.lite SRA
SRX19329747 SRP421822 RIP-Seq SINGLE
GSM7036819: Crosslinked HEK293T, RPS19 size-matched IN, rep2; Homo sapiens; RIP-Seq
Sample: SRS16726691
BioProject: PRJNA933532
BioSample: SAMN33238803
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: control
antibody: none (input)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391962 47550710 4755071000 1439.07 RPS19-IN-2_S2_L001_R1_001.fastq.gz, SRR23391962, SRR23391962.lite SRA
SRR23391963 45517516 4551751600 1396.44 RPS19-IN-2_S2_L002_R1_001.fastq.gz, SRR23391963, SRR23391963.lite SRA
SRX19329748 SRP421822 RIP-Seq SINGLE
GSM7036820: Crosslinked HEK293T, RPS19 size-matched IN, rep3; Homo sapiens; RIP-Seq
Sample: SRS16726692
BioProject: PRJNA933532
BioSample: SAMN33238802
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: control
antibody: none (input)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391960 50896584 5089658400 1528.31 RPS19-IN-3_S3_L001_R1_001.fastq.gz, SRR23391960, SRR23391960.lite SRA
SRR23391961 48896639 4889663900 1488.47 RPS19-IN-3_S3_L002_R1_001.fastq.gz, SRR23391961, SRR23391961.lite SRA
SRX19329749 SRP421822 RIP-Seq SINGLE
GSM7036821: Crosslinked HEK293T, OE RPS19 R101H IP, rep1; Homo sapiens; RIP-Seq
Sample: SRS16726693
BioProject: PRJNA933532
BioSample: SAMN33238801
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 R101H
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391958 37038612 3703861200 1124.86 RPS19-101m-2_S11_L001_R1_001.fastq.gz, SRR23391958, SRR23391958.lite SRA
SRR23391959 35658481 3565848100 1096.95 RPS19-101m-2_S11_L002_R1_001.fastq.gz, SRR23391959, SRR23391959.lite SRA
SRX19329750 SRP421822 RIP-Seq SINGLE
GSM7036822: Crosslinked HEK293T, OE RPS19 R101H IP, rep2; Homo sapiens; RIP-Seq
Sample: SRS16726694
BioProject: PRJNA933532
BioSample: SAMN33238800
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 R101H
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391956 41130975 4113097500 1234.56 RPS19-101m-3_S12_L001_R1_001.fastq.gz, SRR23391956, SRR23391956.lite SRA
SRR23391957 39675103 3967510300 1206.63 RPS19-101m-3_S12_L002_R1_001.fastq.gz, SRR23391957, SRR23391957.lite SRA
SRX19329751 SRP421822 RIP-Seq SINGLE
GSM7036823: Crosslinked HEK293T, OE RPS19 R62W IP, rep1; Homo sapiens; RIP-Seq
Sample: SRS16726695
BioProject: PRJNA933532
BioSample: SAMN33238799
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 R62W
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391954 36868859 3686885900 1123.89 RPS19-62m-1_S7_L001_R1_001.fastq.gz, SRR23391954, SRR23391954.lite SRA
SRR23391955 35278791 3527879100 1090.08 RPS19-62m-1_S7_L002_R1_001.fastq.gz, SRR23391955, SRR23391955.lite SRA
SRX19329752 SRP421822 RIP-Seq SINGLE
GSM7036824: Crosslinked HEK293T, OE RPS19 R62W IP, rep2; Homo sapiens; RIP-Seq
Sample: SRS16726696
BioProject: PRJNA933532
BioSample: SAMN33238798
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 R62W
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391952 35054382 3505438200 1073.58 RPS19-62m-2_S8_L001_R1_001.fastq.gz, SRR23391952, SRR23391952.lite SRA
SRR23391953 33666998 3366699800 1044.77 RPS19-62m-2_S8_L002_R1_001.fastq.gz, SRR23391953, SRR23391953.lite SRA
SRX19329753 SRP421822 RIP-Seq SINGLE
GSM7036825: Crosslinked HEK293T, OE RPS19 R62W IP, rep3; Homo sapiens; RIP-Seq
Sample: SRS16726697
BioProject: PRJNA933532
BioSample: SAMN33238797
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 R62W
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391950 40583420 4058342000 1217.66 RPS19-62m-3_S9_L001_R1_001.fastq.gz, SRR23391950, SRR23391950.lite SRA
SRR23391951 39028200 3902820000 1187.13 RPS19-62m-3_S9_L002_R1_001.fastq.gz, SRR23391951, SRR23391951.lite SRA
SRX19329754 SRP421822 RIP-Seq SINGLE
GSM7036826: Crosslinked HEK293T, OE RPS19 WT IP, rep1; Homo sapiens; RIP-Seq
Sample: SRS16726698
BioProject: PRJNA933532
BioSample: SAMN33238796
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 WT
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391948 44706844 4470684400 1360.6 RPS19-WT-1_S4_L001_R1_001.fastq.gz, SRR23391948, SRR23391948.lite SRA
SRR23391949 42868608 4286860800 1322.23 RPS19-WT-1_S4_L002_R1_001.fastq.gz, SRR23391949, SRR23391949.lite SRA
SRX19329755 SRP421822 RIP-Seq SINGLE
GSM7036827: Crosslinked HEK293T, OE RPS19 WT IP, rep2; Homo sapiens; RIP-Seq
Sample: SRS16726699
BioProject: PRJNA933532
BioSample: SAMN33238795
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 WT
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391946 52308821 5230882100 1577.46 RPS19-WT-2_S5_L001_R1_001.fastq.gz, SRR23391946, SRR23391946.lite SRA
SRR23391947 50209219 5020921900 1534.75 RPS19-WT-2_S5_L002_R1_001.fastq.gz, SRR23391947, SRR23391947.lite SRA
SRX19329756 SRP421822 RIP-Seq SINGLE
GSM7036828: Crosslinked HEK293T, OE RPS19 WT IP, rep3; Homo sapiens; RIP-Seq
Sample: SRS16726700
BioProject: PRJNA933532
BioSample: SAMN33238794
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: HEK293T
cell line: HEK293T
genotype: OE RPS19 WT
antibody: V5 antibody (Bethyl Laboratories)
Original files (1)
HEK293T
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR23391944 42020395 4202039500 1263.99 RPS19-WT-3_S6_L001_R1_001.fastq.gz, SRR23391944, SRR23391944.lite SRA
SRR23391945 40523398 4052339800 1235.13 RPS19-WT-3_S6_L002_R1_001.fastq.gz, SRR23391945, SRR23391945.lite SRA

Linked Publications (2)

Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics · 2023
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics · 2023

Data Files (22)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— RPS19-101m-2_S11_L001_R1_001.fastq.gz RIP-Seq 1.1 GB link
— RPS19-101m-2_S11_L002_R1_001.fastq.gz RIP-Seq 1.1 GB link
— RPS19-101m-3_S12_L001_R1_001.fastq.gz RIP-Seq 1.2 GB link
— RPS19-101m-3_S12_L002_R1_001.fastq.gz RIP-Seq 1.2 GB link
— RPS19-62m-1_S7_L001_R1_001.fastq.gz RIP-Seq 1.1 GB link
— RPS19-62m-1_S7_L002_R1_001.fastq.gz RIP-Seq 1.1 GB link
— RPS19-62m-2_S8_L001_R1_001.fastq.gz RIP-Seq 1.0 GB link
— RPS19-62m-2_S8_L002_R1_001.fastq.gz RIP-Seq 1.0 GB link
— RPS19-62m-3_S9_L001_R1_001.fastq.gz RIP-Seq 1.2 GB link
— RPS19-62m-3_S9_L002_R1_001.fastq.gz RIP-Seq 1.2 GB link
— RPS19-IN-1_S1_L001_R1_001.fastq.gz RIP-Seq 1.3 GB link
— RPS19-IN-1_S1_L002_R1_001.fastq.gz RIP-Seq 1.2 GB link
— RPS19-IN-2_S2_L001_R1_001.fastq.gz RIP-Seq 1.4 GB link
— RPS19-IN-2_S2_L002_R1_001.fastq.gz RIP-Seq 1.4 GB link
— RPS19-IN-3_S3_L001_R1_001.fastq.gz RIP-Seq 1.5 GB link
— RPS19-IN-3_S3_L002_R1_001.fastq.gz RIP-Seq 1.5 GB link
— RPS19-WT-1_S4_L001_R1_001.fastq.gz RIP-Seq 1.3 GB link
— RPS19-WT-1_S4_L002_R1_001.fastq.gz RIP-Seq 1.3 GB link
— RPS19-WT-2_S5_L001_R1_001.fastq.gz RIP-Seq 1.5 GB link
— RPS19-WT-2_S5_L002_R1_001.fastq.gz RIP-Seq 1.5 GB link
— RPS19-WT-3_S6_L001_R1_001.fastq.gz RIP-Seq 1.2 GB link
— RPS19-WT-3_S6_L002_R1_001.fastq.gz RIP-Seq 1.2 GB link