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GSE145984

GSE GEO
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Total RNA-Seq of KHSRP knockdown (KD) and control samples in HepG2 and K562

Organism: Homo sapiens
Platform: GPL20301
Samples: 8
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Feb 26 2020
Last Updated: Dec 11 2020
Status: Public on Nov 11 2020
Contact: Trine Line,Hauge,Okholm (Aarhus University Hospital)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA608915 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP250831

Summary

We profile the expression of circular RNAs (circRNAs) upon KHSRP KD in HepG2 and K562 cells

Overall Design

KHSRP KD and control samples were originally generated for the ENCODE project by Brenton Graveley’s Lab, UConn. We sequenced total RNA to evaluate the expression of circRNAs

Analysis (5 steps)

View Data Processing
Processing steps for GSE145984
  1. Reads were trimmed with Trim Galore v0.4.1 and cutadapt v1.15
  2. Mapping to hg19 was performed with bwa v0.7.17 and samtools v1.9
  3. We used the CIRI2 pipeline v2.0.6 to detect circRNAs.
  4. The CIRI2 pipeline was run with a gene transfer format (GTF) file (hg19) to annotate the overlapping gene of the circRNAs
  5. Expression values of circRNAs were normalized to total reads

Supplementary Files (1)

GSE145984_circRNA_expression_CPM.txt.gz Download
GEO Samples (8)
GSM4340681 GSM4340682 GSM4340683 GSM4340684 GSM4340685 GSM4340686 GSM4340687 GSM4340688

Dataset Citations (1)

Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.
PMID 33287884 · 2020 · Genome medicine
Trine Line Hauge Okholm, Shashank Sathe, Samuel S Park, Andreas Bjerregaard Kamstrup, Asta Mannstaedt Rasmussen, Archana Shankar, Zong Ming Chua, Niels Fristrup, Morten Muhlig Nielsen, Søren Vang, Lars Dyrskjøt, Stefan Aigner, Christian Kroun Damgaard, Gene W Yeo, Jakob Skou Pedersen

SRA Experiments (8) and Runs (8)

Total: 29910 MB
SRX7806815 SRP250831 RNA-Seq PAIRED
GSM4340681: HepG2_KHSRP_1; Homo sapiens; RNA-Seq
Sample: SRS6219850
BioProject: PRJNA608915
BioSample: SAMN14213077
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HepG2_KHSRP
cell line: HepG2
tissue source: Hepatocellular carcinoma
sirna: KHSRP
replicate: 1
Original files (1)
HepG2_KHSRP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186531 35658401 7202997002 3069.51 HepG2_KHSRP_1_S7_L005_R1_001.fastq.gz, HepG2_KHSRP_1_S7_L005_R2_001.f… SRA
SRX7806816 SRP250831 RNA-Seq PAIRED
GSM4340682: HepG2_KHSRP_2; Homo sapiens; RNA-Seq
Sample: SRS6219851
BioProject: PRJNA608915
BioSample: SAMN14213011
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HepG2_KHSRP
cell line: HepG2
tissue source: Hepatocellular carcinoma
sirna: KHSRP
replicate: 2
Original files (1)
HepG2_KHSRP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186532 35951118 7262125836 3054.36 HepG2_KHSRP_2_S8_L005_R1_001.fastq.gz, HepG2_KHSRP_2_S8_L005_R2_001.f… SRA
SRX7806817 SRP250831 RNA-Seq PAIRED
GSM4340683: HepG2_NonTargeting_1; Homo sapiens; RNA-Seq
Sample: SRS6219852
BioProject: PRJNA608915
BioSample: SAMN14213009
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HepG2_NonTargeting
cell line: HepG2
tissue source: Hepatocellular carcinoma
sirna: NonTargeting
replicate: 1
Original files (1)
HepG2_NonTargeting
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186533 54114136 10931055472 4662.61 HepG2_NonTargeting_1_S5_L005_R1_001.fastq.gz, HepG2_NonTargeting_1_S5… SRA
SRX7806818 SRP250831 RNA-Seq PAIRED
GSM4340684: HepG2_NonTargeting_2; Homo sapiens; RNA-Seq
Sample: SRS6219853
BioProject: PRJNA608915
BioSample: SAMN14213008
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: HepG2_NonTargeting
cell line: HepG2
tissue source: Hepatocellular carcinoma
sirna: NonTargeting
replicate: 2
Original files (1)
HepG2_NonTargeting
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186534 52495866 10604164932 4461.87 HepG2_NonTargeting_2_S6_L005_R1_001.fastq.gz, HepG2_NonTargeting_2_S6… SRA
SRX7806819 SRP250831 RNA-Seq PAIRED
GSM4340685: K562_KHSRP_1; Homo sapiens; RNA-Seq
Sample: SRS6219854
BioProject: PRJNA608915
BioSample: SAMN14213006
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: K562_KHSRP
cell line: K562
tissue source: Chronic myelogenous leukemia
sirna: KHSRP
replicate: 1
Original files (1)
K562_KHSRP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186535 44023153 8892676906 3776.81 K562_KHSRP_1_S3_L005_R1_001.fastq.gz, K562_KHSRP_1_S3_L005_R2_001.fas… SRA
SRX7806820 SRP250831 RNA-Seq PAIRED
GSM4340686: K562_KHSRP_2; Homo sapiens; RNA-Seq
Sample: SRS6219855
BioProject: PRJNA608915
BioSample: SAMN14213005
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: K562_KHSRP
cell line: K562
tissue source: Chronic myelogenous leukemia
sirna: KHSRP
replicate: 2
Original files (1)
K562_KHSRP
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186536 48127730 9721801460 4137.87 K562_KHSRP_2_S4_L005_R1_001.fastq.gz, K562_KHSRP_2_S4_L005_R2_001.fas… SRA
SRX7806821 SRP250831 RNA-Seq PAIRED
GSM4340687: K562_NonTargeting_1; Homo sapiens; RNA-Seq
Sample: SRS6219856
BioProject: PRJNA608915
BioSample: SAMN14213004
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: K562_NonTargeting
cell line: K562
tissue source: Chronic myelogenous leukemia
sirna: NonTargeting
replicate: 1
Original files (1)
K562_NonTargeting
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186537 41819740 8447587480 3540.0 K562_NonTargeting_1_S1_L005_R1_001.fastq.gz, K562_NonTargeting_1_S1_L… SRA
SRX7806822 SRP250831 RNA-Seq PAIRED
GSM4340688: K562_NonTargeting_2; Homo sapiens; RNA-Seq
Sample: SRS6219857
BioProject: PRJNA608915
BioSample: SAMN14213003
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: K562_NonTargeting
cell line: K562
tissue source: Chronic myelogenous leukemia
sirna: NonTargeting
replicate: 2
Original files (1)
K562_NonTargeting
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR11186538 37457110 7566336220 3206.54 K562_NonTargeting_2_S2_L005_R1_001.fastq.gz, K562_NonTargeting_2_S2_L… SRA

Linked Publications (1)

Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.
Genome medicine · 2020

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— HepG2_KHSRP_1_S7_L005_R1_001.fastq.gz RNA-Seq 3.0 GB link
— HepG2_KHSRP_2_S8_L005_R1_001.fastq.gz RNA-Seq 3.0 GB link
— HepG2_NonTargeting_1_S5_L005_R1_001.fastq.gz RNA-Seq 4.6 GB link
— HepG2_NonTargeting_2_S6_L005_R1_001.fastq.gz RNA-Seq 4.4 GB link
— K562_KHSRP_1_S3_L005_R1_001.fastq.gz RNA-Seq 3.7 GB link
— K562_KHSRP_2_S4_L005_R1_001.fastq.gz RNA-Seq 4.0 GB link
— K562_NonTargeting_1_S1_L005_R1_001.fastq.gz RNA-Seq 3.5 GB link
— K562_NonTargeting_2_S2_L005_R1_001.fastq.gz RNA-Seq 3.1 GB link