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Sample GSM6998374 Query DataSets for GSM6998374
Status Public on Apr 21, 2023
Title siZFC3H1_3_A375_S9
Sample type SRA
 
Source name A375 melanoma cell line
Organism Homo sapiens
Characteristics tissue: A375 melanoma cell line
cell line: A375
treatment: siZFC3H1 treated
Treatment protocol Stable lines were untreated. Knockdown of ZFC3H1 (Dharmacon, L-020839-02-0005), ZC3H14 (Dharmacon, L-014468-01-0005), or a control knockdown (Dharmacon, D-001810-01-05) were completed on A375 CLOVER cells
Growth protocol A375 human melanoma cells were identity-verified via STR analysis. Mycoplasma testing was done within one week of every experiment using human cell lines (Lonza, Mycoalert PLUS, LT07-710). All cell lines were mycoplasma negative. Cells were grown in DMEM supplemented with 10% FBS, penicillin/streptomycin or selection antibiotics, and L-glutamine.
Extracted molecule polyA RNA
Extraction protocol DNA was removed, and RNA was isolated (Qiagen, 741134). Poly-A selection was undertaken (NEB, E7490).
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina, 016.24
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNA 3' end sequencing
siZFC3H1
Data processing Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013)
Custom Python script to filter reads from each bam file based on the following parameters: 1) Proper mate pairing; 2) orientation of the putative 3’ cleavage end corresponding to the direction of transcription for the gene to which reads mapped; 3) concordant mapping to known chromosomes; 4) no soft clippings; 5) skipped regions must be longer than 70 nucleotides.
Bedtools cluster tool version 2.26.0 (Quinlan and Hall, 2010) and custom Python scripts were used to generate read clusters by grouping any 3’ end coordinates that fell within 40 nucleotides of one another into a single cluster.
Clusters present in >1 replicate were considered to be true termination sites (high confidence termination sites). High confidence termination site reads were reclusters to define a complete and non-redundant 3' cleavage map for all conditions.
3' cleavage site reads were quantified using DEX-seq (Anders et al, 2012).
Assembly: GRCh38
Supplementary files format and content: Read count tables for each replicate at each identified cleavage site
 
Submission date Jan 27, 2023
Last update date Apr 21, 2023
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (2)
GSE131334 Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance
GSE223890 Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance [humanMut3primeseq]
Relations
BioSample SAMN32941450
SRA SRX19200349

Supplementary file Size Download File type/resource
GSM6998374_Human_3pSeq_raw_counts_siZFC3H1_R3.txt.gz 676.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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