|
| Status |
Public on Apr 21, 2023 |
| Title |
siZFC3H1_2_A375_S8 |
| 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 |
SAMN32941451 |
| SRA |
SRX19200348 |
