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| Status |
Public on Jul 06, 2023 |
| Title |
MDA-MB-231_P1__sihnRNP_K |
| Sample type |
SRA |
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| Source name |
Triple-negative breast cancer
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
genotype: parental
treatment: sihnRNP_K
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| Treatment protocol |
For siRNA, RNAimax lipofectamine (Invitrogen, Waltham, MA) was used to transfect HNRNPK smartpool siRNA (Dharmacon) or non-targeting siRNA (Qiagen) according to the manufacturer’s protocol. For overexpression plasmids, jetOptimus DNA transfection reagent (Polyplus, Illkirch, France) was used according to the manufacturer’s protocol.
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| Growth protocol |
MDA-MB-231 cells were authenticated by short-tandem repeat profiling, performed by ATCC. MDA-MB-231 KRT19 KO cells generated using the CRISPR/Cas9 system and cells stably expressing GFP or GFP-KRT19 generated using the lentiviral system, Cells were grown in Dulbecco’s modified essential medium (DMEM; Gibco, Grand Island, NY) supplemented with 10% Fetal Bovine Serum (GE Healthcare, Logan, UT) and 1% penicillin/streptomycin (Gibco) in a humidified incubator at 5% CO2 and 37°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq analysis, total RNAs from three biological replicates each of untransfected parental and KRT19 KO cells, transfected with siHNRNPK, control siRNA, HNRNPK ∆NLS or vector.
Ribosomal RNA was depleted of using the NEBNext® rRNA Depletion Kit and cDNA libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).
RNA was barcoded using the NEBNext Multiplex Oligos for Illumina (NEB).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
bcl2fastq/2.20.0 was used to convert bcl to fastq
For RNA-Seq fastq files were aligned using star/2.7.2b or TopHat(2)
differential expression was done using cuffdiff (cufflinks/2.2.1)
PARCLIP was analysed using Parpipes (https://github.com/ohlerlab/PARpipe)
Assembly: hg38
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| Submission date |
Jan 24, 2023 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Markus Hafner |
| E-mail(s) |
markus.hafner@nih.gov
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| Organization name |
NIH
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| Department |
NIAMS
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| Lab |
Laboratory of Muscle Stem Cells and Gene Regulation
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| Street address |
50 South Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE223603 |
Keratin 19 binds and regulates cytoplasmic HNRNPK mRNA targets in triple-negative breast cancer |
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| Relations |
| BioSample |
SAMN32887264 |
| SRA |
SRX19148532 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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