|
| Status |
Public on Jan 28, 2023 |
| Title |
SUM159PT_Clone321_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SUM159PT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159PT
cell type: Claudinlow Breast Cancer
genotype: NF-YA deltaEx3
treatment: CRISPR/spCas9D10A editing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were extracted with the Tri-Reagent protocol (Sigma-Aldrich). 1 μg of total RNA was retrotranscribed to cDNA by the MMLV Reverse Transcription Mix (GeneSpin). RNA samples for RNA-Seq were extracted from three independent biological replicates for each cell line, treated with DNAse and checked for its quality by RNA ScreenTape Assay with TapeStation System.
BT549: mRNA was enriched using oligo(dT) beads cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was obtained after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. SUM159PT: total RNA was depleted of ribosomal RNA and the RNAseq libraries were prepared with the Illumina TruSeq Stranded Total RNA kit following the manufacturer’s protocol. Amplified libraries were checked on a bioanalyzer 2100 and quantified with picogreen reagent.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
final_tab_SUM159_raw_genes.txt
final_tab_SUM159PT_norm_genes.txt
final_tab_SUM159_norm_isoforms.txt
|
| Data processing |
mRNA expression was calculated from FASTQ files with RSEM (version = 1.3.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes gene-level expected counts for each Sample (raw_genes)
Supplementary files format and content: tab-delimited text file includes gene-level TPM values for each Sample (norm_genes)
Supplementary files format and content: tab-delimited text file includes isoform-level TPM values for each Sample (norm_isoforms)
|
| |
|
| Submission date |
Jul 13, 2022 |
| Last update date |
Jan 28, 2023 |
| Contact name |
Alberto Gallo |
| E-mail(s) |
alberto.gallo1@unimi.it
|
| Phone |
3478054509
|
| Organization name |
Università degli Studi di Milano
|
| Street address |
Via Marconi 11/B
|
| City |
Ceriano Laghetto |
| State/province |
District Of Columbia |
| ZIP/Postal code |
20816 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE208088 |
High levels of NF-YAl drives EMT in Claudinlow tumors |
|
| Relations |
| BioSample |
SAMN29680454 |
| SRA |
SRX16174177 |
