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| Status |
Public on Apr 13, 2020 |
| Title |
HCC1954_siNT_rep1 |
| Sample type |
SRA |
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| Source name |
human breast carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
passage: between 5 and 10
cell line: HCC1954
transfection reagent: Lipofectamine RNAi_Max
sirna/shrna: Negative control siRNA#2
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| Treatment protocol |
Cells were transfected using small interfering RNA (siRNA) directed towards non-targeting #2 (NT Thermo Fisher Scientific ID:4390843), TFAP2C (TFS ID:10.7041) with lipofectamine RNAiMAX reagent (Cat# 13778150, Thermo Fisher Scientific, USA), accordingly a manufacturer’s instruction. After 72 to 96 hours of incubation, cell were immediately analyzed or used in consequent experiments. Cell clones of HCC1954 lines with stable knockdown of TFAP2C (Cat#TRCN0000019745, Sigma, USA) and negative control (Cat#SHC002, Sigma, USA) were generated using lentivirus-mediated shRNA cassette.
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| Growth protocol |
Cell lines HCC1954 and SKBR3 were purchased from the American Type Culture Collection (ATCC; Manassas, VA, USA) and propagated in the appropriate medium as recommended by manufacturer. Additionally, all media were supplemented with 10% FBS (LS26140079, Gibco, USA), 1% 100X Pen/Strep antibiotics (10378016, Gibco, USA), and 0.2% Plasmocin (Cat# ant-mpp, InvivoGen, USA). The cell lines were cultured in a standard humidified incubator at 37° C and 5% CO2 (16). The cells were not tested and authenticated by the authors. Only early passages of cell lines (less than 10) were used for experiments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA from cell lysates were obtained from cell lines using the Rneasy Mini Kit (Qiagen, Valencia, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
transient knockdown
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| Data processing |
Sample processing was done by the University of Nebraska
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cuffdiff was used for FPKM quantification and differential expression
Genome_build: Human Feb.2009 (GRCh37/hg19) (hg19)
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| Submission date |
Feb 21, 2019 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Tiandao Li |
| Organization name |
Washington University
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| Street address |
4444 Forest Park Ave
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| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE126894 |
A TFAP2C Gene Signature is Predictive of Outcome in HER2 Breast Cancer (RNA-Seq) |
| GSE126898 |
A TFAP2C Gene Signature is Predictive of Outcome in HER2 Breast Cancer |
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| Relations |
| BioSample |
SAMN10984820 |
| SRA |
SRX5405618 |
| 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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