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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 26, 2022 |
| Title |
MDA-MB-231-WT rep1 |
| Sample type |
SRA |
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| Source name |
breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: triple-negative breast cancer cells
genotype: WT
cell line: MDA-MB-231
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA.
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 |
BGISEQ-500 |
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| Description |
X231_1
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| Data processing |
In our project, we sequenced 4 samples on BGISEQ-500 Platform in total
After reads filtering, we map clean reads to reference genome (hg38) using HISAT
IGV(Integrative Genomics Viewer) tool can be used to review the mapping result.
we use StringTie to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks ) and predict the coding ability of those new transcripts using CPC
After genome mapping, we use GATK to call SNP and INDEL variant for each sample.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Mar 17, 2021 |
| Last update date |
Jan 26, 2022 |
| Contact name |
Lizhong Wang |
| E-mail(s) |
[email protected]
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| Organization name |
UAB
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| Street address |
740 20th St S
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| City |
Birmingham |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE169128 |
Targeted CRISPR interference and activation of microRNA-3662-HBP1 axis controls tumor progression of triple-negative breast cancer |
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| Relations |
| BioSample |
SAMN18341055 |
| SRA |
SRX10372553 |
| 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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