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| Status |
Public on Oct 25, 2021 |
| Title |
MCF7 multi-omics sample RNA _rep1 |
| Sample type |
SRA |
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| Source name |
breast cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: breast cancer cells
human cell line: MCF7
treatment: none
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| Treatment protocol |
Drug-treated group was treated by Trastuzumab for 72h.
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| Growth protocol |
Cells are all cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lyzed and RNAs/Proteins were captured, reverse transcribed and amplified.
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 NextSeq 500 |
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| Description |
RNA
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| Data processing |
multi-Paired-seq sequencing libraries produce paired-end reads: Read 1 contained a cell barcode (12 bases) and a UMI (8 bases); Read 2 contained mRNA/protein barcode information.
The reads would be preprocessed with the following steps: correcting bead, filtering low-quality reads, trimming read 2 including polyA, adapter and primer, alignment, assigning gene tags, generating digital gene expressing.
The beads with the twenty-first base as A, C or G only were used in our experiments. If the number of continuous T bases at the end of read 1 was less than or equal to 12, we inserted “N” bases before T bases. Otherwise, the pair of reads was dropped. Filtering low-quality reads was based on the base quality of the cell barcode and UMI. Respectively, cell barcode and UMI should have only one base with quality lower than 20 at most. Otherwise, the read pair was discarded. At least 5 contiguous bases of TSO and at least 6 contiguous bases of A with no mismatch were examined for read 2 and were hard clipped off the read. At least 6 contiguous bases of primer with one mismatch allowed considered for read 2 and hard clipped off read.
The read pair was discarded, if the length of read 2 was less than 26 after trimmed. STAR alignment tool was used to align read 2 with the reference genome.
For human and mouse mixed cells, we used hg19_mm10 mentioned in Drop-seq as reference genome. This program from Drop-seq added a tag “GE”. We kept the unique mapping with gene tags. Then unique UMIs for each gene of each cell were counted to generate digital gene expression.
Genome_build: hg19 (GRCh37), mm10 (GRCm38)
Supplementary_files_format_and_content: Digital gene/protein expression in text files.
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| Submission date |
Oct 22, 2021 |
| Last update date |
Oct 26, 2021 |
| Contact name |
Xing Xu |
| E-mail(s) |
xuxing940329@126.com
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| Phone |
086-18850013503
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| Organization name |
Xiamen University
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| Street address |
422 Road, Siming District, Xiamen, China
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| City |
Xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361005 |
| Country |
China |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE186402 |
Decoding Expression Dynamics of Protein and Transcriptome at the Single Cell Level through Multi-Omics Sequencing in Paired Picoliter Chambers |
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| Relations |
| BioSample |
SAMN22504986 |
| SRA |
SRX12735268 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5651034_MCF7_RNA_1_dge.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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