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Sample GSM5651047 Query DataSets for GSM5651047
Status Public on Oct 25, 2021
Title Drug-treated SK-BR-3 multi-omics sample protein _rep1
Sample type SRA
Source name breast cancer cells
Organism Homo sapiens
Characteristics cell type: breast cancer cells
human cell line: SK-BR-3
treatment: Trastuzumab
antibody: anti-human Epcam antibody, anti-human HER2 antibody and anti-human EGFR antibody
Treatment protocol Drug-treated group was treated by Trastuzumab for 72h.
Growth protocol Cells are all cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin.
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.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
Description Protein
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.
Submission date Oct 22, 2021
Last update date Oct 26, 2021
Contact name Xing Xu
Phone 086-18850013503
Organization name Xiamen University
Street address 422 Road, Siming District, Xiamen, China
City Xiamen
State/province Fujian
ZIP/Postal code 361005
Country China
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
BioSample SAMN22504999
SRA SRX12735281

Supplementary file Size Download File type/resource
GSM5651047_Drug-treated_SK-BR-3_protein_1_dge.txt.gz 3.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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