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Status |
Public on Nov 11, 2021 |
Title |
U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d5 |
Sample type |
SRA |
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Source name |
Single cell from U87-3T3 cell mixture
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Organisms |
Homo sapiens; Mus musculus |
Characteristics |
cell line: U87 and 3T3
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Extracted molecule |
polyA RNA |
Extraction protocol |
published scPLATE-Seq protocol published scPLATE-Seq protocol
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
HsMm.csv
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Data processing |
After demultiplexing, UMIs from the barcode read (8nt) were concatenated onto the 5’ part of corresponding mappable reads using a custom Python script. The concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --quantMode TranscriptomeSAM so that output alignments are translated into transcript coordinates for downstream analysis, and --clip5pNbases 8 so that the UMI sequences are not mapped. All other options for STAR are set as default. Specifically, for mix-species experiments, the concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --outFilterMultimapNmax 1 so that only reads that uniquely mapped are considered. The mapped transcripts per gene and mapped reads per gene were quantified using a custom Python script. When measuring mapped transcripts per gene, we use hamming distance threshold 1, which means only if the hamming distance between two UMIs is greater than 1, then they are considered from different transcripts. Genome_build: UCSC hg38 for HEK293 RNA-Seq and scRNA-Seq, and U87 scRNA-Seq. Genome_build: Concatenated UCSC hg38 and mm10 for U87-3T3 cell mixture scRNA-Seq profiles. Supplementary_files_format_and_content: comma separated file including umi matrix, counts matrix and cross-species matrix.
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Submission date |
Oct 02, 2017 |
Last update date |
Nov 11, 2021 |
Contact name |
Hongxu Ding |
E-mail(s) |
hongxuding@arizona.edu
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Organization name |
University of Arizona
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Street address |
The University of Arizona
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City |
Tucson |
State/province |
AZ |
ZIP/Postal code |
85721 |
Country |
USA |
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Platform ID |
GPL19415 |
Series (1) |
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Relations |
BioSample |
SAMN07730573 |
SRA |
SRX3237366 |
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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