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Sample GSM2801986 Query DataSets for GSM2801986
Status Public on Nov 11, 2021
Title U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c4
Sample type SRA
 
Source name Single cell from U87-3T3 cell mixture
Organisms Homo sapiens; Mus musculus
Characteristics cell line: U87 and 3T3
Extracted molecule polyA RNA
Extraction protocol published scPLATE-Seq protocol
published scPLATE-Seq protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description HsMm.csv
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.
 
Submission date Oct 02, 2017
Last update date Nov 11, 2021
Contact name Hongxu Ding
E-mail(s) hongxuding@arizona.edu
Organization name University of Arizona
Street address The University of Arizona
City Tucson
State/province AZ
ZIP/Postal code 85721
Country USA
 
Platform ID GPL19415
Series (1)
GSE104493 Benchmark Data for scPLATE-Seq
Relations
BioSample SAMN07730588
SRA SRX3237353

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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