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Sample GSM2802103

Query DataSets for GSM2802103

Status

Public on Nov 11, 2021

Title

U87-3T3 scRNA-Seq with 15xSMRT, 8xNextera and SPRI U87_3T3_SC_C2_e12

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