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Sample GSM2679966

Query DataSets for GSM2679966

Status

Public on Jan 17, 2018

Title

hs121-mCherry

Sample type

SRA

Source name

embryonic forebrain and 293T/17 cells

Organisms

Homo sapiens; Mus musculus

Characteristics

strain (mouse): FVB
developmental stage (mouse): gestational day e12.5
tissue (mouse): forebrain
enhancer: hs121

Extracted molecule

polyA RNA

Extraction protocol

Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads (ChemGene Beads, Lot 011416B). Cell concentration was set to 50 cells/µl. 2.5% 293T/17 human cells were added to each suspension.
As previously described (PMID: 26000488).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

dropseq_data.digital_expression.txt.gz

Data processing

Raw data analysis and digital expression quantification was carried out using the Drop-seq published pipeline (PMID: 26000488) version 1.11. The alignment was performed using STAR (PMID: 23104886) version 2.4.1d.
For each one of the five libraries, the counts for each transcript were retrieved for the top 10,000 STAMPs. By means of the human cells spiked-in, the purity was determined using a 90% as cutoff (namely, if 90% or more of the transcripts assigned to a STAMP were from human or mouse, that STAMP was assigned to either a human or a mouse cell, otherwise it was considered as a doublet). After that, starting from the 50 STAMPs showing the highest number of detected transcripts, the doublet-rate was estimated as previously described (PMID: 26000488). The 51st STAMP was then added and the doublet-rate re-calculated, and so forth up to the 10,000th STAMP. A threshold on 90% doublet-rate was finally applied to the resulting curve, which in turn allowed the identification of a set of high-quality STAMPs. A further threshold on the minimum number of detected transcripts was applied, so that STAMPs showing less than 1,000 detected molecules were discarded. Results from the five libraries were then merged together.
Genome_build: mm10 (Genome Reference Consortium GRCm38) and hg19 (Genome Reference Consortium GRCh37)
Supplementary_files_format_and_content: dropseq_data.digital_expression.txt.gz: digital expression matrix, flat text files with tab delimiters; mm10_hg19.refFlat.gz: transcriptome combining mm10 genes, hg19 genes and transgenes, refFlat tabular format. Column headers (gene Name, name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds)

Submission date

Jun 22, 2017

Last update date

May 15, 2019

Contact name

Iros Barozzi

E-mail(s)

iros.barozzi@meduniwien.ac.at

Organization name

Medical University Vienna

Street address

Borschkegasse 8a