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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/┬Ál. 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
Organization name Medical University Vienna
Street address Borschkegasse 8a
City Vienna
ZIP/Postal code 1090
Country Austria
Platform ID GPL22245
Series (2)
GSE100384 Ultraconserved Enhancers Are Required for Normal Development [Drop-seq]
GSE100394 Ultraconserved Enhancers Are Required for Normal Development
BioSample SAMN07269891
SRA SRX2948606

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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