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Sample GSM3191999 Query DataSets for GSM3191999
Status Public on Feb 13, 2019
Title Unfixed_SetA
Sample type SRA
Source name Foreskin keratinocytes
Organism Homo sapiens
Characteristics cell type: Foreskin keratinocytes
condition: Unfixed cell
growth conditions: Keratinocyte Serum Free Medium
Extracted molecule polyA RNA
Extraction protocol Reverse Transcription from detergent and heat based lysates, according to the SORT-seq/CELseq2 protocol
CELseq2 library prep
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Read1 and Read2 where swapped to allow compatibility with CELseq2 pipeline
Reads were matched to individual cells using the demultiplexing function of the CELseq2 pipeline
Transcripts were Mapped and UMI corrected using standard settings of the CELseq2 pipeline - Reads were trimmed to 50 bases before mapping to UCSChg38 and hereafter matched to the gencode.v25.basic.annotation transcriptome
A count tables from all six samples was generated ( where UnfixedA, UnfixedB, UnfixedC represent the unfixed cells and RAID-A, RAID-B, RAID-C represent the cells that were fixed and mock-stained according to the RAID procedure
For normalization, 40000 UMI counts were subsampled from all cells and cells with fewer counts were discarded. JPGII170_40K_SUB_GEO.csv.gz is the count table with the sampled counts
Genome_build: UCSChg38
Supplementary_files_format_and_content: The .csv.gz file contains 40000 sampled transcipt UMI counts for the cells from all 6 samples - samples are indicated in cell name
Supplementary_files_format_and_content: The tab.gz file contains contains raw transcipt UMI counts, as obtained from the CELseq2 pipeline, for the cells from all 6 samples - samples are indicated in cell name
Submission date Jun 15, 2018
Last update date Feb 13, 2019
Contact name Jan Patrick Gerlach
Organization name Radboud Institute for Molecular Life Sciences
Department Molecular Developmental Biology
Street address Geert Grooteplein Zuid 28
City Nijmegen
ZIP/Postal code 6500HB
Country Netherlands
Platform ID GPL18573
Series (2)
GSE115861 Comparison of single-cell transcriptomics quality between unfixed cells and cells that were fixed and mock stained according to the RAID procedure
GSE115981 RAID allows multiplexed quantification of intracellular (phospho-)proteins and transcriptomes from fixed single cells
BioSample SAMN09429722
SRA SRX4221217

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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