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Sample GSM2359902 Query DataSets for GSM2359902
Status Public on May 03, 2017
Title Live
Sample type SRA
Source name Cell culture cells, live
Organisms Homo sapiens; Mus musculus
Characteristics human cell line: Flp-In T-Rex 293 HEK
mouse cell line: NIH-3T3 (ACC 59)
condition: live
Treatment protocol Cells were grown to 30 to 60% confluence, dissociated with 0.05% bovine trypsin-EDTA (Invitrogen 25300062), quenched with growth medium, and further processed as described previously (Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1).
Growth protocol Cells were grown in DMEM (Invitrogen 61965-026) without antibiotics containing 10% fetal bovine serum, and confirmed to be mycoplasma-free (LookOut Mycoplasma PCR detection kit, Sigma Aldrich).
Extracted molecule polyA RNA
Extraction protocol Methanol-fixation was adapted from Stöckius et al. 2009 (Nat. Methods). To avoid cell clumping, 8 volumes (800 µl) of methanol p. a. (pre-chilled to -20˚C) were added drop-wise, while gently mixing or vortexing the cell suspension.
Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Drop-seq
Unique lab identifier: NR_CK_027 (ds013_50)
Data processing Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12.
Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12.
Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j.
Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12.
Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12.
Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2.
The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: *txt: Tab-separated text files containing UMI counts per gene and per cell of each sample.
clusters*.txt files generated using Seurat.
Submission date Oct 25, 2016
Last update date May 15, 2019
Contact name Nikos Karaiskos
Organization name Max Delbrück Center for Molecular Medicine
Lab Systems Biology of Gene Regulatory Elements
Street address Hannoversche Str. 28
City Berlin
ZIP/Postal code 10115
Country Germany
Platform ID GPL19415
Series (1)
GSE89164 Cell fixation and preservation for droplet-based single cell transcriptomics
BioSample SAMN05939265
SRA SRX2268041

Supplementary file Size Download File type/resource
GSM2359902_live_dge.txt.gz 2.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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