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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
E-mail(s) nikolaos.karaiskos@mdc-berlin.de
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
Relations
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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