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Sample GSM2277952 Query DataSets for GSM2277952
Status Public on Aug 13, 2016
Title U87_3T3_scRNAseq
Sample type SRA
Source name Brain and embyro
Organisms Homo sapiens; Mus musculus
Characteristics cell line: U87
cell line: 3T3
Extracted molecule polyA RNA
Extraction protocol mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description U87 cells and 3T3 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplimented with 10% (v/v) Fetal Bovine Serum (FBS).
Data processing Read 1 and read 2 fastq files were generated on basespace.
Raw reads from Read 1 were demultiplexed to obtain cell barcode and unique molecular identifier for each read.
Read 2 were pre-processed using faxtx_clipper to remove all poly(A) tails from the 3'-ends of each read. Any resulting fragment shorter than 25 nucleotides were discarded.
Pre-processed reads were then mapped to a concatenated human-murine transcriptome (hg19, UCSC known genes and mm10, UCSC known genes) using bwa-mem. We kept all reads with the correct strandedness that map uniquely to a specific gene with an alignment score that is greater than or equal 85% of the length of the fragment.
Cell barcodes were collapsed to account for PCR duplications. Unique molecular identifiers were collapsed to account for PCR duplications and errors that are associated with unique molecular identifier synthesis, PCR, and sequencing.
All fastq files were generated using Illumina's default pipeline on basespace. Read 1 is 26 bases long which contains cell barcode sequences (12 base long), unique molecular identifier sequences (8 base long) and 6-base long oligo(dT) sequences.Both cell barcode and unique molecular identifier are random sequences. Read 2 is 66 bases long which contains mRNA sequences.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression counts of each individual cell.
Submission date Aug 12, 2016
Last update date May 15, 2019
Contact name Peter Sims
Organization name Columbia University
Street address 3960 Broadway, 2nd Floor, Room 203AC
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platform ID GPL19415
Series (1)
GSE85575 An automatec microwell platform for large-scale single cell RNA-seq.
BioSample SAMN05571437
SRA SRX2019092

Supplementary file Size Download File type/resource 17.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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