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Sample GSM1671930 Query DataSets for GSM1671930
Status Public on May 19, 2015
Title Subject6_PBMC
Sample type SRA
 
Source name Peripheral blood
Organism Homo sapiens
Characteristics collection site and cell type: PBMC APC
bacterial community type: Prevotella dominant
cell type: Antigen presenting cells
Treatment protocol n/a, samples are ex vivo
Growth protocol n/a, samples are ex vivo
Extracted molecule total RNA
Extraction protocol Cells were sorted directly into TriZOL on a FACS Aria III and frozen at -80C. Gen-Elute linear polyacrylamide (Sigma) was added to the RNA in TRIzol, followed by the addition of 0.2 volumes of chloroform and vortexing. After centrifuging at 14,000xg for 5 minutes, the aqueous phase was transferred to a clean tube. Nucleic acid was precipitated with isopropanol and 3M sodium acetate pH 5.5 (Ambion) at -20°C overnight and then centrifuged at maximum speed for 30 minutes at 4°C. The supernatant was discarded and the pellet was washed by adding 0.5mL of 100% ethanol, centrifuging for 15 minutes at 4°C, and discarding the supernatant. The nucleic acid pellet was allowed to dry and was resuspended in 5 μL of molecular grade water.
RNA-DGE derived from the Single Cell RNA Barcoding and Sequencing (SCRB-Seq) strategy
3’ Digital Gene Expression (3’ DGE)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Mapping of read2 on mRNA refseq using BWA
Parsing the output based on cell barcode stored in read1 (first 6bp)
Gene expression computation based on Unique Molecular Identifier (UMI) counts stored in read1 (base 7 to 16)
Concatenation of single cell gene expression in gene expression matrices (processed data files)
DGE file was imported into R. Cervical samples were analyzed separately from PBMC samples. Genes with less than a total of 10 reads across all samples were eliminated from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: gene expression matrix
 
Submission date Apr 30, 2015
Last update date May 15, 2019
Contact name Melis Anahtar
E-mail(s) melis_anahtar@hms.harvard.edu
Organization name Massachusetts General Hospital
Department Ragon Institute of MGH, MIT, Harvard
Lab Kwon Lab
Street address 400 Technology Sq
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL16791
Series (1)
GSE68452 Role of cervicovaginal microbiota in genital inflammation
Relations
BioSample SAMN03577739
SRA SRX1014856

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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