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| Status |
Public on May 19, 2015 |
| Title |
Subject9_Cervical |
| Sample type |
SRA |
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| Source name |
Cervical cytobrush
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| Organism |
Homo sapiens |
| Characteristics |
collection site and cell type: Cervical APC
bacterial community type: Gardnerella dominant
cell type: Antigen presenting cells
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| Treatment protocol |
n/a, samples are ex vivo
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| Growth protocol |
n/a, samples are ex vivo
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Apr 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Melis Anahtar |
| E-mail(s) |
melis_anahtar@hms.harvard.edu
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| Organization name |
Massachusetts General Hospital
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| Department |
Ragon Institute of MGH, MIT, Harvard
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| Lab |
Kwon Lab
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| Street address |
400 Technology Sq
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE68452 |
Role of cervicovaginal microbiota in genital inflammation |
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| Relations |
| BioSample |
SAMN03577743 |
| SRA |
SRX1014860 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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