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Sample GSM3689565 Query DataSets for GSM3689565
Status Public on Dec 26, 2020
Title H1
Sample type SRA
 
Source name Metaplasia
Organism Mus musculus
Characteristics strain: BALB/c
tissue: Metaplasia
replicate: technical replicate 2
Extracted molecule total RNA
Extraction protocol Mice were euthanized and the genital tract was extracted. Endocervix, junction and ectocervix were cut out with a sterile surgical knife. Tissue samples were washed thoroughly in sterile PBS (Gibco, # 14190-094) and minced with surgical scissors. Minced tissue was incubated in 0.5 mg/ml collagenase type II (Calbiochem, # 234155) for 45 mins at 37 °C in a shaker incubator. Tissue and dissociated cells were pelleted by centrifugation (7 min at 1000 g, 4 °C), supernatant discarded, cells resuspended in warm TrypLE express (Gibco, # 12604021) and incubated for 15 min at 37 °C in a shaker incubator. After dissociation, the cell and tissue pellet was resuspended in ADF (Invitrogen) medium and passed through a 40 µM cell strainer (BD Falcon, # 352340) to separate the single dissociated cells from tissue pieces. Cells were pelleted by centrifugation (7 min at 1000xg, 4 °C) and resuspended in PBS containing 0.04% w/v BSA (400 μg/ml) at a concentration of 500-1500 cells/μl.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Data were analyzed using Cell Ranger™ v3.0.1 pipelines and were visualized by Loupe™ Cell Browser v3.0.2 Both are available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: csv format: includes mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.
*tar archives include cell-level data: matrix.mtx, barcodes.tsv and features.tsv
*matrix.h5 files include cell-level data in H5 matrix format
*molecule_info.h5 files include per molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene. Also contain data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
 
Submission date Mar 28, 2019
Last update date Dec 26, 2020
Contact name Antoine-Emmanuel Saliba
E-mail(s) emmanuel.saliba@helmholtz-hzi.de
Phone +49-931-31-81341
Organization name Helmholtz Institute for RNA-based Infection Research
Street address Josef-Schneider-Straße 2 / D15
City Würzburg
ZIP/Postal code 97080
Country Germany
 
Platform ID GPL24247
Series (1)
GSE128987 Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia
Relations
BioSample SAMN11280470
SRA SRX5587884

Supplementary file Size Download File type/resource
GSM3689565_H1_cell-level_data.tar.gz 24.8 Mb (ftp)(http) TAR
GSM3689565_H1_differential_expression.csv.gz 3.4 Mb (ftp)(http) CSV
GSM3689565_H1_filtered_feature_bc_matrix.h5 13.0 Mb (ftp)(http) H5
GSM3689565_H1_molecule_info.h5 156.6 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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