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GEO help: Mouse over screen elements for information. |
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Status |
Public on Dec 26, 2020 |
Title |
H1 |
Sample type |
SRA |
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Source name |
Metaplasia
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Organism |
Mus musculus |
Characteristics |
strain: BALB/c tissue: Metaplasia replicate: technical replicate 2
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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.
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Submission date |
Mar 28, 2019 |
Last update date |
Dec 26, 2020 |
Contact name |
Antoine-Emmanuel Saliba |
E-mail(s) |
emmanuel.saliba@helmholtz-hzi.de
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Phone |
+49-931-31-81341
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Organization name |
Helmholtz Institute for RNA-based Infection Research
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Street address |
Josef-Schneider-Straße 2 / D15
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City |
Würzburg |
ZIP/Postal code |
97080 |
Country |
Germany |
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Platform ID |
GPL24247 |
Series (1) |
GSE128987 |
Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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