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Status |
Public on Nov 12, 2024 |
Title |
COL1 and STIFF, HTO |
Sample type |
SRA |
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Source name |
mammary gland
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Organism |
Mus musculus |
Characteristics |
tissue: mammary gland group: stiff
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Extracted molecule |
total RNA |
Extraction protocol |
Single cells from the mammary gland organoid from Matrigel (MATR), soft (SOFT), collagen (COL1) and stiff (STIFF) condition were dissociated. Dissociated cells were labelled with TotalSeq-A hashtag oligonucleotide (HTO) antibodies. Matrigel and soft, collagen and stiff were pooled and loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2- chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics) and sequenced on an Illumina Novaseq 6000 (paired-end 100bp reads).
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
10X genomics, cell hashing
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Data processing |
Sequencing reads were aligned and annotated with the mm10-2020-A reference dataset as provided by 10X Genomics and demultiplexed using CellRanger (v.5.0.0) Data was demultiplexed based on data from cell hashing, by the function HTODemux() included in Seurat R package (v.4.2.0) with parameter ‘positive.quantile = 0.99’. Further downstream analyses were carried out individually for each of the four samples (MATR, SOFT, COL1 and STIFF). Quality control and downstream analysis were performed using the Seurat R package (v.4.2.0). For each sample, all the cells passed the following criteria: showed expression of more than 2000 and less than 7000 unique genes and had less than 10% UMI counts belonging to mitochondrial sequences. Read counts were normalized using the NormalizeData() function of Seurat, with parameter ‘normalization.method = "LogNormalize" and scale.factor=10000’. A PCA for each sample was calculated using the scaled expression data of the 2000 most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes() function). UMAP calculation and graph-based clustering were performed for each sample using Seurat (default parameters) with the respective 30 PCA results as input. Assembly: mm10-2020-A Supplementary files format and content: .mtx / gene expression matrix Supplementary files format and content: .tsv / genes and cell barcode Library strategy: scRNA-seq, HTO cell hashing
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Submission date |
Sep 15, 2023 |
Last update date |
Nov 12, 2024 |
Contact name |
Yura Song |
E-mail(s) |
yura.song@ulb.be
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Organization name |
Université Libre de Bruxelles
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Lab |
Laboratory of Stem Cells and Cancer
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Street address |
808, route de Lennik
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City |
Bruxelles |
ZIP/Postal code |
1070 |
Country |
Belgium |
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Platform ID |
GPL24247 |
Series (2) |
GSE243335 |
Collagen signaling and matrix stiffness regulate multipotency in glandular epithelial stem cells in mice [scRNA-Seq] |
GSE243338 |
Collagen signaling and matrix stiffness regulate multipotency in glandular epithelial stem cells in mice |
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Relations |
BioSample |
SAMN37411420 |
SRA |
SRX21838755 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7783602_Col-Ab1-PEG7-Ab2_woAb_barcodes.tsv.gz |
52.4 Kb |
(ftp)(http) |
TSV |
GSM7783602_Col-Ab1-PEG7-Ab2_woAb_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
GSM7783602_Col-Ab1-PEG7-Ab2_woAb_matrix.mtx.gz |
107.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
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