NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7783602 Query DataSets for GSM7783602
Status Public on Nov 12, 2024
Title COL1 and STIFF, HTO
Sample type SRA
 
Source name mammary gland
Organism Mus musculus
Characteristics tissue: mammary gland
group: stiff
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).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description 10X genomics, cell hashing
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
 
Submission date Sep 15, 2023
Last update date Nov 12, 2024
Contact name Yura Song
E-mail(s) yura.song@ulb.be
Organization name Université Libre de Bruxelles
Lab Laboratory of Stem Cells and Cancer
Street address 808, route de Lennik
City Bruxelles
ZIP/Postal code 1070
Country Belgium
 
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
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 SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap