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Sample GSM4909302 Query DataSets for GSM4909302
Status Public on Mar 19, 2021
Title ER+ tumour Total cells from Patient 0025
Sample type SRA
 
Source name Mammary gland
Organism Homo sapiens
Characteristics patient: 0025
gender: Female
menopause: NA
parity: NA
cancer type: ER+ tumour
cell population: Total
number of cells: 10592
Treatment protocol none
Growth protocol none
Extracted molecule polyA RNA
Extraction protocol A 10X Genomics Chromium machine was used for single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10X Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of about 750,000 barcodes to separately index each cell’s transcriptome. The R1 primers were added during the GEM incubation and the P5, P7, a sample index and R2 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina NextSeq 500.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Read alignment and count summarization were performed using CellRanger v3.0.2 using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format. The supplementary file features.tsv.gz contains the corresponding Ensembl IDs and gene symbols as tab-delimited text. The barcode.tsv files contain the 10X barcodes used to identify cells. Each matrix market file can be read into R, together with features.tsv.gz, using the read10X function of the edgeR software package.
 
Submission date Nov 16, 2020
Last update date Mar 22, 2021
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL18573
Series (1)
GSE161529 scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells
Relations
BioSample SAMN16809188

Supplementary file Size Download File type/resource
GSM4909302_ER-MH0025-barcodes.tsv.gz 50.3 Kb (ftp)(http) TSV
GSM4909302_ER-MH0025-matrix.mtx.gz 43.6 Mb (ftp)(http) MTX
Processed data provided as supplementary file
Raw data not provided for this record

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