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Sample GSM2510616 Query DataSets for GSM2510616
Status Public on Nov 20, 2017
Title Adult basal cells
Sample type SRA
Source name Mammary gland
Organism Mus musculus
Characteristics strain: FVB/NJ
age: Adult
cell source: Basal
number of cells: 4771
Treatment protocol none
Growth protocol none
Extracted molecule total RNA
Extraction protocol A 10X Genomics Chromium machine was used for 3,000-5000 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 P7 and R2 primers were added during the GEM incubation and the P5, and R1 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 with parameters as recommended by 10X Genomics.
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 v1.2.1 using the Illumina BCL files as input.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.
Submission date Feb 27, 2017
Last update date May 15, 2019
Contact name Gordon K Smyth
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
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 GPL19057
Series (2)
GSE95430 Single cell RNA-seq of eight thousand epithelium cells from the mammary glands of adult mice
GSE103275 Single cell RNA-seq of mouse mammary gland epithelium cells
SRA SRX2595068
BioSample SAMN06472407

Supplementary file Size Download File type/resource
GSM2510616_P4-barcodes.tsv.gz 18.2 Kb (ftp)(http) TSV
GSM2510616_P4-genes.tsv.gz 212.5 Kb (ftp)(http) TSV
GSM2510616_P4-matrix.mtx.gz 4.7 Mb (ftp)(http) MTX
GSM2510616_P4-possorted_genome_bam.bam.bai.gz 1.7 Mb (ftp)(http) BAI
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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