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Sample GSM4827199 Query DataSets for GSM4827199
Status Public on Dec 15, 2020
Title Control N1865 CD45+
Sample type SRA
 
Source name transplant rejection lung
Organism Homo sapiens
Characteristics disease: Control
tissue: lung
cell type: CD45+
Extracted molecule total RNA
Extraction protocol After bronchoalveolar lavage, fresh lung explant tissue was stored in complete media on wet ice overnight. The tissue was washed in HBSS and then thoroughly minced in digestion buffer (HBSS, 2.5mg/mL Collagenase D, 100ug/mL DNAse). Minced tissue was rocked 45 minutes at 37C. Residual tissue material was transferred into fresh digestion buffer and rocked another 45 minutes at 37C. Single cells from both rounds of digest were combined and utilized for downstream analyses. Single cell preparations were labeled with a cocktail of fluorescently labeled antibodies including, CD45(BUV421), EpCAM(PE) , CD31(PE-CY7) , CD90(APC), Live/Dead(eFluor 780), and then subjected to fluorescence-activated cell sorting (FACS) to isolate specific populations.
Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3’ Library and Gel bead kit v2 following the manufacturer’s user guide.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description SAM24351198
Data processing FASTQ files were generated using the Cell Ranger v3.0.2 (10X Genomics) bcl2fastq (Illumina) wrapper.
Sequencing reads were assembled and aligned against the GENCODE basic human reference using Cell Ranger v3.0.2 (10X Genomics) to generate count matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5 gene count matrices
 
Submission date Oct 11, 2020
Last update date Dec 15, 2020
Contact name Jason Anthony Vander Heiden
E-mail(s) vandej27@gene.com
Organization name Genentech
Department Biological Research AI Development
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platform ID GPL20301
Series (1)
GSE159354 Single-cell RNA-seq of sort human lung explants from IPF and SSc-ILD patients
Relations
BioSample SAMN16415325
SRA SRX9276330

Supplementary file Size Download File type/resource
GSM4827199_SAM24351198_filtered_feature_bc_matrix.h5 4.9 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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