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| Status |
Public on Sep 04, 2018 |
| Title |
PP: EpCAM+ CCR10+ |
| Sample type |
SRA |
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| Source name |
Explanted lung tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: lung airway epithelial cells
cell type: EpCAM+ CCR10+
processing: in vitro cultured and expanded
diagnosis: Idiopathic Pulmonary Fibrosis
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| Growth protocol |
Epithelial colonies were derived using CRC medium: 50% senescent lung fibroblast conditioned medium + 50% fibroblast complete medium (DMEM + 15% FBS + antiboitics) and 10 µM of Y27632. After approximately 2 weeks, cells were passaged and cultured overnight in Pneumacult Ex Plus medium (STEMCELL technologies) containing 10 µM Y27632.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell RNA-seq libraries were prepared per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cellular suspensions were loaded on a Chromium Controller instrument (10X Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT were performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). After RT, GEMs were harvested and the cDNAs were amplified, cleaned up with SPRIselect Reagent Kit. Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2), to obtain a sequencing depth of 100K~200K reads per cell.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Single cell RNA sequencing of cultured IPF primary epithelial cells
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| Data processing |
The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) with default parameters, using a custom mm10 transcriptome reference from GENCODE M9 annotation, containing all protein coding and long non-coding RNA genes. Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 1.3.0 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include gene expression for each cell with or without normalization.
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| Submission date |
Jun 19, 2018 |
| Last update date |
Oct 11, 2021 |
| Contact name |
AGCT Core |
| Organization name |
Cedars Sinai Medical Center
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| Department |
BMS
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| Street address |
8687 Melrose Ave, PDC B230
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| City |
West Hollywood |
| State/province |
CA |
| ZIP/Postal code |
90069 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE115982 |
Single cell RNA sequencing of cultured CCR10+ and CCR10- lung airway epithelial cells |
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| Relations |
| BioSample |
SAMN09453173 |
| SRA |
SRX4314691 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3204304_P_P_Expr_norm.csv.gz |
162.9 Mb |
(ftp)(http) |
CSV |
| GSM3204304_P_P_Expr_raw.csv.gz |
17.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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