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| Status |
Public on Dec 15, 2018 |
| Title |
IPF_03 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Homo sapiens |
| Characteristics |
disease condition: Idiopathic pulmonary fibrosis
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| Treatment protocol |
not applicable.
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| Growth protocol |
not applicable.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The lungs were infused with 1 mL dispase (Corning) with DNase I (Sigma). Lungs were incubated at room temperature with gentle agitation for 45 minutes, followed by gentle teasing using forceps into small (1-2 mm) fragments and incubation in digestion buffer for another 15 minutes. Resulting suspension was passed through passed through 70 μm cell strainer (Falcon), washed with DMEM (Corning) supplemented with 5% FBS (Corning), pelleted by centrifugation and erythrocytes were lysed using BD Pharm Lyse (BD Biosciences). Resulting single cell suspension was kept in DMEM/FBS and passed through 40 μm cell strainer (Falcon) two times. Cells were counted using Cellometer K2 (Nexcelom) with nucleic acid binding dyes acridine orange (AO) to calculate total number of nucleated cells and propidium iodide (PI) to count dead cells. All manipulations were performed using wide bore tips (Axygen).
10x Genomics, 3' single-cell RNA-seq, V2 chemistry (Protocol CG00052 Rev B).
single-cell RNA-seq (10x Genomics) sequenced on Illumina HiSeq 4000, 1 librar per lane.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
BaseCalls: HCS 3.4.0 software.
Fastq files were generated using bcl2fastq software (Illumina) as part of CellRanger V2.0 pipeline (10x Genomics) using mkfastq command.
Fastq files processed using CellRanger V2.0 pipeline (10x Genomics), mapping was done to GRCh38 version of human genome.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw and filtered matrices in HDF5 format.
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| Submission date |
Nov 26, 2018 |
| Last update date |
Dec 16, 2018 |
| Contact name |
Alexander V Misharin |
| E-mail(s) |
a-misharin@northwestern.edu
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| Phone |
3125031958
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| Organization name |
Northwestern University
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| Department |
Pulmonary and Critical Care
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| Lab |
Misharin lab
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| Street address |
240 E Huron
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE122960 |
Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis II |
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| Relations |
| BioSample |
SAMN10477936 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3489188_IPF_03_filtered_gene_bc_matrices_h5.h5 |
11.8 Mb |
(ftp)(http) |
H5 |
| GSM3489188_IPF_03_raw_gene_bc_matrices_h5.h5 |
25.1 Mb |
(ftp)(http) |
H5 |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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