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| Status |
Public on Dec 15, 2020 |
| Title |
SSc-ILD S19578 EPCAM+ |
| Sample type |
SRA |
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| Source name |
lung explant
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| Organism |
Homo sapiens |
| Characteristics |
disease: SSc-ILD
tissue: lung
cell type: EPCAM+
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| 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 37C. Residual tissue material was transferred into fresh digestion buffer and rocked another 45 minutes at 37C. 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
SAM24360872
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| 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
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| Submission date |
Oct 11, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Jason Anthony Vander Heiden |
| E-mail(s) |
[email protected]
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| Organization name |
Genentech
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| Department |
Biological Research AI Development
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| Street address |
1 DNA Way
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE159354 |
Single-cell RNA-seq of sort human lung explants from IPF and SSc-ILD patients |
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| Relations |
| BioSample |
SAMN16415316 |
| SRA |
SRX9276293 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4827178_SAM24360872_filtered_feature_bc_matrix.h5 |
14.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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