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| Status |
Public on Oct 11, 2019 |
| Title |
11.18 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Homo sapiens |
| Characteristics |
disease state: IPF
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| Treatment protocol |
Following explantation, lungs were inflated to 30 cm H2O and held at 10 cm H2O pressure inflation while frozen over liquid nitrogen vapor according to previously established protocols.(12) The frozen lung was imaged using a high resolution CT scanner and cut into 2 cm thick slices along the transverse plane for sampling. Cores were systematically sampled from each slice using a 1.4 cm diameter coring drill. For this study, 2 cores were randomly selected from each of upper, mid, and lower lung regions for 6 samples per lung.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using miRNeasy mini kit (Qiagen) from each core. according the manufacturer’s protocol. RNA concentration and integrity were measured by using NanoDrop ND-2000 and 2200 Tape Station
20 ng RNA input was used for library preparation by AmpliSeq™ Transcriptome Human Gene Expression kit according the manufacturer’s protocol . The cDNA was then amplified and barcoded using the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Life Technologies 4475485). The Ion PI™ Chip Kit v2 BC (Life Technologies) 4484270) was then loaded using the Ion Chef™ System (Life Technologies 4484177) with the Ion PI™ IC 200 Kit (Life Technologies 4488377). Afterwards, the chips were run on the Ion Proton™ System for Next-Generation Sequencing (Life Technologies 4476610) using the Ion PI™ IC 200 Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Description |
11.18
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| Data processing |
Basecalling was performed with Ion Torrent Suite 5.0.5
After quality control for adapter contamination and trimming, Fastq files were mapped on human genome ( Hg19) by by combinations of Top Tophat and Bowtie2 softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Jan 04, 2019 |
| Last update date |
Oct 11, 2019 |
| Contact name |
Naftali Kaminski |
| Organization name |
Yale University
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| Street address |
1 Gilbert street
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE124685 |
mRNA Sequencing to identify transcriptional changes in early and late stages of lung in human Idiopathic Pulmonary Fibrosis |
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| Relations |
| BioSample |
SAMN10695371 |
| SRA |
SRX5206550 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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