|
| Status |
Public on Oct 09, 2023 |
| Title |
175_22_CTRL (reanalysis) |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
disease: Control (donor)
subject: 175
surface density: 0.0146
tissue percentage: 29.5
terminal bronchioles/ ml: 3.6
smoking ever: yes
age transplant: 60
gender: Male
|
| 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. 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, 4 cores were randomly selected per lung.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using miRNeasy mini kit (Qiagen) from each core according to the manufacturer 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. The cDNA was then amplified and barcoded using the Ion Xpress RNA-Seq Barcode 1-16 Kit (Life Technologies 4475485). The Ion 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| 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 (Hg38) by combinations of Tophat and Bowtie2 softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1.
Assembly: hg38
Supplementary files format and content: Matrix table with FPKM gene counts for every gene and every sample.
|
| |
|
| Submission date |
Aug 24, 2023 |
| Last update date |
Oct 09, 2023 |
| Contact name |
John McDonough |
| Organization name |
Yale School of Medicine
|
| Street address |
300 Cedar St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE239897 |
Mucosal immune alterations at the early onset of tissue destruction in Chronic Obstructive Pulmonary Disease |
|
| Relations |
| Reanalysis of |
GSM5583914 |
| BioSample |
SAMN21465293 |
| SRA |
SRX12216859 |
