|
| Status |
Public on Jan 12, 2017 |
| Title |
Control SL71048 |
| Sample type |
SRA |
| |
|
| Source name |
FFPE lung tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
tissue: lung
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Five 10-µm slices of the whole lung tissue were cut from FFPE block, excess paraffin was trimmed and slices were treated twice with 1ml xylene for 30 min at 62°C, then washed twice with 100% ethanol. Total RNA was isolated by using MasterPure kit (Epicentre Biotechnologies). Ribosomal RNA was removed by using the RiboZero rRNA removal kit (Epicentre)
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol from 1ug of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava and bcl2fastq-1.8.3 was used for base calling
RNAseq reads were mapped to the hg19 genome assembly using Tophat version v2.0.6 allowing for multiple hits.
Cufflinks version 2.2.0 was used to calculate the FPKMs
Cuffdiff was used to compare FPKMs between groups and genes with a false discovery rate (FDR) adjusted p<0.05 were identified as differentially expressed genes (DEGs).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples except SL32681. this sample was excluded from the final analysis due to low reads number and low mapping rate. According to that raw files for SL32681 were not uploaded.
|
| |
|
| Submission date |
Jun 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Naftali Kaminski |
| E-mail(s) |
naftali.kaminski@yale.edu
|
| Organization name |
Yale School of Medicine
|
| Department |
Pulmonary, Critical Care and Sleep Medicine
|
| Street address |
300 Cedar St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE83717 |
Identification and validation of differentially expressed transcripts by RNA-Sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis |
|
| Relations |
| BioSample |
SAMN05292517 |
| SRA |
SRX1875166 |
