|
| Status |
Public on Jul 20, 2015 |
| Title |
Mes_TNF_1hr_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
small airway epithelial cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tgf-beta treatment: Yes
tnf-alpha treatment: 1 hour
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total cellular RNA was extracted using either RNAqueous™ phenol-free total RNA isolation kits (Life Technologies, CA) or Quick-RNA MiniPrep kits (ZYMO Research) according to the manufacture's recommendations
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Sample Preparation kit under conditions prescribed by the manufacturer (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped with Tophat v2.0.10 with options -p 10 -r 170 --mate-std-dev 40. Reference was hg19.
Reads mapping to genes were counted with HTSeq0.5.4p5/htseq-count
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: excel file with raw read counts per gene
|
| |
|
| Submission date |
Sep 08, 2014 |
| Last update date |
May 22, 2019 |
| Contact name |
Allan Brasier |
| E-mail(s) |
abrasier@wisc.edu
|
| Phone |
409-772-2824
|
| Organization name |
University Texas Medical Branch
|
| Department |
Medicine
|
| Street address |
301 Univ. Blvd
|
| City |
Galveston |
| State/province |
TX |
| ZIP/Postal code |
77555-1060 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE61220 |
Analysis Of The TGFb-Induced Program In Primary Airway Epithelial Cells Shows Essential Role Of NF-kB/RelA Signaling Network In Type II Epithelial Mesenchymal Transition |
|
| Relations |
| BioSample |
SAMN03023941 |
| SRA |
SRX696332 |
