|
| Status |
Public on Aug 03, 2020 |
| Title |
He109: TGF 5 ng/ml |
| Sample type |
SRA |
| |
|
| Source name |
Donor 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Esophagus
cell type: Fibroblast
treatment: TGF 5 ng/ml
|
| Treatment protocol |
Cells pre-starved to serum/growth factor free smooth muscle cell medium with 100u/ml penicilin and 100ug/ml streptomicin. After 16 hours pre-starvation, cells were treated with the specified doses of cytokine diluted on starvation medium, for 24 hours
|
| Growth protocol |
Cells grown and plated for experiments in smooth muscle cell medium supplemented with 2% FBS, 1% SMGS, 100u/ml penicilin and 100ug/ml streptomicin (ScienCell, CA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeasy Micro Kit (Qiagen 217084)
200ng RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490L) prior to NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB E7760L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells
|
| |
|
| Submission date |
Jan 12, 2020 |
| Last update date |
Aug 03, 2020 |
| Contact name |
Mario J. Cabrero Manresa |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California San Diego
|
| Lab |
Aceves laboratory
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE143482 |
Comparison of the LIGHT and TGF-B1 induced transcriptomes in esophageal FBL |
|
| Relations |
| BioSample |
SAMN13830367 |
| SRA |
SRX7543980 |
