|
| Status |
Public on Nov 22, 2017 |
| Title |
Pa213_basal |
| Sample type |
SRA |
| |
|
| Source name |
Cardiac fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: right atrial appendage biopsies
hour: cultured for 24 hours
treatment: No treatment
|
| Treatment protocol |
Cardiac fibroblasts were cultured in serum-free media for at least 16 hours prior to treatment. They were further treated with either TGFB1 or IL11.
|
| Growth protocol |
Growth media contained DMEM (Life technologies) supplemented with 20% fetal bovine serum (FBS, Hyclone) and 1% penicillin/streptomycin (Gibco) . When the cells grew to 80% confluence, they were passaged using standard trypsinization techniques. Fresh media was renewed every 2-3 days to remove cell debris and to maintain a physiological pH.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from human cardiac fibroblasts with RNeasy column kit (Qiagen).
Libraries were constructed with TruSeq Stranded mRNA Library Prep kit (Illumina) using 0.8µg of total RNA. RNA-seq, barcoded libraries were multiplexed and sequenced as paired-end reads on Illumina NextSeq 500 platform using NextSeq High output 150 cycles kit across 4 lanes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Raw_counts_IL11_Basal_6patients.txt; Raw_counts_IL11_Basal_combined.txt
|
| Data processing |
Preprocesing: The adaptor sequences and low quality reads/bases were trimmed using Trimmomatic v0.36 and the read quality was assessed using FastQC v0.11.5
Alignment: High-quality reads were mapped to Ensembl human GRCh38 v86 ref or mouse GRCm38 v86 reference genome using STAR v2.5.2b . Only uniquely mapped reads were reported from STAR by setting the parameter —outFilterMulrimapNmax 1
Read summarization: Strand-specific raw counts of uniquely mapped reads (paired-end) were summarized with featureCounts [Ref:PMID: 24227677] to get gene-level quantification of genomic features
Differential expression analysis: Differential expression (DE) was performed with DESeq2 v1.14.1 by using raw read counts from featureCounts. We performed a minimal pre-filtering to remove genes that have no reads or only 1 read across all samples. Sample IDs were included as co-variates in DESeq2 design formula to remove batch effect due to samples. Basal condition was always used as the reference level for pair wise comparison. Shrinkage MA-plot was generated and points will be colored red if adjusted p value was less than 0.1.
Genome_build: GRCh38 v86
Supplementary_files_format_and_content: Raw_counts_IL11_Basal_4patients.txt: tab-delimited file with raw gene expression counts for each gene and sample for IL11 vs Basal RNA-seq 4 patients; Raw_counts_TGFB1_Basal_4patients.txt: tab-delimited file with raw gene expression counts for each gene and sample for TGFB1 vs Basal RNA-seq 4 patients; Raw_counts_IL11_Basal_6patients.txt: tab-delimited file with raw gene expression counts for each gene and sample for IL11 vs Basal RNA-seq 6 patients;Raw_counts_IL11_Basal_combined.txt: tab-delimited file with raw gene expression counts for each gene and sample for IL11 vs Basal RNA-seq combined;
|
| |
|
| Submission date |
Mar 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sonia Chothani |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke-NUS school of medicine
|
| Lab |
Prof. Stuart Cook
|
| Street address |
8 College Road
|
| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE96975 |
Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis [human] |
| GSE97117 |
Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis |
|
| Relations |
| BioSample |
SAMN06638159 |
| SRA |
SRX2664176 |
