|
| Status |
Public on Oct 28, 2020 |
| Title |
colonsigmoid1_RNA |
| Sample type |
SRA |
| |
|
| Source name |
colon (sigmoid)
|
| Organism |
Homo sapiens |
| Characteristics |
technology: RNA-seq
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from tissue samples with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA-seq libraries were constructed using illumina Truseq stranded mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Reads count was generated by featureCounts.
Normalized RPKM values were generated by edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM matrix
|
| |
|
| Submission date |
Apr 09, 2020 |
| Last update date |
Oct 28, 2020 |
| Contact name |
Xiaolong Cui |
| E-mail(s) |
xiaolong.cui@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Department of Preventive Medicine
|
| Street address |
680 N Lake Shore Drive
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE144530 |
A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation |
|
| Relations |
| BioSample |
SAMN14569954 |
| SRA |
SRX8088943 |
