|
| Status |
Public on Sep 18, 2019 |
| Title |
Ctrl rep3 |
| Sample type |
SRA |
| |
|
| Source name |
anonymous newborn
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: fresh umbilical cords
condition: cultured in the control medium containing potassium chloride
stimulation duration: 24hr
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA isolation was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. Polyadenylated mRNA was further selected using Poly(A) Beads (NEXTflexTM).
Libraries were generated using the NEXTflexTM Rapid RNA-seq Kit (Bio Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
STAR version 2.4.2a was used to align sequenced reads.
Picard AddOrReplaceReadGroups (v1.98) was used to add read groups to the BAM files, which were sorted with Sambamba v0.4.5.
Transcript abundances were quantified with HTSeq-count, version 0.6.1p1, using the union mode.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files contains the raw counts per transcript for each sample.
|
| |
|
| Submission date |
Jun 09, 2019 |
| Last update date |
Sep 18, 2019 |
| Contact name |
Caroline Cheng |
| Organization name |
Universitair Medisch Centrum Utrecht
|
| Department |
Nephrology and Hypertension
|
| Street address |
Heidelberglaan 100
|
| City |
Utrecht |
| State/province |
Nederland |
| ZIP/Postal code |
3584 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE132410 |
Indoxyl sulfate stimulates angiogenesis by regulating reactive oxygen species production via CYP1B1 |
|
| Relations |
| BioSample |
SAMN11996103 |
| SRA |
SRX6021967 |
