|
| Status |
Public on Jun 01, 2017 |
| Title |
136b |
| Sample type |
SRA |
| |
|
| Source name |
full thickness intestine
|
| Organism |
Homo sapiens |
| Characteristics |
age: 2 month
status: unfed
diagnosis: necrotizing enterocolitis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Full thickness section of intestine was removed, and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer.
Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing QC: FastQC
Trimming of reads for quality: Trimmomatic
Alignment: STAR
Read binning: Htseq-count
Differential Gene Expression: RUVSeq, edgeR
Genome_build: GRCh38.p3 (Gencode 24)
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values, counts, DE statistics and Annotation
|
| |
|
| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tracy Grikscheit |
| E-mail(s) |
tgrikscheit@chla.usc.edu
|
| Organization name |
Children's Hospital Los Angeles
|
| Street address |
4650 Sunset Boulevard Mailstop#100
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90027 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE82147 |
Genome wide impact of loss of mechanoluminal stimulation on neonatal intestine |
|
| Relations |
| BioSample |
SAMN05196252 |
| SRA |
SRX1816601 |
