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Sample GSM2184758 Query DataSets for GSM2184758
Status Public on Jun 01, 2017
Title 117a
Sample type SRA
 
Source name full thickness intestine
Organism Homo sapiens
Characteristics age: 3 month
status: fed
diagnosis: focal intestinal perforation
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 SAMN05196249
SRA SRX1816598

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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