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Sample GSM4635574 Query DataSets for GSM4635574
Status Public on Oct 12, 2020
Title VU13_Col_R3
Sample type SRA
 
Source name Colon
Organism Homo sapiens
Characteristics Sex: Female
race: Caucasian
age: 33
sequencer: NovaSeq 6000
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Micro® kit (Ambion) as described in May-Zhang et al. Jove 2018. Briefly, 1-3 Arcturus XT laser capture caps were pooled for each sample after collecting sufficient quantities of enteric ganglia. Lysates were incubated at 26C for 30 min in 250uL of Buffer RLT with repeated brief vortexing. Lysates were frozen at -80C and stored for up to 2 months before isolating RNA.
cDNA libraries were prepared using the Takara SMARTer kit according to llumina's instructions. Libraries were sequenced using the NovaSeq as 1x100bp single-end reads. Each sample had a mean depth of approximately 138 million reads and a mean alignment rate of 99.01%.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Base calls and demultiplexing were performed with Illumina’s bcl2fastq software
RNA-Seq reads were then aligned to their respective Ensembl release 76 human or mouse top-level assemblies with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned, unambiguous reads by Subread:featureCount version 1.4.5
Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.13.
Sequencing performance was then assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
Genome_build: Ensembl release 76 human assembly
Supplementary_files_format_and_content: counts matrix
 
Submission date Jun 24, 2020
Last update date Oct 12, 2020
Contact name E Michelle Southard-Smith
E-mail(s) michelle.southard-smith@vanderbilt.edu
Phone 615-293-4236
Organization name Vanderbilt University Medical Center
Department Medicine, Genetic Medicine
Street address 2215 Garland Ave,
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL24676
Series (2)
GSE153198 Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ [Human Enteric Ganglia]
GSE153202 Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ
Relations
BioSample SAMN15361736
SRA SRX8610801

Supplementary file Size Download File type/resource
GSM4635574_vu13_col_r3.GCCGTTT-TTGAGGC.gene_counts.txt.gz 5.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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