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Sample GSM2186531 Query DataSets for GSM2186531
Status Public on Jun 19, 2017
Title HESC_SIO_3
Sample type SRA
 
Source name hESC derived organoids
Organism Homo sapiens
Characteristics origin: hESC derived organoids
time in culture: 4 weeks
genotype: wt
Growth protocol hESCs were subjected to a 3 day activin endoderm differentiation, followed by 4 days of posterior endoderm differentiation in the presence of CHIR and FGF4. After that they were grown in matrigel beads for 4 weeks adding CHIR, EGF and B27 as a supplement for samples MCH1 and 2. Samples MCW1 & 2 were differentiated according to the protocol publisjed by Spence et al. Nature 2011.
Extracted molecule total RNA
Extraction protocol organoids were obtained by dislodging the matrigel beads pipetting up and down. Then, total RNA was extracteed with the Absolutely RNA nanoprep Agilent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for low-quality sequences and adapter sequences by using cutadapt with parameters "-O 5 -m 45 -q 10"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene
 
Submission date Jun 03, 2016
Last update date May 15, 2019
Contact name Shuibing Chen
E-mail(s) shuibing.chen@gmail.com
Phone 2127465431
Organization name Weill Cornell Medical College
Department Surgery
Street address A 827B, 1300 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL20301
Series (1)
GSE82207 Total RNA sequencing of WT intestinal orgaonids.
Relations
BioSample SAMN05200859
SRA SRX1818609

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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