|
Status |
Public on Jun 19, 2017 |
Title |
HESC_CO_4 |
Sample type |
SRA |
|
|
Source name |
hESC derived Colonic organoids
|
Organism |
Homo sapiens |
Characteristics |
origin: hESC derived Colonic 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 |
SAMN05200858 |
SRA |
SRX1818608 |