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Sample GSM1590874 Query DataSets for GSM1590874
Status Public on May 07, 2015
Title Organoid 7 derived from patient 31
Sample type SRA
Source name Colonic Adenocarcinoma derived organoid
Organism Homo sapiens
Characteristics sample type: Organoid culture
tissue: Colonic Adenocarcinoma derived organoid
protocol: CEL-seq (Hashimshony et al., Cell reports 2012)
subject: patient 31
Growth protocol Organoids derived from colorectal cancer cases were resuspended in matrigel. Subseqeuntly, droplets of matrigel (10 ul), were put in a dish. After letting the Matrigel solidy, Human Intestinal Stem Cell medium (HISC) (Basal culture medium with 50% Wnt conditioned medium, 20% R-Spondin conditioned medium, 10% Noggin conditioned medium, 1 x B27, 1,25 mM n-Acetyl Cysteine, 10 mM Nicotinamide, 50 ng/ml human EGF, 10 nM Gastrin, 500 nM A83-01, 3 uM SB202190, 10 nM Prostaglandine E2 and 1 x Primocin (Vivogen)) minus Wnt was added and the cells were incubated at 37 oC.
Extracted molecule total RNA
Extraction protocol For single organoid mRNA sequencing, organoids were hand-picked and deposited into trizol (life technologies).
The RNA was extracted using chloroform and precipitated with iso-propanol. The RNA-pellet was then processed using the CEL-seq protocol (Hashimshony et al., 2012) and sequenced on an Illumina Nextseq using 75bp paired end sequencing.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
Description mRNA
Data processing After sequencing, read 1 was aligned to the hg19 RefSeq human transcriptome downloaded from the UCSC genome browser (Meyer et al., 2013) using bwa (Li and Durbin, 2010) with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL-seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Samples with less than 500.000 reads were discarded after which the remaining samples were rpm normalized.
Genome_build: hg19
Supplementary_files_format_and_content: mRNA count data for all samples, each column is a sample each row is a gene
Submission date Jan 23, 2015
Last update date May 15, 2019
Contact name Lennart Kester
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
Platform ID GPL18573
Series (1)
GSE65253 Prospective derivation of a 'Living Organoid Biobank' of colorectal cancer patients
BioSample SAMN03292611
SRA SRX852124

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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