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Sample GSM4188828 Query DataSets for GSM4188828
Status Public on Nov 23, 2019
Title 15CON_re-used
Sample type SRA
Source name cerebral organoids
Organism Homo sapiens
Characteristics cell type: Human iPSC derieved cerebral organoids
age: 6 months of differentiation
diagnosis: healthy control
Growth protocol Lancaster protocol (
Extracted molecule total RNA
Extraction protocol Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description sample_20
Data processing Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample
Submission date Nov 22, 2019
Last update date Nov 27, 2019
Contact name Annie Kathuria
Organization name Mass Gen Hospital
Street address 185 cambridge street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platform ID GPL24676
Series (1)
GSE140843 Total RNA sequencing for human induced pluripotent derived cerebral organoids [controls only]
Alternative to GSM3954326
BioSample SAMN13353025
SRA SRX7202310

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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