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Sample GSM3954336 Query DataSets for GSM3954336
Status Public on Apr 01, 2020
Title 25BPI.2
Sample type SRA
 
Source name cerebral organoids
Organism Homo sapiens
Characteristics diagnosis: Bipolar Disorder
cell type: Human iPSC derived cerebral organoids
state: 6 months of differention
Treatment protocol None
Growth protocol Lancaster protocol (https://www.nature.com/articles/nature12517)
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
 
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 Jul 18, 2019
Last update date Oct 10, 2022
Contact name Annie Kathuria
E-mail(s) kathu003@gmail.com
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)
GSE134497 Total RNA sequecing for human induced pluripotent derived cerebral organoids
Relations
BioSample SAMN12315331
SRA SRX6466845

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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