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Sample GSM8089328 Query DataSets for GSM8089328
Status Public on May 01, 2024
Title PC1_rep1
Sample type SRA
 
Source name PC1
Organism Homo sapiens
Characteristics cell line: PC1
genotype: SHANK2 Mutation
Extracted molecule polyA RNA
Extraction protocol RNA-seq: To extract the total RNAs, organoids were collected and lysed with 1 ml TRIzol reagent (MRC, TR118-200), followed by adding 200 μL chloroform. After centrifugation (14,000 ×g for 10 min at 4°C), the total RNAs in the supernatant were precipitated with isopropanol. 1ug RNAs were subjected to RNA-seq library construction.
scRNA-seq: Brain organoids at D21 and D30 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153).
RNA-seq: RNA Sequencing libraries were prepared according to the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme).
scRNA-seq: 3'-library was constructed using Chromium Single Cell Reagent Kits v2 (10X GENOMICS).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description D9
Data processing RNA-seq: Data quality control for raw data using FastQC (v0.11.4)
RNA-seq: Preprocessing of raw reads using cutadapt (version 2.6)
RNA-seq: Read aligned to the human reference genome using STAR (version 2.7.10a)
RNA-seq: Quantification of gene expression of RNA-seq using RSEM (v1.2.28)
scRNA-seq: Data quality control for raw data using FastQC (v0.11.4)
scRNA-seq: Read aligned to the human reference genome using STARsolo (version 2.7.10a)
scRNA-seq:The BAM files in the results of STARsolo were visualized using IGV(2.8.9)
Assembly: hg38
Supplementary files format and content: RNA-seq: tab-delimited table containing gene count values, TPM values, FPKM values
Supplementary files format and content: RNA-seq: tab-delimited table containing isoform count values, TPM values, FPKM values
 
Submission date Feb 20, 2024
Last update date May 01, 2024
Contact name Yingying Zhao
E-mail(s) zhao_yingying@gibh.ac.cn
Organization name Guangzhou Institutes of Biomedicine and Health
Department Chinese Academy of Sciences Guangzhou Branch
Street address Kaiyuan Avenue
City Guangzhou
ZIP/Postal code 510530
Country China
 
Platform ID GPL18573
Series (1)
GSE256210 Autism patient derived SHANK2BY29X mutation affects ALDH1A1 negative dopamine neuron development

Supplementary file Size Download File type/resource
GSM8089328_PC1_rep1.genes.results.gz 2.6 Mb (ftp)(http) RESULTS
GSM8089328_PC1_rep1.isoforms.results.gz 4.5 Mb (ftp)(http) RESULTS
Raw data are available in SRA

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