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Sample GSM8089332 Query DataSets for GSM8089332
Status Public on May 01, 2024
Title WT
Sample type SRA
 
Source name midbrain
Organism Mus musculus
Characteristics tissue: midbrain
strain: C57BL/6
genotype: WT
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 single cell
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description E13.5
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 GPL19057
Series (1)
GSE256210 Autism patient derived SHANK2BY29X mutation affects ALDH1A1 negative dopamine neuron development
Relations
BioSample SAMN40008332
SRA SRX23678606

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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