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Status |
Public on May 01, 2024 |
Title |
WT |
Sample type |
SRA |
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Source name |
midbrain
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Organism |
Mus musculus |
Characteristics |
tissue: midbrain strain: C57BL/6 genotype: WT
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
E13.5
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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
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Submission date |
Feb 20, 2024 |
Last update date |
May 01, 2024 |
Contact name |
Yingying Zhao |
E-mail(s) |
zhao_yingying@gibh.ac.cn
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Organization name |
Guangzhou Institutes of Biomedicine and Health
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Department |
Chinese Academy of Sciences Guangzhou Branch
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Street address |
Kaiyuan Avenue
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City |
Guangzhou |
ZIP/Postal code |
510530 |
Country |
China |
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Platform ID |
GPL19057 |
Series (1) |
GSE256210 |
Autism patient derived SHANK2BY29X mutation affects ALDH1A1 negative dopamine neuron development |
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Relations |
BioSample |
SAMN40008332 |
SRA |
SRX23678606 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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