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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 18, 2024 |
| Title |
Mouse cortex, WT, E15.5, Rep1 |
| Sample type |
SRA |
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| Source name |
Mouse, Cortex, CDYLloxp/loxp
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| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse, Cortex, CDYLloxp/loxp
cell line: NA
cell type: whole cortex
genotype: CDYLloxp/loxp
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8-2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150 bp read length).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
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| Description |
Mouse RNA-Seq.csv
WT_1
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| Data processing |
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg38 & mm38
Supplementary files format and content: Read counts in .csv files
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| Submission date |
Sep 04, 2024 |
| Last update date |
Sep 18, 2024 |
| Contact name |
Liang-Yu Ni |
| E-mail(s) |
nly123@pku.edu.cn
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| Phone |
18075062311
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| Organization name |
Peking University
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| Street address |
Peking university Health Science center
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
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| Platform ID |
GPL34328 |
| Series (1) |
| GSE276320 |
Chromodomain protein CDYL confers forebrain identity to human cortical organoids by inhibiting neuronatin [RNA-seq] |
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| Relations |
| BioSample |
SAMN43496461 |
| Supplementary data files not provided |
| Raw data are available in SRA |
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