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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 08, 2024 |
| Title |
S4 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
srain: C57BL/6
tissue: heart
gender: female
genotype: TECRL-/-
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| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were removed, flash fronzen in liquid nitrogen and RNA was extracted using Trizol reagant.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.6.1p2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (v1.26.0). Pvalue < 0.05 and absolute log2 (fold change) > 0.58 were set as the threshold for significantly differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
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| Submission date |
Dec 17, 2021 |
| Last update date |
Feb 08, 2024 |
| Contact name |
Shujia Lin |
| E-mail(s) |
linshujia96@sjtu.edu.cn
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| Organization name |
Shanghai Children’s Hospital
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| Street address |
No. 355 Luding Road, Shanghai, China
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| City |
Shanghai |
| ZIP/Postal code |
200062 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE191112 |
RNA-sequencing analysis reveals the different gene expression in male and female wild type and TECRL knockout mice. |
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| Relations |
| BioSample |
SAMN24155267 |
| SRA |
SRX13435920 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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