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| Status |
Public on Jun 20, 2021 |
| Title |
AA1 |
| Sample type |
SRA |
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| Source name |
chondrocytes
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| Organism |
Mus musculus |
| Characteristics |
genotype: control
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| Extracted molecule |
total RNA |
| Extraction protocol |
fresh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.
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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 |
Basecalls performed using Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM
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| Submission date |
Jun 14, 2021 |
| Last update date |
Jun 20, 2021 |
| Contact name |
Mingliang Ji |
| E-mail(s) |
jimingliang558@outlook.com
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| Organization name |
Zhongda Hospital,school of medicine, southeast university
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| Street address |
Dingjiaqiao Road 87
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210009 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE178091 |
The long noncoding RNA ELDR serves as an epigenetic driver in aging and injury-induced chondrocyte senescence [chondrocytes part2] |
| GSE178092 |
Dynamic chromatin accessibility tuning of long noncoding RNA ELDR accelerates chondrocyte senescence and osteoarthritis |
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| Relations |
| BioSample |
SAMN19692020 |
| SRA |
SRX11136748 |
| 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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