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Status |
Public on Mar 27, 2024 |
Title |
WT rep2 |
Sample type |
SRA |
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Source name |
bone marrow B220+ cells
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Organism |
Mus musculus |
Characteristics |
cell type: bone marrow B220+ cells genotype: WT
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the TRIzol reagent. RNA quality and quantity were determined using a Nano Drop and Agilent 2100 bioanalyzer. Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSEQ platform.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12). Differential expression was performed using DESeq2 (version 1.4.5). Assembly: GCF_000001635.26_GRCm38.p6 Supplementary files format and content: WT_and_PELI2_CKO_genes.fpkm.anno.txt: Tab-delimited text file includes FPKM values for each Sample.
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Submission date |
Apr 04, 2023 |
Last update date |
Mar 27, 2024 |
Contact name |
Yan Xu |
E-mail(s) |
[email protected]
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Organization name |
Shandong University
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Street address |
No. 44 Wenhua West Road
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City |
Jinan City |
ZIP/Postal code |
250014 |
Country |
China |
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Platform ID |
GPL17021 |
Series (1) |
GSE228984 |
Effect of PELI2 deficiency on the gene expression of bone marrow B220+ cells |
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Relations |
BioSample |
SAMN34072407 |
SRA |
SRX19868736 |
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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