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| Status |
Public on Jun 22, 2022 |
| Title |
CD_P2_RNAseq |
| Sample type |
SRA |
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| Source name |
CD, P18
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: CD
developmental stage: pregnant (day18)
tissue: kidney
age: two-month
Sex: female
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| Treatment protocol |
pregnancy
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| Growth protocol |
6-8 week-old female rats
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| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN AllPrep DNA/RNA/miRNA Universal Kit protocol
RRBS: NuGen Ovation RRBS Methyl-Seq protocol with QIAGEN EpiTech Fast DNA Bisulfite Kit for bisulfite conversion. RNA-seq NuGen Universal RNA-seq library protocol for rat.
RRBS: Bisulfite-seq (reduced representation). RNA-seq: total stranded RNA with ribosomal RNA depletion.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
stranded, rRNA depletion
RNAseq_counts.csv
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| Data processing |
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RRBS fastq header contained 6 nt index sequence and 6 random nt (N6 NuGen RRBS duplicate information). Adaptors and low quality reads were trimmed with Trim_galore v0.4.5. and reads containing adapter were discarded. Following adaptor and quality trimming, the fastq files were further trimmed with NuGEN custom python script trimRRBSdiversityAdaptCustomers.py. Potential PCR or optical duplicates were removed using NuGEN python script Nudup.py
Trimmed reads was aligned to rat genome Rnor_6.0, allowing for 1 mismatch and retaining only uniquely mapped reads. Bam files were generated using Bismark v0.16.34. CpG coverage reports were generated using MethylKit (v1.16.1) from bam files.
RNA-seq fastq files were trimmed with trimmomatic, aligned to rat genome with STAR (v2.5.2), and reads were qunatified with Htseq_count (v0.6.1). Gene differential expression was analyzed using edgeR (v3.26.8) with FPKM threshold of 1.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Processed methylation data is uploaded as CpG reports in txt format. Process RNA-seq data is uploaded raw count matrix in csv format.
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| Submission date |
Apr 26, 2021 |
| Last update date |
Jun 22, 2022 |
| Contact name |
Charles Wang |
| E-mail(s) |
chwang@llu.edu
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| Phone |
(909) 558-4325
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| Organization name |
Loma Linda University
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| Department |
Department of Basic Sciences
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| Lab |
Center for Genomics
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| Street address |
11021 Campus Street
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| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92350 |
| Country |
USA |
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| Platform ID |
GPL25029 |
| Series (1) |
| GSE173380 |
Illumina NGS RNA-seq and RRBS Sequencing on Rat Kidney |
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| Relations |
| BioSample |
SAMN18875792 |
| SRA |
SRX10682985 |
| 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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