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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 05, 2021 |
Title |
WT D0 rep2 |
Sample type |
SRA |
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Source name |
liver
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Organism |
Mus musculus |
Characteristics |
strain: B6D2F1/Crl tissue: liver age: 8-12 week gender: male genotype: wild type ccl4-treated time: Day 0
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Treatment protocol |
Once or repeated injections of CCl4 (Sigma) were performed respectively to produce acute and long-term liver injuries. Corn oil was used to dilute CCl4 (Sigma) to form 40% CCl4 and intraperitoneal injected into 9-12-week-old male mice at 2 ml kg-1 body mass.
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Extracted molecule |
total RNA |
Extraction protocol |
Isolate mice liver and remove gall bladder. Cut the liver into small pieces and place them in RNAlater (Thermo). Liver tissues were ground in liquid nitrogen after added lysis buffer. Then extract the RNAs with mirVana™ miRNA Isolation Kit (Thermo, AM1561). Isolate 14-40 nt RNAs by PAGE. Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’ -adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Pretreated total RNA of each sample was taken for tRF & tiRNA-seq library preparation. Library preparation procedures included: 1) 3’-adapter ligation; 2) 5’-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~134-160bp PCR amplified fragments (corresponding to ~14-40nt small RNAs). The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results, and used for sequencing on the instrument. tRF-seq
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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Description |
tRNA derived fragments
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Data processing |
Basecalling was performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8) Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5’, 3’-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. tRNA sequences of cytoplasmic were downloaded from GtRNAdb. tRNA sequences of mitochondrial were predicted with tRANscan-SE software. To generate the mature tRNA libraries, we removed the predicted intronic sequences (if present) and added an additional 3’-terminal “CCA” to each tRNA. To generate the precursor tRNA libraries, we included 40 nucleotides of flanking genomic sequence on either side of the original tRNA sequence. The abundance of tRF & tiRNA is evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). For each tRF & tiRNA, estimated the expression level using the mapped reads number and given an ID. Then the tRF & tiRNA are filtered if CPM less than 20 in all samples. tRFdb & GtRNAdb Supplementary_files_format_and_content: [Aligned Results, txt]: The trimmed reads (14-40nt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. [Trimmed Sequence Data, fastq]: Subsequently, the 5’, 3’-adapter sequence are trimmed from the clean reads by cutadapt and the reads with lengths shorter than 14nt or longer than 40 were discarded. The trimmed reads are collapsed into FASTA format. The identifier line, which begin with‘>’, gives a name that are divided into three parts by underline. The first part of the character indicate sample name, the second part of the integer indicate rank the i-th out of all sequences, the third part is made up of character and integer. For example, the identifier line ‘>samplei_1_x123’, the character ‘samplei’indicate sample name, the integer ‘1’ indicate rank the first out of all sequences, the character ‘x’as an identifier and the subsequent integer ‘123’indicate the sequence have occur 123 time. [xlsx files]: the data of expressed tRFs and differentially expressed tRFs, and their normalized data.
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Submission date |
Feb 03, 2020 |
Last update date |
Jun 05, 2021 |
Contact name |
Sunyang YING |
E-mail(s) |
yingsunyang@ioz.ac.cn
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Phone |
13021027424
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Organization name |
Chinese Academy of Sciences
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Department |
State key laboratory of stem cell and reproductive biology
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Lab |
Zhou
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Street address |
1-5 Beichen West Road, Chaoyang District, Beijing
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City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100101 |
Country |
China |
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Platform ID |
GPL19057 |
Series (1) |
GSE144698 |
tRF-seq landscapes the variation of tRNA derived fragments after mouse liver injury |
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Relations |
BioSample |
SAMN13976819 |
SRA |
SRX7667771 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4293944_2_2.fa.gz |
2.5 Mb |
(ftp)(http) |
FA |
GSM4293944_Alignment_2_2.txt.gz |
281.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
Processed data provided as supplementary file |
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