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| Status |
Public on Jun 13, 2019 |
| Title |
HEK293_1ug_R2 |
| Sample type |
SRA |
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| Source name |
HEK293 cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: HEK293 cell line
rna input: 1ug input of total RNA
library construction method: TruSeq
spike-in: no
strain: --
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| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA library construction strategies of Illumina TruSeq, our CAS-seq and our previous 10ng-seq were utilized. Details were in the online method of our article.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
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| Description |
small RNA-seq of HEK293 cell lines detected by TruSeq with 1ug input of total RNA, technical replicate 2
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| Data processing |
The raw reads in fastq files were trimmed to 50nt, then these reads were quality filtered and collapsed with FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Read sequences longer than 17 nt after adapter trimming were aligned to the reference genome (hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey) with Bowtie allowing no mismatch. The perfectly mapped reads were assigned to known miRNAs, rRNAs, sn/snoRNAs and tRNAs successively. The reads that couldn’t be mapped to these known small RNAs were used to predict piRNAs, endo-siRNAs and xiRNAs successively. For the reads that could be mapped to multiple genome loci, we used the program reallocate (http://www.smallrnagroup-mainz.de/software.html) to apportion the read counts of multiply mapped sequences according to their local transcription level calculated by uniquely mapped sequences within 5 kb flanking regions. The reads with low sequence complexity (>=75% of the sequence consists of one nucleotide) were removed from the datasets. The relative abundance of these small RNAs was normalized as reads assigned per million genome mapped reads (RPM).
Genome_build: hg38 for human, mm10 for mouse, macFas5 for crab-eating monkey
Supplementary_files_format_and_content: sequence of miRNA, endo-siRNA, piRNA and their expression (RPM) in each sample were provided
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| Submission date |
Feb 22, 2017 |
| Last update date |
Jun 13, 2019 |
| Contact name |
Ligang Wu |
| E-mail(s) |
lgwu@sibcb.ac.cn
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| Phone |
+86-21-54921321
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| Organization name |
Chinese Academy of Sciences
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| Department |
Shanghai Institutes for biological Sciences
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| Lab |
Wu ligang
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE95218 |
Single-cell CAS-seq reveals a class of short PIWI-interacting RNAs in human oocytes |
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| Relations |
| BioSample |
SAMN06392704 |
| SRA |
SRX2582561 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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