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| Status |
Public on Jun 04, 2020 |
| Title |
HCT116_spike-in_40 |
| Sample type |
SRA |
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| Source name |
HCT116 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol and treated with RQ1 DNase (Promega) to remove DNA
Total RNA was partially fragmented with RNase T1. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads. 3’ adaptor was added to purified mRNAs, followed by reverse transcription performed with RT primer harboring 5' adaptor sequence and randomized hexamer. The cDNAs were purified and PCR amplified for library construction for Illumina HiSeq X Ten system.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
processed data file: length_statistic.txt
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| Data processing |
NextSeq Control Software 1.4 was used for basecalls.
Reads were trimmed for polyG sequence, and polyA sequence shorter than 11nt were discarded. PolyA lengths were counted from basecalls.
Sequenced reads were trimmed for polyA and adaptor sequence, and reads longer than 20nt were mapped to GRCH38 whole genome using tophat2 with parameters -a 8 -m 0 -g 2 --microexon-search --report-secondary-alignments --read-edit-dist 4 N 2 --b2-N 1
the median of polyA sequence length was calculated of each gene.
Genome_build: GRCH38
Supplementary_files_format_and_content: txt file, the median distribution of polyA length of genes in each sample
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| Submission date |
Sep 03, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
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| Department |
Center for Genome Analysis
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| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE84287 |
A novel method for genome-wide profiling of poly(A)-tail lengths |
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| Relations |
| BioSample |
SAMN12676133 |
| SRA |
SRX6792725 |
| 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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