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| Status |
Public on Oct 13, 2016 |
| Title |
CLIP-ALKBH1-replicate3 |
| Sample type |
SRA |
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| Source name |
CLIP-ALKBH1-replicate3
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
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| Growth protocol |
HeLa cell line was purchased from ATCC (CCL-2) and grown in DMEM (Gibco, 11965) media supplemented with 10% FBS (Gibco, 10438-026) and 1× Pen/Strep (Gibco, 15140).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA Clean & Concentrator was used to further clean the final recovered RNA sample (Zymo Research) followed by library construction with small-RNA sample preparation kit (New England BioLabs Inc) prior to the cDNA reverse transcription. To avoid the sequencing bias, which is caused by the heavily modified status of tRNAs, we used TGIRT reverse transcriptase enzyme. Using the TGIRT reverse transcriptase enzyme, we also constructed the input library with the same procedure with the exception of the ALKBH1 immunoprecipitation step.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw reads from CLIP samples were first trimmed according to recommended settings using cutadpt with a minimum length of 15 nucleotides
Processed reads were combined to unique sequences then mapped to the human small RNA database (Rfam)
Genome_build: hg19
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| Submission date |
Apr 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Guan-Zheng Luo |
| Organization name |
UChicago
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| Department |
Chemistry
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| Street address |
929 E 57th St
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE65299 |
ALKBH1-Mediated Transfer RNA Demethylation |
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| Relations |
| BioSample |
SAMN04600576 |
| SRA |
SRX1674965 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2107200_ABH1_CLIP_3_ncRNA.txt.gz |
587.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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