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| Status |
Public on Jul 09, 2019 |
| Title |
HeLaS3FlpIn_Control_Rep2 |
| Sample type |
SRA |
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| Source name |
HeLaS3FlpIn cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLaS3FlpIn
flag status: None
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| Growth protocol |
RPMI+10%FBS+PSQ in Spinner Flasks at 75 rpm
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy MinElute Cleanup Kit
TGIRT-seq
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RNA from FLAG eluates
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| Data processing |
For all datasets, sequence quality was verified by FastQC and reads were aligned using STAR.
Reads were aligned against a custom reference composed of miRBase, tRNAdb, mitotRNAdb, piRNAdb, and rRNA from the UCSC Browser track annotations. Alignments were split based on length (over/under 50bp) and counted using samtools idxstats.
Genome_build: Custom
Supplementary_files_format_and_content: Tab-delimited text files contain read counts were each row is a small RNA feature, the first colum is the feature name, and the second column is the read count
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| Submission date |
May 09, 2019 |
| Last update date |
Jul 11, 2019 |
| Contact name |
Blerta Xhemalce |
| Organization name |
University of Texas at Austin
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| Street address |
2500 Speedway
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| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE130951 |
BCDIN3D regulates tRNAHis 3’ fragment processing |
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| Relations |
| BioSample |
SAMN11609528 |
| SRA |
SRX5811136 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3756744_HeLaS3FlpIn_Control_Rep2_over50_counts.txt.gz |
63.5 Kb |
(ftp)(http) |
TXT |
| GSM3756744_HeLaS3FlpIn_Control_Rep2_under50_counts.txt.gz |
67.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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