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| Status |
Public on Apr 04, 2016 |
| Title |
HeLa_LowRNase |
| Sample type |
SRA |
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| Source name |
human HeLa cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
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| Treatment protocol |
HEK293T Cells were induced for 8 hours with 1 μg/ml Doxycycline before AMT crosslinking.
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| Growth protocol |
HeLa-S3 cells were cultured in DMEM+ 10% FBS + Pen/Strep at 37ºC with 5% CO2. Flp-In HEK293T-REx cells express doxycycline inducible 3XFLAG-DDX3X at a level comparable to endogenous DDX3X. The 293T cells were cultured with DMEM + 10% Tetracycline-free FBS (Clontech, Tet System Approved FBS, 631106) + Pen/Strep + 2mM Glutamax (Gibco). J1 mouse ES cells (male) were cultured on gelatin coated plates at 37ºC with mES media: 500ml Knockout DMEM (Gibco), 90ml FBS, 6ml non-essential amino acid (MEM NEAA, 100x, Gibco), 6ml glutamine or glutamax (200mM stock solution), 6ml Pen/Strep, 1ml BME and 60ul LIF (Millipore, ESG1106).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were digested with S1 nuclease, proteinase K and RNA was extracted using TRIzol.
See previous publication for the protocol (PMID: 25799993)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
remove 5' and 3' adapters using trimmomatic-0.32.jar SE -threads 16 -phred33
removed PCR duplicates using splitFastqLibrary (in the icSHAPE pipeline)
mapped reads using STAR, version 2.4, with the following parameters: --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --runThreadN 16
secondary mappings were removed using samtools
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: read count was calculated using bedtools v2.22.0
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| Submission date |
Oct 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhipeng Lu |
| E-mail(s) |
zhipengluchina@gmail.com
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| Organization name |
Stanford University
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| Department |
Department of Dermatology
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| Lab |
Howard Chang
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE74353 |
RNA duplex map in living cells reveals higher order transcriptome structure |
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| Relations |
| BioSample |
SAMN04215494 |
| SRA |
SRX1382444 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1917753_HeLa_LowRNase_count.txt.gz |
295.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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