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Status |
Public on Jul 21, 2020 |
Title |
HeLa_E203Q_Proseq_r2 |
Sample type |
SRA |
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Source name |
HeLa
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Organism |
Homo sapiens |
Characteristics |
cell line: HeLa cell type: cervical adenocarcinoma modification: shINTS11-Tet-pLKO-neo/ Cumate-pLenti-Cloning-2A-WT
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Biomaterial provider |
ATCC#CCL-2
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Growth protocol |
HeLa stable containing INTS11 shRNA and overexpression E203Q mutant INTS11 cell lines were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS, puromycin (2 μg/ml) and G418 (200 μg/ml). Knockdowns were induced by adding of 1 μg/ml oxycycline (Dox) into the culture medium daily for 3 days
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Extracted molecule |
total RNA |
Extraction protocol |
PRO-seq experiments were performed as described previously (Mahat, D. B. et al. 2016). Nuclei were isolated by Dounce homogenizer with loose pestle. 1x107 nuclei were subjected to nuclear run-on (30oC, 3min) in the presence of 25 μM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer). Total RNA was extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min). PRO-seq libraries used biotinylated nascent RNAs were purified by Dynabeads M-280 streptavidin (Invitrogen). Following adaptor ligation as described in previously (Mahat, D. B. et al. 2016), cDNA synthesis, and PCR amplification 140–350 bp libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science).
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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Description |
E203Q
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Data processing |
Library strategy: PRO-seq Proseq: FASTQ data were trimmed by Cutadapt 1.14 and Trimmomatic v0.32. Proseq: Reads were aligned on hg19 or dm3 genome by bowtie 1.1.2 26. Strand-specific single nucleotide ends of aligned reads were generated by Bedtools v2.26 with genomecov as bedgraph format. Bedgraph data were normalized by the number of reads mapped to spike-in dm3 genome, and then converted to bigwig files. Genome_build: hg19 Supplementary_files_format_and_content: The processed data files are in bigWig format: Proseq: bigwigs were with Bedtools v2.26 with genomecov.
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Submission date |
Jan 23, 2019 |
Last update date |
Jul 21, 2020 |
Contact name |
Felipe Beckedorff |
E-mail(s) |
beckedorff@gmail.com
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Organization name |
University of Miami
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Street address |
1501 NW 10th Avenue room 731.G , Miami, FL
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City |
Miami |
State/province |
FL |
ZIP/Postal code |
33136 |
Country |
USA |
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Platform ID |
GPL18573 |
Series (1) |
GSE125535 |
The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts |
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Relations |
BioSample |
SAMN10794310 |
SRA |
SRX5283857 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3576731_Proseq_EQ_r2_spike_norm_forward.bw |
120.8 Mb |
(ftp)(http) |
BW |
GSM3576731_Proseq_EQ_r2_spike_norm_reverse.bw |
116.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data provided as supplementary file |
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