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| Status |
Public on Sep 30, 2021 |
| Title |
WT_empty1 |
| Sample type |
SRA |
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| Source name |
HEK293T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293T
genotype: wild type
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| Growth protocol |
HEK293T were obtained from ATCC and HeLa were obtained from ECACC. All cell lines were cultured at 37°C and 5% CO2 in Iscove's Modified Dulbecco's Medium (IMDM, Sigma-Aldrich) supplemented with 10% fetal calf serum (FCS, Gibco), 1x GlutaMAX (Gibco), and 100 U/mL penicillin/streptomycin (Gibco).
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
RIPseq: Lysates from UV-treated cells were clarified from sonicated nuclei and RNA-protein complexes were isolated with anti-HA magnetic beads. ChIPseq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K9me3 antibody.
RIPseq: Immunoprecipitated RNA was subjected to DNA library preparation using SMARTer Stranded Total RNA-Seq Kit V3 – Pico Input Mammalian (Takara Bio, USA) kit according to the manufacturer’s instructions and following conditions: initial fragmentation at 94°C for 3-4 min, ribosomal RNA depletion step included, 5 PCR cycles for PCR adding adapters and indexes and 12 for final library amplification). The library quality was determined using Bioanalyzer, and sequenced using Illumina MiniSeq System with the following specifications: 32 bp (R1) and 43 bp (R2), paired-end reads were sequenced using MiniSeq High-Output 75 cycles kit. ChIPseq: ChIP DNA and input DNA were subjected to library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instructions. Libraries were purified, quantified, multiplexed (with NEBNext Multiplex Oligos for Illumina) and sequenced with 2× 50-bp pair-end reads on Illumina Novaseq platform (Genomics Core, Cancer Research UK Cambridge Institute).
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiniSeq |
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| Description |
control RIPseq
WTempty.dedup.bw
WTHA.v2.bed
ripseq_genes.txt
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| Data processing |
The data was processed as described in the methods section of the associated manuscript. Details about the analysis are available in https://github.com/semacu/hush
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files contain quantification of signal in genes of interest, bed files contain peaks calculated with a tailored peak calling strategy and bigwig capture genomic signal. Data was processed jointly with RNA-seq and ChIP-seq data available in GSE95374
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| Submission date |
Jul 29, 2021 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Sergio Martínez Cuesta |
| E-mail(s) |
sermarcue@gmail.com
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| Organization name |
AstraZeneca
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| Department |
Data Sciences and Quantitative Biology, Discovery Sciences
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| Street address |
1 Francis Crick Avenue
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0AA |
| Country |
United Kingdom |
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| Platform ID |
GPL22790 |
| Series (1) |
| GSE181113 |
Genome surveillance through repression of intronless mobile elements by the HUSH complex |
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| Relations |
| BioSample |
SAMN20478161 |
| SRA |
SRX11600464 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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