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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 25, 2023 |
| Title |
HeLa, shLUC, EGF, RNAPII, biol rep2 |
| Sample type |
SRA |
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| Source name |
HeLa
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
cell type: cervical epithelial
genotype: wt
treatment: shLuciferase, serum starved in DMEM media containin 0.3% serum overnight and then treated with epidermal growth factor (EGF) for 15 minutes
chip antibody: RNAPII (Barbieri et al., Mol Cell, 2018, 71, 103-116 e107.)
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| Treatment protocol |
WT HeLa cells were starved in DMEM media containing 0.3% super calf serum for 72 hours and then treated with 0.1ug/mL EGF for 15 minutes. HL-60 cells were differentiated with 100nM phorbol myristate acetate (PMA) for 16 hours where noted. Where noted, HeLa cells were either infected with lentivirus containing shRNAs for Luciferase (control) or C7orf26, starved overnight in 0.3% serum containing-DMEM media and then treated with 0.1ug/mL EGF.
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| Growth protocol |
HeLa cells were maintained in DMEM high glucose media, supplemented with 10%(v/v) super calf serum (GEMcell) and 2 mM of L-glutamine. HL-60 cells were maintained in RPMI high glucose media, supplemented with 10% (v/v) super calf serum and 2mM L-glutamine.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei (Covaris S220), and protein-DNA complexes were isolated with antibody-conjugated Dynabeads
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Inc.)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
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| Description |
RNAPII ChIP-seq in shLuciferase(Control), serum-starved HeLa cells treated with 0.1ug/mL EGF
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| Data processing |
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment (ChIPseq): BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)
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| Submission date |
May 26, 2022 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Sarah R Offley |
| E-mail(s) |
offley@upenn.edu, soffley@wistar.org, Sarah.offley@pennmedicine.upenn.edu
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| Organization name |
The Wistar Institute
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| Lab |
Alessandro Gardini
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| Street address |
3601 Spruce St
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| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19103 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE204932 |
A combinatorial approach to uncover a novel Integrator subunit [ChIP-seq I] |
| GSE204936 |
A combinatorial approach to uncover a novel Integrator subunit |
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| Relations |
| BioSample |
SAMN28686201 |
| SRA |
SRX15475756 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6202510_Hela-shLUC-EGF-Pol2-ChIP-rep3_mem_srt_q10_rmdup_nSiN.bw |
90.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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