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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 03, 2023 |
| Title |
ATAC-seq, naive_hESC_dCAS9-KRAB+sgRNA_rep1 |
| Sample type |
SRA |
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| Source name |
WIBR3dPE hESC
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| Organism |
Homo sapiens |
| Characteristics |
cell line: WIBR3dPE hESC
treatment: CRISPRi in naive
media: KN/2iL media
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| Treatment protocol |
ATAC-seq was performed on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs
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| Growth protocol |
Conventional (primed) human ESC lines were maintained in mTSER for H1 (Male) and IPS on Matrigel, for WIBR3 (Female) on irradiated inactivated mouse embryonic fibroblast (MEF) feeders in human ESC medium (hESM) and passaged with collagenase and dispase, followed by sequential sedimentation steps in hESM to remove single cells while naïve ES cells, primed H1 and IPS were passaged by Accutase in single cells. hES media composition: DMEM/F12 supplemented with 15% fetalbovine serum, 5% KnockOut Serum Replacement, 2 mM L-glutamine, 1% nonessential amino acids, 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol and 4 ng/ml FGF2. Naïve media composition: 500 mL of medium was generated by including: 240 mL DMEM/F12, 240 mL Neurobasal, 5 mL N2 supplement, 10 mL B27 supplement, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin-streptomycin, 50 μg/ml BSA. In addition for 4i/LA: PD0325901 (1 μM), SB590885 (0.5 μM), WH4-023 (1 μM), Activin A (10 ng/mL), 20 ng/ml hLIF, Y-27632 (10 μM) and IM-12 (0-1 μM). In addition for KN/2i media: PD0325901 (1 μM), CHIR99021 (1 μM), 20 ng/ml hLIF and Doxycycline (2 µg/ml). For conversion of primed human ESC lines (WIBR3), we seeded 2-3e105 trypsinized single cells on an MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (10 mM). Two days later, medium was switched to 4i/LA (+/- IM12)-containing naïve hESM (Theunissen et al., 2016). WIBR3dPE cells (OCT4 GFP knock-in depleted for its primed specific Proximal Enhancer (dPE) were converted in naïve with DOX-inducible KLF2 and NANOG transgenes and maintained in 2i/L/DOX (Theunissen et al., 2014).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as in (Buenrostro et al., 2013) on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs
Library were made using Nextera DNA Library Prep Kit (Illumina #FC-121-1030)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequenced reads were de-multiplexed to attribute each read to a DNA sample and then aligned with bowtie2. Mitochondrial reads were removed.
Accessible sites were called using MACS2, only peaks with a score higher than 5 (–log10 p-value) were kept. Then differential analysis between conditions was done using unique reads (filter for MAPQ > 10)
Assembly: hg19
Supplementary files format and content: A bed file containing the output of the peak called by MACS2
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| Submission date |
Jul 03, 2023 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Julien Duc |
| E-mail(s) |
julien.duc@epfl.ch
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| Organization name |
EPFL
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| Department |
School of Life Science
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| Lab |
LVG
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| Street address |
Station 19 CH-1015 Lausanne
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| City |
Lausanne |
| State/province |
VAUD |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE208403 |
Statistical learning quantifies transposable element-mediated cis-regulation |
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| Relations |
| BioSample |
SAMN36278195 |
| SRA |
SRX20871822 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7548162_16_03_17_g2_S2_peaks_score5.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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