 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 22, 2021 |
| Title |
Asynchronous_IPSc_wt_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
passage: Passage 19
genotype: Wild-type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Transposase-accessible chromatin was obtained from frozen human IPSc and D. Melanogaster S2 cells according to ATAC-seq protocol (Buenrostro et al. 2013; 2015), with modifications. Briefly, 100 000 IPSc cells per replicate were spiked-in with 200 S2 cells, washed in PBS and lysed in cell lysis buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin) for 3 minutes (Corces et al. 2017). Lysates were washed with washing buffer (10 mM Tris-Hcl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and pelleted. Isolated nuclei were resuspended in transposase reaction mix (25 ul 2X TD buffer, 16.5 ul 1X PBS, 0.5 ul 10% Tween-20, 0.5 ul 1% digitonin, 2.5 ul of Tn5 Transposase and 5 ul of nuclease-free H2O) and incubated at 37°C for 30 minutes on thermomixer at 1000 rpm. Transposase reaction was terminated by addition of stop buffer (50 mM Tris-Hcl pH 8, 10 mM EDTA, 1% SDS) (Stewart-Morgan, Reverón-Gómez, and Groth 2019). Reaction components were removed with DNA Clean&Concentrator kit (Zymo) and extracted chromatin was used for library construction and subsequent sequencing.
Standard DNA library prep (Buenrostro et al 2015)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
mapped with Bowtie2 to hg38 and dm6
filtered to remove non-primary, unmapped, duplicate and mitochondrial reads
spike-in scaling factors calculated from dm6 mapped reads with ChIPseqSpike
scaled with spike-in scaling factors and RPKM normalized with Deeptools to produce bigwig files
Genome_build: hg38
|
| |
|
| Submission date |
Nov 09, 2020 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Argyris Papantonis |
| E-mail(s) |
[email protected]
|
| Organization name |
University Medical Center Goettingen
|
| Department |
Department of Pathology
|
| Street address |
Robert-Koch-Str 40
|
| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE161118 |
Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology [ATAC-Seq] |
| GSE161120 |
Impaired CHD6 function links misregulation of autophagy and DNA damage response to premature ageing |
|
| Relations |
| BioSample |
SAMN16709822 |
| SRA |
SRX9462617 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
