|
| Status |
Public on Jun 28, 2019 |
| Title |
Repli-seq, early, RPE, CRISPRa, GRID2, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Repli-seq_early_RPE_CRISPRa_GRID2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RPE-1
genotype/variation: SunCas CRISPRa RPE
transfected protein: GRID2
|
| Treatment protocol |
sgRNAs were cloned into Lentiguide-Puro vector (Addgene #52963) using restriction enzyme BsmBI, and Lentivirus was prepared. RPE-1 cells stably expressing SunTag-CRISPRa were infected with LentiGuide virus and selected with 10 µg/µl Puromycin for one week to obtain stable polyclonal cell pools.
|
| Growth protocol |
Cells were cultured according to 4DNucleome SOP, https://www.4dnucleome.org/cell-lines.html
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RepliSeq was performed as described in Marchal et al. 2018, PMID 29599440; Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nat Protoc 13, 819-839 (2018).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RPE171R1E_S28
|
| Data processing |
Data analysis of RepliSeq samples: Repi-seq reads from early and late replicating fraction were processed in the same way as DamID reads in this study, i.e., they were mapped to GATC fragments.
Genome_build: hg19
|
| |
|
| Submission date |
Jun 27, 2019 |
| Last update date |
Jun 30, 2019 |
| Contact name |
Bas van Steensel |
| E-mail(s) |
b.v.steensel@nki.nl
|
| Phone |
+ 31 20 512 2040
|
| Fax |
+31 20 669 1383
|
| URL |
http://www.nki.nl/nkidep/vansteensel
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
division of Molecular Biology
|
| Lab |
van Steensel group
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE133274 |
Effects of transcription on genome - nuclear lamina interactions: Repli-seq data |
| GSE133275 |
Effects of transcription on genome - nuclear lamina interactions |
|
| Relations |
| BioSample |
SAMN12145566 |
| SRA |
SRX6369513 |
