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Sample GSM3908063 Query DataSets for GSM3908063
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,
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
Phone + 31 20 512 2040
Fax +31 20 669 1383
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
BioSample SAMN12145566
SRA SRX6369513

Supplementary file Size Download File type/resource
GSM3908063_RPE_171_r1_E-gatc.counts.txt.gz 46.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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