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Sample GSM3908060 Query DataSets for GSM3908060
Status Public on Jun 28, 2019
Title Repli-seq, early, RPE, CRISPRa, ADAM22, rep2
Sample type SRA
 
Source name Repli-seq_early_RPE_CRISPRa_ADAM22
Organism Homo sapiens
Characteristics cell line: RPE-1
genotype/variation: SunCas CRISPRa RPE
transfected protein: ADAM22
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 RPE187R2E_S34
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 SAMN12145569
SRA SRX6369510

Supplementary file Size Download File type/resource
GSM3908060_RPE_187_r2_E-gatc.counts.txt.gz 46.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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