|
Status |
Public on Jun 28, 2019 |
Title |
RNA-seq, RPE, CRISPRa, GRID2, rep2 [4862_6_plb171_GGCTACA] |
Sample type |
SRA |
|
|
Source name |
RNA-seq_RPE_CRISPRa_GRID2
|
Organism |
Homo sapiens |
Characteristics |
cell line: RPE-1 genotype/variation: stably expressing SunTag-CRISPRa 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 |
polyA RNA |
Extraction protocol |
total RNA was extracted using TRIsure and selected for polyadenylated fraction
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
4862_6_plb171_GGCTACA_S19
|
Data processing |
Reads were aligned to hg19 using TopHat version 2.1, with Ensembl genome build 75. Genome_build: GRCh37.75
|
|
|
Submission date |
Jun 25, 2019 |
Last update date |
Jun 28, 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 |
GPL16791 |
Series (2) |
GSE133273 |
Effects of transcription on genome - nuclear lamina interactions: RNA-seq data |
GSE133275 |
Effects of transcription on genome - nuclear lamina interactions |
|
Relations |
BioSample |
SAMN12136043 |
SRA |
SRX6366111 |