|
| Status |
Public on Jun 28, 2019 |
| Title |
RNA-seq, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep1 [4861_11_plb184_3_GTCCGCA] |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq_RPE_CRISPRa_ABCB4+ABCB1+ADAM22+RUNDC3B
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RPE-1
genotype/variation: stably expressing SunTag-CRISPRa
transfected protein: ABCB4+ABCB1+ADAM22+RUNDC3B
|
| 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 |
4861_11_plb184_3_GTCCGCA_S11
|
| 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 |
SAMN12136034 |
| SRA |
SRX6366120 |
