|
| Status |
Public on Jan 11, 2022 |
| Title |
WAPL/MED12 rep 3C RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Hap1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hap1
genotype/variation: WAPL/MED12
|
| Treatment protocol |
CRISPRs targeting WAPL (5’-CACCGCGTTCCATAGTATCCTGTA-3’) and SCC4 (5’-CACCGTACGGGCCTCGATGCGCTG-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL and ∆SCC4 HAP1 clones were generated by insertion of a Blasticidine or Puromycin cassette respectively, as previously described (Blomen et al., 2015). ∆WAPL/∆SCC4 cells were generated by knocking out SCC4 in ∆WAPL cells.
|
| Growth protocol |
HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 1% Ultraglutamin (Lonza).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cultured cells was extracted using TRIzol reagent (Invitrogen).
Strand-specific libraries were generated using the TruSeq PolyA Stranded mRNA sample preparation kit (iIlumina). In brief, polyadenylated RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random-primed and reserve transcribed using SuperScript II Reverse Transcriptase (Invitrogen). The generated cDNA was 3’ end-adenylated and ligated to Illumina Paired-end sequencing adapters and amplified by PCR using HiSeq SR Cluster Kit v4 cBot (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped to hg19 using TopHat 2.0.9 and HTSeq-count was used to generate transcript-counts.
DESeq2 1.10.1 was used to infer differentially expressed genes with basic settings.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq output
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Robin H. van der Weide |
| Organization name |
Hubrecht Institute
|
| Lab |
Kind Lab
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE125618 |
A Mediator-cohesin axis controls heterochromatin domain formation [RNA-seq] |
| GSE125672 |
A Mediator-cohesin axis controls heterochromatin domain formation. |
|
| Relations |
| BioSample |
SAMN10815718 |
| SRA |
SRX5288835 |
