|
| Status |
Public on Jul 15, 2015 |
| Title |
ACTC1_VPR 20nt Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: dCas9-VPR and a gRNA of length 20nt targeting ACTC1
cell line: HEK293T
|
| Treatment protocol |
Cells were transfected with Lipofectamine 2000 (Life Technologies)
|
| Growth protocol |
HEK-293T cells were cultivated in Dulbecco’s Modified Eagle Medium (Life Technologies) with 10% FBS (Life Technologies) and Penicillin/Streptomycin (Life Technologies). Incubator conditions were 37 oC and 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were lysed and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen). For each sample, 200 ng of total RNA was polyA selected using Dynabeads mRNA Purification Kit (Life Technologies). The RNA was then DNAse treated with Turbo DNase (Life Technologies) and cleaned up with Agenocourt RNAClean XP Beads (Beckman Coulter).
RNA-Seq Libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s instructions with NEBNext Multiplex Oligos (New England BioLabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were combined from the four different flow cells using a custom script
Reads were aligned to the hg19 UCSC Known Genes annotations using RSEM v1.2.1
Using paired end setting (not strand specific)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of RSEM output with TPM, Counts, FPKM
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
George Chruch |
| E-mail(s) |
gchurch@genetics.med.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Street address |
77 Ave Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE70694 |
Cas9 gRNA engineering for selectable genome editing, activation and repression |
|
| Relations |
| BioSample |
SAMN03853166 |
| SRA |
SRX1091351 |
