|
| Status |
Public on Nov 07, 2022 |
| Title |
dCas9-KRAB DF1, Mock control_B |
| Sample type |
SRA |
| |
|
| Source name |
DF1
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: DF1
cell type: Embryonic fibroblast
genotype: dCas9-KRAB
treatment: Mock control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Zymo DirectZol mini
mRNA library preparation (poly A enrichment)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
KRAB_Mock_B
|
| Data processing |
Raw read quailty trimming and adaptor removal: TrimGalore (version 0.6.7)
Read alignment against bGalGal1.mat.broiler.GRCg7b (NCBI annotation release 106): STAR (version 2.7.10a)
Raw read count extraction from bam files: htseq-count (version 0.13.5)
Assembly: bGalGal1.mat.broiler.GRCg7b (NCBI annotation release 106)
Supplementary files format and content: csv, raw read counts of annotated genes in matrix format across all samples
|
| |
|
| Submission date |
Nov 04, 2022 |
| Last update date |
Nov 07, 2022 |
| Contact name |
Tae Hyun Kim |
| E-mail(s) |
tpk5258@psu.edu
|
| Organization name |
Penn State University
|
| Street address |
317 AVBS
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE217310 |
Targeted modulation of chicken genes in vitro using CRISPRa and CRISPRi toolkit |
|
| Relations |
| BioSample |
SAMN31610274 |
| SRA |
SRX18173621 |
