|
| Status |
Public on Dec 22, 2023 |
| Title |
LCL8664-DNA_in_GM12878-cells_RNA_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878/LCL8664
|
| Organisms |
Macaca mulatta; Homo sapiens |
| Characteristics |
cell line: GM12878/LCL8664
cell type: Lymphoblasotid cell line (immortalized B cells)
biomaterial provider: https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878
molecule type: reporter RNA
|
| Growth protocol |
We cultured both cell lines with RPMI 1640 Media containing 15% fetal bovine serum, 2mM GlutaMAX, 100 units/mL penicillin and 100 μg/mL streptomycin. Cells were cultured at 37°C, 80% relative humidity, and 5% CO2. Cell density was maintained between 0.2×106 and 1.5×106 cells/mL with a 50% media change every 2-4 days. All cell lines were regularly screened for mycoplasma contamination.
|
| Extracted molecule |
other |
| Extraction protocol |
ATAC-STARR-seq samples were extracted 24hrs after transfection with the reporter plasmid library. For RNA-seq, total RNA was harvested using TRIzol™ Reagent and Phasemaker™ Tubes Complete System 24 hours after transfection with hSTARR_ORI plasmid.
ATAC-STARR-seq libraries were generated following the protocols described in Hansen & Hodges 2022. RNA-seq libraries were generated from total RNA using the SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian from Takara bio.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MH_active.regions.bed
MH_merged-reps_RNA-to-DNA_log2.crossmap.bw
HH_active.regions.bed
HH_merged-reps_RNA-to-DNA_log2.bw
conserved_active.regions.bed
human-specific.regions.bed
macaque-specific.regions.bed
human-specific_cis.bed
human-specific_trans.bed
macaque-specific_cis.bed
macaque-specific_trans.bed
human-specific_cis-only.bed
human-specific_trans-only.bed
human-specific_cis+trans.bed
macaque-specific_cis-only.bed
macaque-specific_trans-only.bed
macaque-specific_cis+trans.bed
|
| Data processing |
library strategy: ATAC-STARR-seq
active regions for each condition were called using a custom process described in the manuscript
activity signal was created using a custom process described in the manuscript
cis/trans regions were called using a custom process described in the manuscript
normalized RNA-seq counts were generated using a custom process described in the manuscript
Assembly: hg38 or rheMac10
Supplementary files format and content: region files (BED/narrowPeak)
Supplementary files format and content: ATAC-STARR-seq signal files (bigWig)
Supplementary files format and content: normalized RNA-seq count data (tsv)
|
| |
|
| Submission date |
Oct 31, 2022 |
| Last update date |
Dec 22, 2023 |
| Contact name |
Tyler J Hansen |
| E-mail(s) |
tyler.j.hansen@vanderbilt.edu
|
| Organization name |
Vanderbilt University
|
| Department |
Biochemistry
|
| Street address |
2215 Garland Ave
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL32794 |
| Series (1) |
| GSE216917 |
Human gene regulatory evolution is driven by divergence in cis and trans |
|
| Relations |
| BioSample |
SAMN31535889 |
| SRA |
SRX18088862 |
