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Status |
Public on Dec 22, 2023 |
Title |
GM12878-DNA_in_LCL8664-cells_RNA_Rep2 |
Sample type |
SRA |
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Source name |
GM12878/LCL8665
|
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
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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.
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Library strategy |
ATAC-seq |
Library source |
other |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
HM_active.regions.bed HM_merged-reps_RNA-to-DNA_log2.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
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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)
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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 |
SAMN31535894 |
SRA |
SRX18088857 |