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Sample GSM6697726 Query DataSets for GSM6697726
Status Public on Dec 22, 2023
Title GM12878-DNA_in_LCL8664-cells_RNA_Rep2
Sample type SRA
 
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
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 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
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 SAMN31535894
SRA SRX18088857

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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