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Sample GSM6431616 Query DataSets for GSM6431616
Status Public on Jun 26, 2024
Title Ancestralized AHR, 0.05% DMSO, 4h, biol rep 6
Sample type SRA
 
Source name H9
Organism Homo sapiens
Characteristics cell line: H9
cell type: embryonic stem cells
genotype: ancestralized AHR (A381)
treatment: 0.05% DMSO
Treatment protocol Cells were treated with the indicated ligand concentration (in 0.05% DMSO) or 0.05% DMSO for four 4 h prior to cell lysis
Growth protocol Cells were grown on Matrigel matrix (Corning, 35248) coated dishes in mTeSR1 medium (StemCell Technologies, 85850) supplemented with MycoZap Plus-CL (Lonza, VZA-2012)
Extracted molecule total RNA
Extraction protocol RNA was harvested using Rneasy mini plus kit (Qiagen). 300 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Collibri Stranded RNA Library Prep Kit for Illumina Systems with Human/Mouse/Rat rRNA Depletion Kit (Thermo Fisher Scientific) following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description ANC_DMSO_6
Data processing Illumina’s Bustard was used for base calling and adapters were trimmed using leeHom (Renaud et al. 2014)
Reads were aligned to the human reference (GRCh37.87) using tophat2 (v2.0.14) using default parameters (Kim et al. 2013)
Aligned reads were assigned to protein coding genes using the featureCounts software (Liao et al. 2014)
Assembly: GRCh37.87
Supplementary files format and content: csv file includes raw read count values for each sample, ENSEMBL IDs, HUGO gene names and gene length
 
Submission date Aug 04, 2022
Last update date Jun 26, 2024
Contact name Svante Paabo
E-mail(s) paabo@eva.mpg.de
Organization name Max-Planck-Institute for Evolutionary Anthropology
Department Department of Evolutionary Genetics
Street address Deutscher Platz 6
City Leipzig
ZIP/Postal code 04177
Country Germany
 
Platform ID GPL16791
Series (1)
GSE210514 Ancestralization of the modern human aryl hydrocarbon receptor by genome editing
Relations
BioSample SAMN30148907
SRA SRX16842634

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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