|
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.
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|
|
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
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|
|
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 |