|
| Status |
Public on Sep 24, 2020 |
| Title |
Dolinoy_RNA_Blood_DEHP_3week_Female_biorep3 |
| Sample type |
SRA |
| |
|
| Source name |
3week_Blood
|
| Organism |
Mus musculus |
| Characteristics |
strain: Avy
age: 3 week
gender: Female
tissue: Blood
treatment: DEHP (bis (2-ethylhexyl) phthalate) 25mg DEHP/kg
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Sample collection was performed by Dana Dolinoy lab at University of Michigan. 3 week mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Dana Dolinoy lab at University of Michigan. mRNA and nuclei from 3 weekmice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
UUID:5c71e72d1bf4744d59c74814,QC_score:3,QC_stats:Pass
|
| Data processing |
RNA-seq and ATAC-seq were sequenced by data production centers and processed by the TaRGET II DCC with standardized data processing pipelines. Library QC was assayed based on key QC parameters. Please refer to the TaRGET II data portal for detailed pipeline description and QC standard (https://data.targetepigenomics.org).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak output for ATAC-seq and gene count table for RNA-seq
|
| |
|
| Submission date |
Sep 23, 2020 |
| Last update date |
Sep 25, 2020 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
|
| Phone |
(314) 286-0866
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue
|
| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE146508 |
Transcriptome and open chromatin analysis of 5-month mouse liver and blood by the TaRGET II consortium |
|
| Relations |
| BioSample |
SAMN16249688 |
| SRA |
SRX9180243 |
