|
| Status |
Public on Oct 18, 2022 |
| Title |
18lo_biorep1 |
| Sample type |
SRA |
| |
|
| Source name |
Male Germ Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: CD1 hybrid
allele: DND1(EGFP/EGFP)
developmental stage: E18.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Testes were collected from DND1(EGFP/EGFP) fetuses at E16.5 and E18.5, testes were disassociated, male germ cells were sorted as DND1-lo and DND1-hi using FACS for GFP, total RNA was extracted using Qiagen RNeasy Micro Kit (Qiagen #74004)
Sample libraries were prepared with SMART-SeqRTM v4 UltraRTM Low Input RNA Kit (Takara Clontech Kit Cat# 63488).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Supp_ScriptFull.txt
DND1seq__Supp_DND1seqFilters.RData
DND1seq_Supp_Dnd1Terseq_Unique.csv
DND1seq_Supp_GCList_Junique.csv
DND1seq_Supp_GCList_Lunique.csv
DND1seq_Supp_GCList_T_Iunique.csv
DND1seq_Supp_GCList_T_T1unique.csv
DND1seq_Supp_GO-0000077(DNAdamage).csv
DND1seq_Supp_GO-0003723(RNAbinding).csv
DND1seq_Supp_GO-0006119(OxidativePhosphorylation).csv
DND1seq_Supp_GO-0006412(Translation).csv
DND1seq_Supp_GO-0007010(CytoOrg).csv
DND1seq_Supp_GO-0007049(CellCycle).csv
DND1seq_Supp_GO-0016570(HistoneModification).csv
DND1seq_Supp_GO-0030198(ECMorg).csv
DND1seq_Supp_GO-0033182(HistUbi).csv
DND1seq_Supp_GO-0044391(RibosomalSubunit).csv
DND1seq_Supp_GO-0045786(NegCellCycle).csv
DND1seq_Supp_GO-0045787(PosCellCycle).csv
DND1seq_Supp_GO-0048193(Golgi).csv
DND1seq_Supp_GO-0051276(ChroOrg).csv
DND1seq_Supp_GO-0061621(CanonicalGlycolysis).csv
DND1seq_Supp_GO-0071103(DNAconCha).csv
DND1seq_Supp_GO-1902275(RchrOrg).csv
DND1seq_Supp_lohiGeneList.csv
DND1seq_Supp_RIPgeneList.csv
DND1seq_Supp_SomaList_Junique.csv
DND1seq_Supp_SomaList_Sunique.csv
DND1seq_Supp_SomaList_Tunique.csv
Proc_DND1seq_Filtering.xlsx
hiloRNAseq_Supp_DND1-GFP_hiloRNA-seq.RData
hiloRNAseq_Supp_MGIBatchReport_hilo.csv
Proc_hiloRNAseq_hiloRNAseqMaster.xlsx
|
| Data processing |
Basecalling performed on Illumina NovaSeq 6000 as 50bp paired-end reads
Reads mapped to the mm10 (GRCm38) mouse genome using Salmon (v1.3.0)
Mapped reads annotated using the Ensemble Mus musculus reference (version 79)
Differential gene expression analysis performed using DeSeq2 (v1.32.0)
Further annnotation and filtering was performed in RSQLite (v2.2.8)
Genome_build: GRCm38
Supplementary_files_format_and_content: intermediate and supporting files, including full pipeline script and Rdata environment, final output as excel file with TPM and differential expression values for each sample
|
| |
|
| Submission date |
Feb 28, 2022 |
| Last update date |
Oct 18, 2022 |
| Contact name |
Victor A Ruthig |
| E-mail(s) |
Victor.Ruthig@CUAnschutz.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pediatrics, Section of Developmental Biology
|
| Street address |
12800 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE197610 |
The RNA Binding Protein Dead End1 Is Differentially Expressed in Male Germ Cells During Late Gestation and Targets Chromatin Modifiers and Translational Machinery |
|
| Relations |
| BioSample |
SAMN26314824 |
| SRA |
SRX14319260 |
