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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 01, 2021 |
| Title |
PGCLC_100nM BPA_Rep1 |
| Sample type |
SRA |
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| Source name |
PGCLC_100nM BPA
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell line: in vitro derived PGCLC (d5)
genotype: Blimp1-mVenus; Stella-ECFP (BVSC)
treatment: 100nM BPA
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| Treatment protocol |
For EpiLC exposure, 100nM BPA containing media was added 24 hours after seeding and cells were cultured for 24 hours.
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| Growth protocol |
BVSC ESCs were grown in 2i + LIF for 2-3 days, before harvesting and culturing in EpiLC Media. After 48 hours of culture, EpiLCs were harvested, counted and cultured in in U-bottom well plates in PGCLC media
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| Extracted molecule |
total RNA |
| Extraction protocol |
For EpiLCs, cells were harvested using TrypLETM Select (ThermoFisher Scientific), before counting, pelleting and snap-freezing. For PGCLCs, Blimp1+Stella+ were FACS purified from TrypLETM Select dissociated aggregates.
Strand-specific RNA-seq libraries were prepared with Universal Plus mRNA-Seq kit (Nugen), according to the manufacturer’s protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
C1_DP1_S7
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| Data processing |
Data quality check was performed using Illumina Sequencing Analysis Viewer (SAV) software
Demultiplexing was performed with Illumina Bcl2fastq2 v 2.19.1.403 program
Fastq reads were checked for overall quality by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 using STAR (Dobin, 2013) with parameters --runThreadN 20 --readFilesCommand zcat --runMode alignReads --outFilterMultimapNmax 1 --outSAMtype BAM Unsorted --quantMode GeneCounts --twopassMode Basic
Read counts were obtained using HTSeq (https://htseq.readthedocs.io/en/master/) using the following commands: htseq-count --mode=union --stranded=no --idattr=gene_id -r pos -f sam
Output files were filtered to remove genes with 9 or fewer read counts, Gene counts were normalized using the trimmed mean of M-values normalization (TMM) method (Robinson, 2010) before determining counts per million (cpm) values
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: BVSC_H18_d5_cpm_FC_FDR.xlsx: Analysis of RNA-seq data from day 5 BVSC-H18 PGC like cells (PGCLCs) derived from either untreated or 100nM Bisphenol A exposed epiblast like cells (EpiLCs). Table shows trimmed mean of M-values (TMM)-normalised counts per million (cpm) of genes indicated. Note, data set pre-filtered to remove genes with a low number of reads (< 10 reads). In addition, columns show log10 fold-change, p-value and Benjamini-Hochberg adjusted p-value (FDR).
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| Submission date |
Sep 06, 2020 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Steen Kian Thye Ooi |
| E-mail(s) |
steen001@g.ucla.edu
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| Organization name |
UCLA
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| Department |
Institute for Society and Genetics
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| Lab |
Allard
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| Street address |
621 Charles E. Young Drive S.
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE157570 |
Physiologically-relevant Bisphenol A levels alter the developmental trajectory of an in vitro model of mouse Primordial Germ Cells |
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| Relations |
| BioSample |
SAMN16071023 |
| SRA |
SRX9085167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4770808_PGCLC_100nM_BPA_Rep1.txt.gz |
79.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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