|
| Status |
Public on Feb 03, 2023 |
| Title |
TE glucose 1 |
| Sample type |
SRA |
| |
|
| Source name |
trophectoderm
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: trophectoderm
treatment: Glucose
|
| Growth protocol |
In vitro development in Global medium supplemented with 10% of human sera albumin and supplemented with Insulin:1.7 μM and/or Glucose 15mM in humidified atmosphere with 5% O2 and CO2 at 38°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). 750pg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-seq V4 ultra low input RNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
raw data were obtain from an Illumina NextSeq NB552053 after demultiplexing performed with bcl2fastq2 v2.2.18.12 and adaptor trimming with Cutadapt 1.15
after deleting poor quality base (under 30) at the end of the sequence, reads longer than 35 bp were kept
reads were mapped using the splice junction mapper TopHat (v2.1.1) with parameters -N 2 --read-edit-dist 2 --b2-sensitive --no-coverage-search
the gene count table was performed with featureCounts (v1.6.0) with parameters -p -B -C
Data normalization and single-gene level analysis of the differential expression were performed using the DESeq2 package
Assembly: Ensembl 98 Oryctolagus cuniculus 2.0
Supplementary files format and content: tab-delimited text files include normalized expression values for each Sample
|
| |
|
| Submission date |
Nov 15, 2022 |
| Last update date |
Feb 03, 2023 |
| Contact name |
Sophie Calderari |
| E-mail(s) |
[email protected]
|
| Phone |
+33134652075
|
| Organization name |
INRAE UMR1198 BREED
|
| Street address |
Allée de Vilvert
|
| City |
Jouy-en-josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL24886 |
| Series (1) |
| GSE218009 |
Effect of insulin and glucose supplementation during in vitro developpement of rabbit embryo |
|
| Relations |
| BioSample |
SAMN31740456 |
| SRA |
SRX18273214 |
