|
| Status |
Public on May 15, 2017 |
| Title |
ZZ@E3 |
| Sample type |
SRA |
| |
|
| Source name |
Lysates of E6.25 epiblast (E) or extra-embryonic (ExE) tissues
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Epiblast
genotype: Tet1gt/gt
age: E6.25
|
| Growth protocol |
Lysates of E6.25 epiblast (E) and extra-embryonic (ExE) tissues were pooled, based on retrospective genotyping, from at least 6 embryos (collected from 2-3 litters). Four pooled biological replicates were collected for each tissue compartment and each genotype (wt, Zwt and ZZ); in 3 of 4 pooled replicates, the E and ExE samples were obtained from the same litters and given the same numbering. One ExE sample of ZZ was lost.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was purified using the RNeasy micro Kit (Qiagen) to obtain 1-10 ng of RNA per pool. RNA quality was assessed using a Bioanalyzer 6000 Pico chip and only samples with RNA integrity number (RIN) > 8.0 were processed further.
First-strand cDNA synthesis and amplification was performed by using the SMARTer Ultra Low Input RNA amplification kit v3 (Clontech). Libraries were prepared using NEBNext Ultra DNA library prep for Illumina and sequenced on NextSeq 500 in high-output to generate 75-bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and cutadapt 1.7.1.
Using FastX and ShortRead 1.16.3, we filtered subsequently small reads (length < 35 bp), polyA-reads (>90% of the bases equal A), ambiguous reads (containing N) and low quality reads (>50% of the bases < Q25).
The reads are aligned to the reference genome with Tophat v2.0.12. As parameter options we use: --library-type unstranded --min-intron-length 70 --max-intron-length 500000.
Counting per gene was performed using the function summarizeOverlap() from the R package GenomicAlignment 1.2.2, using union method and TxDb.Mmusculus.UCSC.mm10.knownGene library for gene annotation.
Genome_build: GRCm38.73 (mm10)
Supplementary_files_format_and_content: raw counts in txt format
|
| |
|
| Submission date |
Aug 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE71744 |
Lineage-specific functions of TET1 in the post-implantation mouse embryo |
|
| Relations |
| BioSample |
SAMN03959766 |
| SRA |
SRX1133868 |
