 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 26, 2019 |
| Title |
cfp1_B5 |
| Sample type |
SRA |
| |
|
| Source name |
The material is RNA extracted from C. elegans embryos using the Nucleozol preparation protocol from Macherey Nagel.
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: embryos
genotype: mutant cfp1
|
| Treatment protocol |
RNA were extracted from frozen early stage embryos prepared by hypochlorite treatment of young adults
|
| Growth protocol |
Nematode strain maintenance was as described previously (Brenner, 1974).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNAs were extracted with NucleoZol [Macherey-Nagel] according to manufacturer’s instructions and treated with DNAse [Turbo-free DNAse, Ambion]. Integrity of RNA was assessed on Tape Station 4200 [Agilent].
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, Part Number RS-122-2101). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Replicate 3
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Mapping & QC-mapped with rna-STAR (2.4.1d) & Samtools (0.1.19)
Gene expression analysis with HTSeq-count (Version 0.7.2) & package DESeq2 (1.10.1 using R version 3.2.4)
Genome_build: WS254
Supplementary_files_format_and_content: 4 CSV files containing genes differentially (cfp1 vs WT, set2 vs WT, sin3 vs WT) and raw counts
|
| |
|
| Submission date |
Feb 02, 2018 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Hélène Polvèche |
| E-mail(s) |
hpolveche@istem.fr
|
| Organization name |
I-Stem
|
| Street address |
28, Rue Henri Desbruères
|
| City |
Corbeil-Essonnes |
| ZIP/Postal code |
91100 |
| Country |
France |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE110072 |
Physical and functional interaction between the SET1 complex component CFP-1/CXXC and the Sin-3S/HDAC complex in C. elegans embryos |
|
| Relations |
| BioSample |
SAMN08457490 |
| SRA |
SRX3643697 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
