|
| Status |
Public on Jan 28, 2019 |
| Title |
hybrid hermaphrodite germlines from K27me3 M+P-, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hybrid hermaphrodite germlines from K27me3 M+P-
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: hybrid (hawaii mother and bristol father)
genotype: mes-3/+; fem-2/+
tissue: distal gonad arms cut at the late-pachytene gonad bend
|
| Treatment protocol |
L4 hermaphrodites or L4 males were transferred to new plates, and dissected the next day (1 day old young adults).
|
| Growth protocol |
C. elegans strains were maintained at 20°on OP50 bacteria as described (Brenner 1974).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were purified using Trizol/chloroform extraction protocol.
Ribosomal RNA was depleted using an NEBNext rRNA Depletion kit (E6310), and libraries were prepared using an NEBNext Ultra RNA Library Prep Kit for Illumina (E7530).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Pp.v.Pm.deseq.output.csv.gz
P.v.Pm.deseq.output.csv.gz
|
| Data processing |
TopHat2 was used to align the RNA-seq reads to the C. elegans transcriptome (WS220) with default parameters allowing either 1 mismatch or 0 mismatches. For all read analysis, all R1 reads were mapped allowing 1 mismatch. For SNP analysis, SNP-containing R1 and R2 reads were mapped twice, once allowing 0 mismatches and once allowing 1 mismatch.
HTSeq was used to obtain read counts per transcript. For all read analysis, all read counts per transcript were obtained. For SNP analysis, SNP-containing read counts per transcript were obtained for reads that mapped with 0 mismatches and those that mapped allowing 1 mismatch.
Differentially expressed genes were determined with DESeq2 in R using HTSeq counts from the all reads analysis and a FDR < 0.05 or < 0.1 (see methods) as the significance cutoff.
Genome_build: WS220
Supplementary_files_format_and_content: Text files for each sample with HTSeq counts per transcript (tab delimited), and DESeq output for differential expression analysis performed (comma delimited). Gene identifiers are Gene Sequence Names as obtained from Wormbase version WS220.
|
| |
|
| Submission date |
Dec 06, 2018 |
| Last update date |
Jan 30, 2019 |
| Contact name |
Susan Strome |
| E-mail(s) |
sstrome@ucsc.edu
|
| Organization name |
UC Santa Cruz
|
| Department |
MCD Biology
|
| Street address |
1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE123415 |
RNA-seq transcriptome profiling of hybrid (hawaii mother and bristol father) C. elegans H3K27me3 M+P+ vs. M+P- hermaphrodite germlines |
|
| Relations |
| BioSample |
SAMN10526585 |
| SRA |
SRX5099844 |
