|
| Status |
Public on Jan 01, 2018 |
| Title |
SC_plate1 |
| Sample type |
SRA |
| |
|
| Source name |
C. elegans, synthetic community
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
food: Synthetic community
environment: Plate
tissue: whole body
age: day 1 adult
truseq index #: 5
|
| Growth protocol |
Synthetic community was comprised of 30 gut isolates; soil was autoclaved before inoculating with either E. coli or the soil microbiota; worms were harvested for mRNA after 3 days of growth (day 1 adults).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a modified CTAB protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
mRNA to cDNA
Processed data file: kallisto_RNAseq_count_table_isoforms.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to WBcel235 genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were aligned, and transcript counts were estimated using Kallisto.
Genome_build: WBcel235
Supplementary_files_format_and_content: kallisto_RNAseq_count_table_isoforms.txt: Tab-delimited text file includes a count matrix for all samples.
|
| |
|
| Submission date |
Apr 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maureen Berg |
| Organization name |
UC Berkeley
|
| Street address |
3040 Valley Life Sciences Building # 3140
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3140 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE97934 |
The role of the TGF-β/DBL-1 pathway in shaping the C. elegans gut microbiota |
|
| Relations |
| BioSample |
SAMN06763369 |
| SRA |
SRX2744286 |
