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| Status |
Public on Dec 11, 2014 |
| Title |
mpfc_200_rep1 |
| Sample type |
SRA |
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| Source name |
multicellular embryo tp 15
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| Organism |
Caenorhabditis elegans |
| Characteristics |
experiment set: Whole embryo, 10min intervals
time: minutes passed the 2-cell stage: 220
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| Growth protocol |
The five lineages were cultured in a humid chamber in EGM.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Egg shells were removed from C. elegans embryos and the resulting blastomeres cultured. For the blastomere sampling, the egg shell and vitelline membrane were removed at the two cell stage, and the embryo separated to the AB and P1 blastomeres by pipetting. P1 was allowed to undergo one cell division and separated to EMS and P2, or two cell divisions before being separated to MS, E, C and P3 blastomeres. All lineages from a single embryo were frozen at the same time
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence both RNA from the whole embryos and the cultured blastomeres. CEL-seq multiplexing barocdes were used.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
200 minutes past the 4-cell stage embryo
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| Data processing |
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (minimum quality of 20, max 1 exception. trimming not required).
RNA-seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing 1 mismatch in the 5 first letters of the barcode.
BWA mapping, version 0.6.1, against c. elegans genome WBCel215 (bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -M 3 -O 11 -E 4)
Read counting with htseq-count version 0.5.3p1. Using a custom annotation,based on WS230 exon annotation (union of overlapping reads).
Genome_build: WBcel215
Supplementary_files_format_and_content: Expression matrix, transcripts per million - whole-embryo timecourse. Meaned (Samples 1-56), 50 stages.
Supplementary_files_format_and_content: Expression matrix, transcripts per million - 5 lineages ,11 timepoints. Meaned (Samples 57-184), 55 stages.
Supplementary_files_format_and_content: Expression matrix, read count. (Samples 1-184, unmeaned).
Supplementary_files_format_and_content: Expression matrix, read count. Spikeins (Samples 1-184, unmeaned)
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| Submission date |
Sep 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Itai Yanai |
| E-mail(s) |
yanai@technion.ac.il
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| Organization name |
Technion - Israel Institute of Technology
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| Department |
Biology
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| Lab |
Yanai
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| Street address |
Technion City
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| City |
Haifa |
| ZIP/Postal code |
30200 |
| Country |
Israel |
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| Platform ID |
GPL13657 |
| Series (1) |
| GSE50548 |
Spatiotemporal embryonic transcriptomics reveals the evolutionary history of the endoderm germ layer |
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| Relations |
| BioSample |
SAMN02343493 |
| SRA |
SRX343175 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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