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| Status |
Public on Mar 22, 2023 |
| Title |
4_r2_1 |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: 4c
cell type: embryonic cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Egg shells were removed from a C. elegans embryo, blastomeres were separated manually, collected and individually frozen
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence RNA from collected blastomeres. CEL-seq2 multiplexing barocdes were used.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
sample name: 59
Embryonic blastomere transcriptome
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| Data processing |
Libraries were sequenced on the Illumina HiSeq2500 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 (barcode minimum quality of 20. trimming of read2 to 35 bases).
CEL-seq2 (Hashimshony, et a. 2016) demultiplexing of second mate, using first mate barcode, allowing no mismatches in the barcode.
bowtie2, version 2.1.0
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting.
Genome_build: WS230
Supplementary_files_format_and_content: Expression matrix, number of transcript molecules
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| Submission date |
Jun 20, 2016 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Alison G Cole |
| Organization name |
University of Vienna
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| Department |
Neurosciences and Developmental Biology
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| Street address |
Djerassiplatz 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE83523 |
Transcriptome characterization of embryogenesis at a single cell resolution [C. elegans] |
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| Relations |
| BioSample |
SAMN05274120 |
| SRA |
SRX1865459 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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