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Sample GSM1221016 Query DataSets for GSM1221016
Status Public on Dec 11, 2014
Title 1_cell
Sample type SRA
 
Source name 1-cell embryo
Organism Caenorhabditis elegans
Characteristics experiment set: Whole embryo
time: minutes passed the 2-cell stage: n/a
Growth protocol The five lineages were cultured in a humid chamber in EGM.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description 1-cell embryo
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).
CEL-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)
 
Submission date Sep 03, 2013
Last update date May 15, 2019
Contact name Itai Yanai
E-mail(s) yanai@technion.ac.il
Organization name Technion - Israel Institute of Technology
Department Biology
Lab Yanai
Street address Technion City
City Haifa
ZIP/Postal code 30200
Country Israel
 
Platform ID GPL13657
Series (1)
GSE50548 Spatiotemporal embryonic transcriptomics reveals the evolutionary history of the endoderm germ layer
Relations
BioSample SAMN02343497
SRA SRX343159

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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