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| Status |
Public on Aug 17, 2016 |
| Title |
st561_tossed_16-cell_r9 |
| Sample type |
SRA |
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| Source name |
embryonic cell
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| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: N2
cell type: tossed
embryo stage: 16-cell
replicate: 9
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| Treatment protocol |
Gravid adults were dissected, embryos were treated with bleach, chitinase and chymotripsin to weaken eggshells, cells were dissociated from each other manually by aspiration.
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| Growth protocol |
N2 worms were grown at 20°C
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were simultaneously lysed and flash frozen in liquid nitrogen and stored at -80°C
mRNA libraries were generated using the Clontech SMARTer Ultra Low Input - HV kit and the Nextera XT library preparation kit, according to manufacturers recommendations.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Identical reads were collapsed to one copy using fastx_collapser (FASTX Toolkit 0.0.13.2), using the option -Q33
Reads were aligned to the ce10 genome using Tophat2 (v2.0.11), allowing for 1 splice mismatch, no coverage search and a mate inner distance of 200
Alignments were sorted and indexed using samtools v1.3
Bedgraphs were generated using bedtools genomecov -bg -split -ibam
Read counts were generated using htseq-count (with WBcel235.78.gtf as reference file). These counts were used to generate RPKMs by our own calculations, based on gene length and total number of reads in experiment.
Genome_build: ce10
Supplementary_files_format_and_content: RPKM tables have four colums; gene name, number of reads that mapped to gene locus, gene length, RPKM normalized to gene length and number of reads in transcriptome
Supplementary_files_format_and_content: .bed files have four columns; chromosome number, start position on chromosome, end position, and score (which corresponds to number of reads that aligned to this region of the genome)
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| Submission date |
Feb 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sophia C Tintori |
| E-mail(s) |
sophia.tintori@gmail.com
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| Organization name |
New York University
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| Street address |
29 Washington Pl - rm 951
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE77944 |
Single-cell transcriptomes of each cell of the C. elegans embryo until the 16-cell stage |
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| Relations |
| SRA |
SRX1585619 |
| BioSample |
SAMN04504113 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2062086_st561.bed.gz |
12.2 Mb |
(ftp)(http) |
BED |
| GSM2062086_st561_RPKM.txt.gz |
195.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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