Sticking together an updated model for temporary adhesion

This zenodo dataset contains raw sequencing data (Illumina total RNA-seq, Illumina differential RNA-seq, Illumina genomic DNA, Nanopore high molecular weight genomic DNA) of the polyclad flatworm Theama mediterranea. This data was used to de-novo assemble a draft genome (Flye assembler), a de-novo transcriptome (Trinity assembler), a positional tail-specific differential RNA-seq dataset (DESeq2), and a genome guided gene prediction (braker2). 

1) RNA-seq (Illumina PE150)
Theama_Transcriptome_1_S76_L007_R1_001.fastq.gz
Theama_Transcriptome_1_S76_L007_R2_001.fastq.gz
Theama_Transcriptome_2_S77_L007_R1_001.fastq.gz
Theama_Transcriptome_2_S77_L007_R2_001.fastq.gz
Theama_Transcriptome_3_S78_L007_R1_001.fastq.gz
Theama_Transcriptome_3_S78_L007_R2_001.fastq.gz
Theama_Transcriptome_4_S79_L007_R1_001.fastq.gz
Theama_Transcriptome_4_S79_L007_R2_001.fastq.gz
 

2) Transcriptome 
>>> Theama_mediterranea_20200402.fasta_annotated_shortHeaders.fa (=transcriptome)
TrinityStats.txt

3) diff-RNA-seq 

'head'
4884-S1_S1_L005_R1_001.fastq.gz
4884-S2_S2_L005_R1_001.fastq.gz
4884-S3_S3_L005_R1_001.fastq.gz

'tail'
4884-S4_S4_L005_R1_001.fastq.gz
4884-S5_S5_L005_R1_001.fastq.gz
4884-S6_S6_L005_R1_001.fastq.gz

cdhit-est 0.95 identity "transcriptome"
Theama_mediterranea_20200402.fasta_annotated_shortHeaders_CDHIT95.fa
Theama_mediterranea_20200402.fasta_annotated_shortHeaders_CDHIT95.fa.clstr

'head quantification'
4884-S1_S1_L005_R1_001.fastq.gz.quant.sf
4884-S2_S2_L005_R1_001.fastq.gz.quant.sf
4884-S3_S3_L005_R1_001.fastq.gz.quant.sf

'tail quantification'
4884-S4_S4_L005_R1_001.fastq.gz.quant.sf
4884-S5_S5_L005_R1_001.fastq.gz.quant.sf
4884-S6_S6_L005_R1_001.fastq.gz.quant.sf

'DESeq2'
Assay_Tail_Vs_Head_clean.csv
R_session

'transcripts on genomic contigs"
Transcripts_on_genomic_contigs.ods

'primer list'
Theama_primerlist.xlsx

4) Genomic DNA Illumina reads

Theama_gDNA_illumina_1_R1.fastq.gz
Theama_gDNA_illumina_1_R1.fastq.gz

5) Final polished draft genome

'unmasked polished genome'
Theama_guppy5015_SUP_q7_flye283_4000ovl_medaka_1_pilon_round4_purgehaplo+mito.fasta

'repeat-masking'
genome-families.fa
genome-families.fa
>>> Theama_guppy5015_SUP_q7_flye283_4000ovl_medaka_1_pilon_round4_purgehaplo+mito.masked (=genome)

5) Augustus gene prediction
augustus.hints.aa
augustus.hints.codingseq
augustus.hints.gff3