view test-data/Metadata_files/DRR011117.tsv @ 1:3f1ee30e39e9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 4f31c74918fc999e01c3e8bc1156ecd79efbc39b

run_accession	experiment_title	sample_accession	project_name	submission_accession	library_min_fragment_size	bam_md5	assembly_software	library_prep_longitude	library_selection	pcr_isolation_protocol	chip_protocol	sequencing_primer_provider	serotype	environment_feature	last_updated	submitted_galaxy	extraction_protocol	germline	secondary_project	culture_collection	submission_tool	sra_bytes	read_strand	rna_purity_280_ratio	hi_c_protocol	collected_by	submitted_ftp	restriction_enzyme_target_sequence	isolate	fastq_bytes	instrument_platform	variety	sequencing_date_format	temperature	sra_aspera	ecotype	submitted_aspera	sampling_campaign	bam_ftp	tissue_lib	environmental_sample	control_experiment	sex	submitted_md5	checklist	fastq_galaxy	library_gen_protocol	specimen_voucher	library_prep_latitude	submitted_bytes	taxonomic_identity_marker	run_date	country	ncbi_reporting_standard	sample_description	sra_galaxy	sample_prep_interval	fastq_md5	secondary_study_accession	experimental_protocol	read_count	study_title	bio_material	rna_prep_5_protocol	host_body_site	local_environmental_context	assembly_quality	collection_date_end	sample_capture_status	sample_title	host_genotype	host_phenotype	environmental_medium	cultivar	instrument_model	faang_library_selection	target_gene	bam_bytes	library_max_fragment_size	experiment_target	sequencing_date	description	nominal_sdev	chip_ab_provider	environment_material	host_tax_id	sample_material	sample_storage_processing	sra_md5	cell_type	fastq_ftp	disease	sample_prep_interval_units	broker_name	sub_strain	base_count	library_strategy	restriction_site	serovar	investigation_type	location	library_source	sra_ftp	age	library_layout	experimental_factor	sequencing_primer_catalog	environment_biome	rna_purity_230_ratio	dnase_protocol	dev_stage	library_prep_date_format	bam_aspera	binning_software	datahub	rna_integrity_num	library_prep_date	location_start	marine_region	aligned	file_location	sample_collection	chip_target	nominal_length	broad_scale_environmental_context	sequencing_location	status	completeness_score	lon	fastq_aspera	tax_lineage	host_sex	library_pcr_isolation_protocol	sample_alias	mating_type	collection_date_start	sub_species	contamination_score	run_alias	restriction_enzyme	depth	submitted_read_type	library_construction_protocol	host_growth_conditions	collection_date	experiment_alias	host_gravidity	center_name	identified_by	cell_line	sampling_site	host	library_name	tag	first_created	lat	strain	experiment_accession	scientific_name	host_status	tax_id	study_accession	submitted_format	submitted_host_sex	bisulfite_protocol	altitude	rt_prep_protocol	host_scientific_name	bam_galaxy	accession	secondary_sample_accession	sample_storage	cage_protocol	sampling_platform	taxonomic_classification	location_end	protocol_label	elevation	salinity	sequencing_method	sequencing_primer_lot	first_public	transposase_protocol	study_alias
DRR011117	454 GS Junior sequencing: HXVJWSB01__Yaku_0782__ITS3	SAMD00008419	rhizosphere metagenome	DRA001010					PCR						2015-06-19							163157								23102	LS454				fasp.sra.ebi.ac.uk:/vol1/drr/DRR011/DRR011117											ftp.sra.ebi.ac.uk/vol1/fastq/DRR011/DRR011117/DRR011117.fastq.gz						1352764800000		Generic	HXVJWSB01__Yaku_0782__ITS3	ftp.sra.ebi.ac.uk/vol1/drr/DRR011/DRR011117		b737064403c17493036beee0987a0556	DRP001052		104	Complex community structure of ectomycorrhizal, arbuscular-mycorrhizal and root-endophytic fungi in a mixed subtropical forest of ectomycorrhizal and arbuscular-mycorrhizal plants								HXVJWSB01__Yaku_0782__ITS3					454 GS Junior							454 GS Junior sequencing: HXVJWSB01__Yaku_0782__ITS3							105143a627249be0bcc20c7755c1adcf		ftp.sra.ebi.ac.uk/vol1/fastq/DRR011/DRR011117/DRR011117.fastq.gz					51498	AMPLICON					METAGENOMIC	ftp.sra.ebi.ac.uk/vol1/drr/DRR011/DRR011117		SINGLE										dcc_metagenome												public			fasp.sra.ebi.ac.uk:/vol1/fastq/DRR011/DRR011117/DRR011117.fastq.gz	1;2787823;12908;408169;410657;939928			SAMD00008419					DRR011117				We sequenced fungal ITS sequences based on a tag-encoded massively-parallel pyrosequencing. For each root sample, the entire ITS region and partial ribosomal large subunit region was amplified using the fungus-specific high-coverage primer ITS1F_KYO2 and the universal primer LR3 (http://www.biology.duke.edu /fungi/mycolab/primers.htm). PCR was conducted using a temperature profile of 95??C for 10 min, followed by 20 cycles at 94??C for 20 s, 50??C for 30 s, 72??C for 120 s and a final extension at 72??C for 7 min with a buffer system of Ampdirect Plus and BIOTAQ HS DNA Polymerase (Shimadzu, Kyoto, Japan). The PCR product of each root sample was subjected to a second PCR step targeting the ITS2 region. The second PCR was conducted with a universal primer ITS3_KYO2 fused with the 454 Adaptor A and each sample-specific molecular ID, and the reverse universal primer LR_KYO1b (5'-MGC WGC ATT CCC AAA CWA-3') fused with the 454 Adaptor B. A buffer system of Taq DNA Polymerase with Standard Taq Buffer (New England BioLabs, Ipswich, MA, USA) was used under a temperature profile of 95??C for 1 min, followed by 40 cycles at 94??C for 20 s, 50??C for 30 s, 72??C for 60 s and a final extension at 72??C for 7 min. The ITS amplicons of the second PCR step were subjected to pyrosequencing. The first 576 and the second 624 samples were sequenced separately using a GS Junior sequencer (Roche). The rbcL amplicons of the first 480 root samples were pooled and purified using ExoSAP-IT (GE Healthcare) and QIAquick PCR Purification Kit (QIAGEN). The sequencing of the first 576 samples was conducted as instructed by the manufacturer. Likewise, the amplicons of the remaining 624 samples were pooled and purified, and then sequenced in the second run.			DRX010073		KYOTO_HE					HXVJWSB01__Yaku_0782__ITS3		2014-04-28			DRX010073	rhizosphere metagenome		939928	PRJDB2078								DRR011117	DRS009918											2014-04-28		PRJDB2078