diff --git a/runs/merged_isa_metadata/merged_isa.tsv b/runs/merged_isa_metadata/merged_isa.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..24bea101e89b855a18d5d294556d6d0f0ca4f170
--- /dev/null
+++ b/runs/merged_isa_metadata/merged_isa.tsv
@@ -0,0 +1,7 @@
+"Sample.Name.3"	"Sample.Name.2"	"Source.Name"	"Characteristics.[Organism]"	"Term.Source.REF.(NFDI4PSO:0000030)"	"Term.Accession.Number.(NFDI4PSO:0000030)"	"Characteristics.[Biological.replicate]"	"Term.Source.REF.(NFDI4PSO:0000042)"	"Term.Accession.Number.(NFDI4PSO:0000042)"	"Characteristics.[Organism.part]"	"Term.Source.REF.(NFDI4PSO:0000032)"	"Term.Accession.Number.(NFDI4PSO:0000032)"	"Characteristics.[age]"	"Term.Source.REF.(NFDI4PSO:0000033)"	"Term.Accession.Number.(NFDI4PSO:0000033)"	"Characteristics.[Developmental.Stage]"	"Term.Source.REF.(NFDI4PSO:0000070)"	"Term.Accession.Number.(NFDI4PSO:0000070)"	"Characteristics.[study.type]"	"Term.Source.REF.(PECO:0007231)"	"Term.Accession.Number.(PECO:0007231)"	"Parameter.[growth.chamber.company]"	"Term.Source.REF.().x"	"Term.Accession.Number.().x"	"Characteristics.[plant.growth.medium.exposure]"	"Term.Source.REF.(PECO:0007147)"	"Term.Accession.Number.(PECO:0007147)"	"Parameter.[Flower.pot]"	"Term.Source.REF.(#2).x"	"Term.Accession.Number.(#2).x"	"Characteristics.[Growth.day.length]"	"Term.Source.REF.(NFDI4PSO:0000041)"	"Term.Accession.Number.(NFDI4PSO:0000041)"	"Characteristics.[light.intensity.exposure]"	"Unit.x"	"Term.Source.REF.(PECO:0007224)"	"Term.Accession.Number.(PECO:0007224)"	"Characteristics.[Humidity.Day]"	"Unit.(#2).x"	"Term.Source.REF.(NFDI4PSO:0000005)"	"Term.Accession.Number.(NFDI4PSO:0000005)"	"Characteristics.[Humidity.Night]"	"Unit.(#3)"	"Term.Source.REF.(NFDI4PSO:0000006)"	"Term.Accession.Number.(NFDI4PSO:0000006)"	"Characteristics.[Temperature.Day]"	"Unit.(#4)"	"Term.Source.REF.(NFDI4PSO:0000007)"	"Term.Accession.Number.(NFDI4PSO:0000007)"	"Characteristics.[Temperature.Night]"	"Unit.(#5)"	"Term.Source.REF.(NFDI4PSO:0000008)"	"Term.Accession.Number.(NFDI4PSO:0000008)"	"Characteristics.[watering.exposure]"	"Term.Source.REF.(PECO:0007383)"	"Term.Accession.Number.(PECO:0007383)"	"Characteristics.[Sample.Collection.Date]"	"Term.Source.REF.(NFDI4PSO:0000075)"	"Term.Accession.Number.(NFDI4PSO:0000075)"	"Characteristics.[Sample.Collected.By]"	"Term.Source.REF.(NFDI4PSO:0000076)"	"Term.Accession.Number.(NFDI4PSO:0000076)"	"Characteristics.[Time.point]"	"Term.Source.REF.(NFDI4PSO:0000034)"	"Term.Accession.Number.(NFDI4PSO:0000034)"	"Parameter.[Sample.Collection.Method]"	"Term.Source.REF.(NFDI4PSO:0000009)"	"Term.Accession.Number.(NFDI4PSO:0000009)"	"Parameter.[Metabolism.quenching.method]"	"Term.Source.REF.(NFDI4PSO:0000010)"	"Term.Accession.Number.(NFDI4PSO:0000010)"	"Parameter.[Sample.storage]"	"Term.Source.REF.(NFDI4PSO:0000011)"	"Term.Accession.Number.(NFDI4PSO:0000011)"	"Factor.[Photosynthesis.mode]"	"Term.Source.REF.(#3)"	"Term.Accession.Number.(#3)"	"Parameter.[Bio.entity]"	"Term.Source.REF.(NFDI4PSO:0000012)"	"Term.Accession.Number.(NFDI4PSO:0000012)"	"Factor.[Biosource.amount]"	"Unit.y"	"Term.Source.REF.(NFDI4PSO:0000013)"	"Term.Accession.Number.(NFDI4PSO:0000013)"	"Parameter.[Extraction.method]"	"Term.Source.REF.(NFDI4PSO:0000054)"	"Term.Accession.Number.(NFDI4PSO:0000054)"	"Parameter.[Extraction.buffer]"	"Term.Source.REF.(NFDI4PSO:0000050)"	"Term.Accession.Number.(NFDI4PSO:0000050)"	"Parameter.[Extraction.buffer.volume]"	"Unit.(#2).y"	"Term.Source.REF.(NFDI4PSO:0000051)"	"Term.Accession.Number.(NFDI4PSO:0000051)"	"Factor.[RNA.quality.check]"	"Term.Source.REF.(NFDI4PSO:0000062)"	"Term.Accession.Number.(NFDI4PSO:0000062)"	"Parameter.[Library.strategy]"	"Term.Source.REF.(NFDI4PSO:0000035)"	"Term.Accession.Number.(NFDI4PSO:0000035)"	"Parameter.[Library.Selection]"	"Term.Source.REF.(NFDI4PSO:0000036)"	"Term.Accession.Number.(NFDI4PSO:0000036)"	"Parameter.[Library.layout]"	"Term.Source.REF.().y"	"Term.Accession.Number.().y"	"Parameter.[rRNA.Depletion]"	"Term.Source.REF.(#2).y"	"Term.Accession.Number.(#2).y"	"Parameter.[Library.preparation.kit]"	"Term.Source.REF.(NFDI4PSO:0000037)"	"Term.Accession.Number.(NFDI4PSO:0000037)"	"Parameter.[Library.preparation.kit.version]"	"Term.Source.REF.(NFDI4PSO:0000038)"	"Term.Accession.Number.(NFDI4PSO:0000038)"	"Factor.[Adapter.sequence]"	"Term.Source.REF.(NFDI4PSO:0000039)"	"Term.Accession.Number.(NFDI4PSO:0000039)"	"Unit"	"Term.Source.REF.(NFDI4PSO:0000016)"	"Term.Accession.Number.(NFDI4PSO:0000016)"	"Parameter.[Next.generation.sequencing.instrument.model]"	"Term.Source.REF.(NFDI4PSO:0000040)"	"Term.Accession.Number.(NFDI4PSO:0000040)"	"Parameter.[Base-calling.Software]"	"Term.Source.REF.(NFDI4PSO:0000017)"	"Term.Accession.Number.(NFDI4PSO:0000017)"	"Parameter.[Base-calling.Software.Version]"	"Term.Source.REF.(NFDI4PSO:0000018)"	"Term.Accession.Number.(NFDI4PSO:0000018)"	"Parameter.[Library.strand]"	"Term.Source.REF.(NFDI4PSO:0000020)"	"Term.Accession.Number.(NFDI4PSO:0000020)"	"Data.File.Name"	"Parameter.[Raw.data.file.format]"	"Term.Source.REF.(NFDI4PSO:0000021)"	"Term.Accession.Number.(NFDI4PSO:0000021)"
+"1"	"CAM_01_ext"	"CAM_01"	"DB_097"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep1"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	80	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"CAGATC"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_097_CAMMD_CAGATC_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"2"	"CAM_02_ext"	"CAM_02"	"DB_099"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep2"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	78	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.7 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"CTTGTA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"3"	"CAM_03_ext"	"CAM_03"	"DB_103"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep3"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"12 days drought"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"CAM"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	93	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 6.5 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"AGTCAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"4"	"reC3_01_ext"	"reC3_01"	"DB_161"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep1"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	82	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.8 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTCCGC"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"5"	"reC3_02_ext"	"reC3_02"	"DB_163"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep2"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	96	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTGAAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
+"6"	"reC3_03_ext"	"reC3_03"	"DB_165"	"Talinum triangulare"	"user-specific"	"user-specific"	"rep3"	"user-specific"	"user-specific"	"Leaf"	"PO"	"http://purl.obolibrary.org/obo/PO_0025034"	"28 days after germination"	"user-specific"	"user-specific"	"Mature"	"user-specific"	"user-specific"	"growth chamber study"	"PECO"	"http://purl.obolibrary.org/obo/PECO_0007269"	"Environmental Growth Chambers, Ohio"	"user-specific"	"user-specific"	"Miracle-Gro Potting Mix"	"user-specific"	"user-specific"	"Stuewe and Sons \"Short-One\" treepots, 1.6 L"	"user-specific"	"user-specific"	"12 hr light / 12 hr dark"	"user-specific"	"user-specific"	425	"microeinstein per square meter per second"	"UO"	"http://purl.obolibrary.org/obo/UO_0000160"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	37	"percent"	"UO"	"http://purl.obolibrary.org/obo/UO_0000187"	30	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	22	"degree Celsius"	"UO"	"http://purl.obolibrary.org/obo/UO_0000027"	"2 days rewatered"	"user-specific"	"user-specific"	41669	"user-specific"	"user-specific"	"Dominik Brilhaus"	"user-specific"	"user-specific"	"6 Zeitgeber time"	"user-specific"	"user-specific"	"Manually. Cut leave with scissors. "	"user-specific"	"user-specific"	"Shock-freeze in liquid nitrogen"	"user-specific"	"user-specific"	"Freezer -80 <U+00B0>C"	"user-specific"	"user-specific"	"reC3"	"user-specific"	"user-specific"	"mRNA"	"user-specific"	"user-specific"	78	"milligram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000022"	"Roboklon EURx GeneMATRIX Universal RNA Purification version 2.3 September 2011"	"user-specific"	"user-specific"	"Roboklon commercial buffers"	"user-specific"	"user-specific"	300	"microliter"	"UO"	"http://purl.obolibrary.org/obo/UO_0000101"	"RIN 7.6 (Agilent Bioanalyzer 2100 expert_Plant RNA Nano)"	"user-specific"	"user-specific"	"RNA-Seq"	"user-specific"	"user-specific"	"cDNA method"	"user-specific"	"user-specific"	"single"	"user-specific"	"user-specific"	"DNase (New England Biolabs)"	"user-specific"	"user-specific"	"Illumina TruSeq RNA Sample Prep Kit"	"user-specific"	"user-specific"	"version 2"	"user-specific"	"user-specific"	"GTGAAA"	"user-specific"	"user-specific"	"microgram"	"UO"	"http://purl.obolibrary.org/obo/UO_0000023"	"Illumina HiSeq 2000 Rapid Run"	"user-specific"	"user-specific"	"Illumina Cassava"	"user-specific"	"user-specific"	"v1.8.2"	"user-specific"	"user-specific"	"Forward"	"user-specific"	"user-specific"	"DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"	"*.fastq.gz"	"user-specific"	"user-specific"
diff --git a/workflows/merge_isa_metadata.R b/workflows/merge_isa_metadata.R
new file mode 100644
index 0000000000000000000000000000000000000000..4af0582c61dbd55afb9cd3f7eb014c0315157e96
--- /dev/null
+++ b/workflows/merge_isa_metadata.R
@@ -0,0 +1,91 @@
+#!/usr/bin/env Rscript
+
+################################################
+#### Test area
+################################################
+
+# arc_root <- "~/03_DataPLANT_gitlab/samplearc_rnaseq/"
+# in_isa_study <- "studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth"
+# in_isa_assay <- "assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq"
+# out_folder <- "runs/merged_isa_metadata"
+
+################################################
+#### Load required library
+################################################
+
+library(openxlsx)
+# library(tidyverse)
+
+################################################
+#### Read arguments from CLI
+################################################
+
+args <- commandArgs(trailingOnly = T)
+
+arc_root <- args[1]
+in_isa_study <- args[2]
+in_isa_assay <- args[3]
+out_folder <- args[4]
+
+# setwd(arc_root)
+
+################################################
+#### Read metadata from isa excel workbooks
+################################################
+
+isa_study <- unlist(strsplit(paste(arc_root, in_isa_study, sep = "/"), split = ":"))
+isa_assay <- unlist(strsplit(paste(arc_root, in_isa_assay, sep = "/"), split = ":"))
+
+isa_sheets <- list()
+for(i in 2:length(isa_study))
+{
+  isa_sheets[[length(isa_sheets) + 1]] <- readWorkbook(isa_study[1], isa_study[i], startRow = 1)
+}
+
+for(i in 2:length(isa_assay))
+{
+  isa_sheets[[length(isa_sheets) + 1]] <- readWorkbook(isa_assay[1], isa_assay[i], startRow = 1)
+}
+
+################################################
+#### Merge consecutively right (Source.Name) to left (Sample.Name)
+################################################
+
+isa_merged <- isa_sheets[[1]]
+
+for(j in 2:length(isa_sheets))
+# for(j in 2)
+{
+  isa_merged <- merge(isa_merged,
+                    isa_sheets[[j]],
+                    by.x = "Sample.Name",
+                    by.y = "Source.Name",
+  )
+
+  # Rename duplicated Sample.Name column
+
+  colnames(isa_merged)[which(colnames(isa_merged) == "Sample.Name")] <- paste("Sample.Name", j, sep = ".")
+  colnames(isa_merged)[which(colnames(isa_merged) == "Sample.Name.y")] <- "Sample.Name"
+
+}
+
+
+## remove empty columns
+isa_merged <- isa_merged[, !apply(isa_merged, 2, function(x) {
+  sum(is.na(x)) == nrow(isa_merged)
+})]
+
+
+################################################
+#### Write to file
+################################################
+
+## Create directory 
+dir.create(paste(arc_root, out_folder, sep = "/"), recursive = T, showWarnings = F)
+# dir.create(out_folder, recursive = T, showWarnings = F)
+
+## Write 
+write.table(isa_merged, file = paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t")
+
+
+# View(read.csv(paste(arc_root, out_folder, "merged_isa.tsv", sep = "/"), sep = "\t"))
diff --git a/workflows/merge_isa_metadata.cwl b/workflows/merge_isa_metadata.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..d812914728833fca5140a2b9347c5e6994aa52ce
--- /dev/null
+++ b/workflows/merge_isa_metadata.cwl
@@ -0,0 +1,37 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+inputs:
+- id: r_script
+  type: File
+  inputBinding:
+    position: 0
+- id: arc_root
+  type: string
+  inputBinding:
+    position: 1
+- id: in_isa_study
+  type: string
+  inputBinding:
+    position: 2
+- id: in_isa_assay
+  type: string
+  inputBinding:
+    position: 3
+- id: out_folder
+  type: string
+  inputBinding:
+    position: 4
+
+outputs:
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
+
+baseCommand:
+- Rscript
diff --git a/workflows/merge_isa_metadata.yml b/workflows/merge_isa_metadata.yml
new file mode 100644
index 0000000000000000000000000000000000000000..27806b37bcecb76072082d9b59c706795309468f
--- /dev/null
+++ b/workflows/merge_isa_metadata.yml
@@ -0,0 +1,8 @@
+cores: 1
+r_script:
+  class: File
+  path: ./merge_isa_metadata.R
+arc_root: /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/
+in_isa_study: studies/TalinumFacultativeCAM/isa.study.xlsx:plant_growth
+in_isa_assay: assays/Talinum_RNASeq_minimal/isa.assay.xlsx:2EXT01_RNA:3ASY01_RNASeq
+out_folder: runs/merged_isa_metadata
\ No newline at end of file