Source Name	Comment[ENA_SAMPLE]	Material Type	Characteristics[organism]	Protocol REF	ParameterValue [culture passage]	Sample Name	Material Type	Characteristics [cell type]	Protocol REF	Protocol REF	Extract Name	Material Type	Comment[LIBRARY_LAYOUT]	Comment[LIBRARY_SOURCE]	Comment[LIBRARY_STRATEGY]	Comment[LIBRARY_SELECTION]	Protocol REF	Performer	ParameterValue [SEQUENCE_LENGTH]	ParameterValue [number of reads]	Assay Name	Technology Type	Comment[ENA_EXPERIMENT]	Scan Name	Comment[SUBMITTED_FILE_NAME]	Comment[ENA_RUN]	Comment[FASTQ_URI]	Protocol REF	ParameterValue [number uniquely mapped]	Derived Array Data File	Comment [Derived ArrayExpress FTP file]	Protocol REF	Derived Array Data File	Comment [Derived ArrayExpress FTP file]	FactorValue [cell type]	FactorValue [culture passage]
Pt51	ERS697294	whole organism	Homo sapiens	P-MTAB-44161	0	Human cystic duct monolayer culture from patient 51, unpassaged (biological replicate A)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD51p0_LA7_A	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	11,246,414	CD51p0_LA7_A-GATCAG	sequencing assay	ERX922986	FGC0379_s_1_GATCAG.fastq.gz	FGC0379_s_1_GATCAG.fastq.gz	ERR842905	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842905/ERR842905.fastq.gz	P-MTAB-44165	7,183,891	FGC0379_s_1_GATCAG.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.2.zip	P-MTAB-44166	FGC0379_s_1_GATCAG.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	0
Pt51	ERS697294	whole organism	Homo sapiens	P-MTAB-44161	0	Human cystic duct monolayer culture from patient 51, unpassaged (biological replicate B)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD51p0_LA7_B	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	8,045,992	CD51p0_LA7_B-TAGCTT	sequencing assay	ERX922977	FGC0379_s_1_TAGCTT.fastq.gz	FGC0379_s_1_TAGCTT.fastq.gz	ERR842904	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842904/ERR842904.fastq.gz	P-MTAB-44165	5,136,283	FGC0379_s_1_TAGCTT.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.2.zip	P-MTAB-44166	FGC0379_s_1_TAGCTT.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	0
Pt50	ERS697292	whole organism	Homo sapiens	P-MTAB-44160	4	Human cystic duct 3D culture from patient 50, passage 4 (biological replicate A)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD50p4_orgA	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	20,816,784	CD50p4_orgA-AGTCAA	sequencing assay	ERX922984	FGC0379_s_1_AGTCAA.fastq.gz	FGC0379_s_1_AGTCAA.fastq.gz	ERR842913	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842913/ERR842913.fastq.gz	P-MTAB-44165	1,096,900	FGC0379_s_1_AGTCAA.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.2.zip	P-MTAB-44166	FGC0379_s_1_AGTCAA.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	4
Pt50	ERS697292	whole organism	Homo sapiens	P-MTAB-44160	4	Human cystic duct 3D culture from patient 50, passage 4 (biological replicate B)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD50p4_orgB	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	11,989,045	CD50p4_orgB-GTTTCG	sequencing assay	ERX922976	FGC0379_s_1_GTTTCG.fastq.gz	FGC0379_s_1_GTTTCG.fastq.gz	ERR842908	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842908/ERR842908.fastq.gz	P-MTAB-44165	537,932	FGC0379_s_1_GTTTCG.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.2.zip	P-MTAB-44166	FGC0379_s_1_GTTTCG.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	4
Pt51	ERS697294	whole organism	Homo sapiens	P-MTAB-44161	1	Human cystic duct monolayer culture from patient 51, passage 1	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD51p1_LA7	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	11,519,735	CD51p1_LA7-CGTACG	sequencing assay	ERX922978	FGC0379_s_1_CGTACG.fastq.gz	FGC0379_s_1_CGTACG.fastq.gz	ERR842906	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842906/ERR842906.fastq.gz	P-MTAB-44165	7,990,047	FGC0379_s_1_CGTACG.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.3.zip	P-MTAB-44166	FGC0379_s_1_CGTACG.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	1
Pt50	ERS697292	whole organism	Homo sapiens	P-MTAB-44161	7	Human gallbladder monolayer culture from patient 50, passage 7 (biological replicate A)	cell	gall bladder cell	P-MTAB-44162	P-MTAB-44163	GB50p7_LA7A	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	12,500,486	GB50p7_LA7A-GTAGAG	sequencing assay	ERX922975	FGC0379_s_1_GTAGAG.fastq.gz	FGC0379_s_1_GTAGAG.fastq.gz	ERR842917	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842917/ERR842917.fastq.gz	P-MTAB-44165	8,773,298	FGC0379_s_1_GTAGAG.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.4.zip	P-MTAB-44166	FGC0379_s_1_GTAGAG.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	gall bladder cell	7
Pt50	ERS697292	whole organism	Homo sapiens	P-MTAB-44161	7	Human gallbladder monolayer culture from patient 50, passage 7 (biological replicate B)	cell	gall bladder cell	P-MTAB-44162	P-MTAB-44163	GB50p7_LA7B	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	13,172,728	GB50p7_LA7B-GAGTGG	sequencing assay	ERX922983	FGC0379_s_1_GAGTGG.fastq.gz	FGC0379_s_1_GAGTGG.fastq.gz	ERR842903	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842903/ERR842903.fastq.gz	P-MTAB-44165	9,631,776	FGC0379_s_1_GAGTGG.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.5.zip	P-MTAB-44166	FGC0379_s_1_GAGTGG.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	gall bladder cell	7
Pt50	ERS697292	whole organism	Homo sapiens	P-MTAB-44161	6	Human gallbladder monolayer culture from patient 50, passage 6 (biological replicate A)	cell	gall bladder cell	P-MTAB-44162	P-MTAB-44163	GB50p6_LA7A	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	9,315,656	GB50p6_LA7A-GTCCGC	sequencing assay	ERX922979	FGC0379_s_1_GTCCGC.fastq.gz	FGC0379_s_1_GTCCGC.fastq.gz	ERR842911	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842911/ERR842911.fastq.gz	P-MTAB-44165	6,596,788	FGC0379_s_1_GTCCGC.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.6.zip	P-MTAB-44166	FGC0379_s_1_GTCCGC.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	gall bladder cell	6
Pt50	ERS697292	whole organism	Homo sapiens	P-MTAB-44161	6	Human gallbladder monolayer culture from patient 50, passage 6 (biological replicate B)	cell	gall bladder cell	P-MTAB-44162	P-MTAB-44163	GB50p6_LA7B	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	13715209	GB50p6_LA7B-GGTAGC	sequencing assay	ERX922973	FGC0379_s_1_GGTAGC.fastq.gz	FGC0379_s_1_GGTAGC.fastq.gz	ERR842914	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842914/ERR842914.fastq.gz	P-MTAB-44165	9894454	FGC0379_s_1_GGTAGC.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.7.zip	P-MTAB-44166	FGC0379_s_1_GGTAGC.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	gall bladder cell	6
Pt49	ERS697293	whole organism	Homo sapiens	P-MTAB-44160	3	Human cystic duct 3D culture from patient 49, passage 3 (biological replicate A)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD49p3_orgA	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	21007617	CD49p3_orgA-GTGAAA	sequencing assay	ERX922982	FGC0379_s_1_GTGAAA.fastq.gz	FGC0379_s_1_GTGAAA.fastq.gz	ERR842907	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842907/ERR842907.fastq.gz	P-MTAB-44165	607629	FGC0379_s_1_GTGAAA.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.7.zip	P-MTAB-44166	FGC0379_s_1_GTGAAA.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	3
Pt49	ERS697293	whole organism	Homo sapiens	P-MTAB-44160	3	Human cystic duct 3D culture from patient 49, passage 3 (biological replicate B)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD49p3_orgB	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	8012036	CD49p3_orgB-GGCTAC	sequencing assay	ERX922974	FGC0379_s_1_GGCTAC.fastq.gz	FGC0379_s_1_GGCTAC.fastq.gz	ERR842915	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842915/ERR842915.fastq.gz	P-MTAB-44165	2050770	FGC0379_s_1_GGCTAC.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.7.zip	P-MTAB-44166	FGC0379_s_1_GGCTAC.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	3
Pt52	ERS697290	whole organism	Homo sapiens	P-MTAB-44160	none	Human cystic duct cells (fresh from tissue specimen) from patient 52	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD52_tB	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	21121590	CD52_tB-CTTGTA	sequencing assay	ERX922971	FGC0379_s_1_CTTGTA.fastq.gz	FGC0379_s_1_CTTGTA.fastq.gz	ERR842916	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842916/ERR842916.fastq.gz	P-MTAB-44165	14110694	FGC0379_s_1_CTTGTA.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.8.zip	P-MTAB-44166	FGC0379_s_1_CTTGTA.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	none
Pt34	ERS697291	whole organism	Homo sapiens	P-MTAB-44160	6	Human gallbladder 3D culture from patient 34, passage 6 (biological replicate A)	cell	gall bladder cell	P-MTAB-44162	P-MTAB-44163	GB34p6_orgA	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	3539447	GB34p6_orgA-ATCACG	sequencing assay	ERX922980	FGC0379_s_1_ATCACG.fastq.gz	FGC0379_s_1_ATCACG.fastq.gz	ERR842918	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842918/ERR842918.fastq.gz	P-MTAB-44165	721027	FGC0379_s_1_ATCACG.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.8.zip	P-MTAB-44166	FGC0379_s_1_ATCACG.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	gall bladder cell	6
Pt34	ERS697291	whole organism	Homo sapiens	P-MTAB-44160	6	Human gallbladder 3D culture from patient 34, passage 6 (biological replicate B)	cell	gall bladder cell	P-MTAB-44162	P-MTAB-44163	GB34p6_orgB	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	4268401	GB34p6_orgB-AGTTCC	sequencing assay	ERX922972	FGC0379_s_1_AGTTCC.fastq.gz	FGC0379_s_1_AGTTCC.fastq.gz	ERR842909	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842909/ERR842909.fastq.gz	P-MTAB-44165	377301	FGC0379_s_1_AGTTCC.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.8.zip	P-MTAB-44166	FGC0379_s_1_AGTTCC.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	gall bladder cell	6
Pt48	ERS697295	whole organism	Homo sapiens	P-MTAB-44160	0	Human cystic duct 3D culture from patient 48, unpassaged (biological replicate A)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD48p0_orgA	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	6868123	CD48p0_orgA-ATGTCA	sequencing assay	ERX922981	FGC0379_s_1_ATGTCA.fastq.gz	FGC0379_s_1_ATGTCA.fastq.gz	ERR842912	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842912/ERR842912.fastq.gz	P-MTAB-44165	755390	FGC0379_s_1_ATGTCA.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.8.zip	P-MTAB-44166	FGC0379_s_1_ATGTCA.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	0
Pt48	ERS697295	whole organism	Homo sapiens	P-MTAB-44160	0	Human cystic duct 3D culture from patient 48, unpassaged (biological replicate B)	cell	cystic duct cell	P-MTAB-44162	P-MTAB-44163	CD48p0_orgB	synthetic_DNA	SINGLE	TRANSCRIPTOMIC	RNA-Seq	cDNA	P-MTAB-44164	Penn Functional Genomics Core (FGC)	50	9227081	CD48p0_orgB-CCGTCC	sequencing assay	ERX922985	FGC0379_s_1_CCGTCC.fastq.gz	FGC0379_s_1_CCGTCC.fastq.gz	ERR842910	ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR842/ERR842910/ERR842910.fastq.gz	P-MTAB-44165	891135	FGC0379_s_1_CCGTCC.hsa_mirna.bed	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.8.zip	P-MTAB-44166	FGC0379_s_1_CCGTCC.hsa_mirna.mature-sart.tab	ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3464/E-MTAB-3464.processed.1.zip	cystic duct cell	0