PRPF4 RNA-Seq in HepG2


RBP	PRPF4
Cell_Line	HepG2
Method	shRNA
Exp_Name	PRPF4-BGHLV37-HepG2
ENCODE_series_ID	ENCSR360MWJ
Batch_ID	BGHLV37
Pool ID	Pool-181119
Local_Set_Name	set41_spikeins
ENCODE_KD_Exp_ID	ENCSR466NRW
ENCODE_CN_Exp_ID	ENCSR093ERJ
Rep1	PRPF4-BGHLV37-41D
Rep2	PRPF4-BGHLV37-42D
CN1	NT-BGHLV37-1D
CN2	NT-BGHLV37-2D
Rep1_qPCR	64.7
Rep2_qPCR	73.5
Rep1_WB	51.0
Rep2_WB	53.8
Antibody Cat#	RN093PW
Antibody Lot#	RN093PW
Antibody DCC ID	ENCAB624FBH
Status	Released
Project	ENCODE4
ID	882

	BGHLV37-41	BGHLV37-42
idx	953	954
TRCN#_or_BGC#	TRCN0000074772	TRCN0000074772
shRNA_or_gRNA_sequence	GCAAAGTGATGGGCCTAGATA	GCAAAGTGATGGGCCTAGATA
PAM
Name	PRPF4	PRPF4
Sample_ID	BGHLV37-41	BGHLV37-42
transduction_Date	9/1/16	9/1/16
days
RBP_name	PRPF4	PRPF4
qPCR_result	64.7	73.5
Ave_qPCR	69.1
RT-qPCR_primer-F	ctgcatcaggaaggccatag
RT-qPCR_primer-R	aaactcgaccaaatgcatcc
protein_conc	4127	4400
WB_result	51.0	53.8
Ave_WB	52.4
WB_DONE_date	9/16/16	WES
MW	60kDa
IP	1	1
antibody_Cat#	RN093PW	RN093PW
Antibody DCC ID	ENCAB624FBH	ENCAB624FBH
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library	5/11/17	5/11/17
Note
ID	3046	3047

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-42	BGHLV37-42	BGHLV37-42
Sample #			63			64
Sample Name	PRPF4-BGHLV37-41	PRPF4-BGHLV37-41B	PRPF4-BGHLV37-41D	PRPF4-BGHLV37-42	PRPF4-BGHLV37-42B	PRPF4-BGHLV37-42D
Sample_Name_Alias	PRPF4_BGHLV37-41	PRPF4-BGHLV37-41B		PRPF4_BGHLV37-42	PRPF4-BGHLV37-42B
Index Well Position	S25	S07	S07	S27	S08	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-11-03	2017-05-11	2018-11-19	2016-11-03	2017-05-11	2018-11-19
Lib_ID	Lib-161103	Lib-170511	Lib-181119	Lib-161103	Lib-170511	Lib-181119
Tecan_Location
Tecan
Tecan_date
Size_bp			283			287
Peak_Molarity			72.30			62.50
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/G3.png	DNA_Library_set39/set2/G5.png	DNA_Library_set41/set1/G7.png	DNA_Library_LV37-38/set1/H3.png	DNA_Library_set39/set2/H5.png	DNA_Library_set41/set1/H7.png
RIN	9.8	9.8	9.8	10.0	10.0	10.0
libSample_RNA_Well	RNA_Library_LV37_38/set1/G1.png	RNA_Library_LV37_38/set1/G1.png	RNA_Library_LV37_38/set1/G1.png	RNA_Library_LV37_38/set1/H1.png	RNA_Library_LV37_38/set1/H1.png	RNA_Library_LV37_38/set1/H1.png
SampleQC_method			TapeStation			TapeStation
SampleQC_date			2022-03-01			2022-03-01
Sample_ID	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-42	BGHLV37-42	BGHLV37-42
RBP	PRPF4	PRPF4	PRPF4	PRPF4	PRPF4	PRPF4
Batch_ID	BGHLV37	BGHLV37	BGHLV37	BGHLV37	BGHLV37	BGHLV37
WB_result	51.000	51.000	51.000	53.800	53.800	53.800
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B	D		B	D
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE3	ENCODE3	ENCODE4
ID	2984	3034	3240	2985	3035	3241

Sequencing Information

	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-42	BGHLV37-42	BGHLV37-42
Sample_ID	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-42	BGHLV37-42	BGHLV37-42
Sample Name	PRPF4_BGHLV37-41	PRPF4-BGHLV37-41B	PRPF4-BGHLV37-41D	PRPF4_BGHLV37-42	PRPF4-BGHLV37-42B	PRPF4-BGHLV37-42D
Pool ID	Pool-161129	Pool-170911	Pool-181119	Pool-161129	Pool-170911	Pool-181119
LocalServer_folder	set37	set39_H	set41_spikeins	set37	set39_H	set41_spikeins
total_reads	101,000,000	61,541,404	29,595,770	40,762,928	70,124,694	30,625,840
total_aligned_reads	92,089,690	54,197,186	28,241,278	35,504,512	62,195,920	28,338,852
unique_aligned_reads	86,620,222	50,993,724	26,492,888	32,982,366	58,417,676	26,610,794
percent_uniqueAligned	0.85763	0.82861	0.89516	0.80913	0.83305	0.86890
correlation_replicates	0.721942	0.994598	0.999257	0.721942	0.994598	0.999257
spikein_reads	336,362	6	69,620	734	284	54,504
percent_spikeins	0.00333		0.00235	0.00002		0.00178
original_ReadLength	100	100	100	100	100	100
QC_Status	BadCorrelation	Submitted	Submitted	BadCorrelation	Submitted	Submitted
ID	1633	1689	1953	1634	1690	1954

	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-42	BGHLV37-42
ENCODE_alias	brenton-graveley:PRPF4-BGHLV37-B	brenton-graveley:PRPF4-BGHLV37-HepG2_A	brenton-graveley:PRPF4-BGHLV37-D	brenton-graveley:L-PRPF4-BGHLV37-41D	brenton-graveley:PRPF4-BGHLV37-HepG2	brenton-graveley:PRPF4-BGHLV37-41B	brenton-graveley:L-PRPF4-BGHLV37-42D	brenton-graveley:PRPF4-BGHLV37-42B
ENCODE_accession	ENCSR215FRI	ENCSR714IVS	ENCSR466NRW	ENCLB068KGS	ENCSR360MWJ	ENCBS528KLM	ENCLB294KUJ	ENCBS334WBP
object_type	experiment	experiment	experiment	library	gene_silencing_series	biosample	library	biosample
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-41	BGHLV37-42	BGHLV37-42
Sample Name	PRPF4-BGHLV37-41B	PRPF4-BGHLV37-41B	PRPF4-BGHLV37-41D	PRPF4-BGHLV37-41D	PRPF4-BGHLV37-41D	PRPF4-BGHLV37-41B	PRPF4-BGHLV37-42D	PRPF4-BGHLV37-42B
Selected	Yes	No	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2022-03-07	2019-03-13	2022-03-07	2019-03-13
Project	ENCODE3	ENCODE3	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
				LV41_library_protocol_spikeins		LV39_biosample_protocol	LV41_library_protocol_spikeins	LV39_biosample_protocol
protocol_URL				L-PRPF4-BGHLV37-41D.pdf		PRPF4-BGHLV37-41B.pdf	L-PRPF4-BGHLV37-42D.pdf	PRPF4-BGHLV37-42B.pdf
ID	3208	6867	7377	7395	7418	7426	7396	7427

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
PRPF4_BGHLV37-41_ACTGAT_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1633	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22040
PRPF4_BGHLV37-41_ACTGAT_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1633	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22056
PRPF4_BGHLV37-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1633					GRCh38	V40	PRPF4_BGHLV37-41_ACTGAT_L006_001.R1.fastq.gz,PRPF4_BGHLV37-41_ACTGAT_L006_001.R2.fastq.gz		ENCORE2	22072
PRPF4_BGHLV37-41_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1633					GRCh38	V40	PRPF4_BGHLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	22088
PRPF4_BGHLV37-41_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1633					GRCh38	V40	PRPF4_BGHLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	22104
PRPF4_BGHLV37-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1633					GRCh38	V40	PRPF4_BGHLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	22120
PRPF4_BGHLV37-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1633					GRCh38	V40	PRPF4_BGHLV37-41/Aligned.sortedByCoord.out.bam		ENCORE2	22136
PRPF4_BGHLV37-41_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1633					GRCh38	V40	PRPF4_BGHLV37-41_ACTGAT_L006_001.R1.fastq.gz,PRPF4_BGHLV37-41_ACTGAT_L006_001.R2.fastq.gz		ENCORE2	22152
PRPF4-BGHLV37-41B_CAGATC_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1689	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R1.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE3	22284
PRPF4-BGHLV37-41B_CAGATC_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1689	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R2.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE3	22308
PRPF4-BGHLV37-41B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1689					GRCh38	V40	PRPF4-BGHLV37-41B_CAGATC_ACBE67ANXX_L001_001.R1.fastq.gz,PRPF4-BGHLV37-41B_CAGATC_ACBE67ANXX_L001_001.R2.fastq.gz		ENCORE2	22332
PRPF4-BGHLV37-41B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1689					GRCh38	V40	PRPF4-BGHLV37-41B/Aligned.sortedByCoord.out.bam		ENCORE2	22356
PRPF4-BGHLV37-41B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1689					GRCh38	V40	PRPF4-BGHLV37-41B/Aligned.sortedByCoord.out.bam		ENCORE2	22380
PRPF4-BGHLV37-41B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1689					GRCh38	V40	PRPF4-BGHLV37-41B/Aligned.sortedByCoord.out.bam		ENCORE2	22404
PRPF4-BGHLV37-41B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1689					GRCh38	V40	PRPF4-BGHLV37-41B/Aligned.sortedByCoord.out.bam		ENCORE2	22428
PRPF4-BGHLV37-41B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1689					GRCh38	V40	PRPF4-BGHLV37-41B_CAGATC_ACBE67ANXX_L001_001.R1.fastq.gz,PRPF4-BGHLV37-41B_CAGATC_ACBE67ANXX_L001_001.R2.fastq.gz		ENCORE2	22452
PRPF4-BGHLV37-41D_CAGATC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1953	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27421
PRPF4-BGHLV37-41D_CAGATC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1953	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27449
PRPF4-BGHLV37-41D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1953					GRCh38	V40	PRPF4-BGHLV37-41D_CAGATC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BGHLV37-41D_CAGATC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27477
PRPF4-BGHLV37-41D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1953					GRCh38	V40	PRPF4-BGHLV37-41D/Aligned.sortedByCoord.out.bam		ENCORE2	27505
PRPF4-BGHLV37-41D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1953					GRCh38	V40	PRPF4-BGHLV37-41D/Aligned.sortedByCoord.out.bam		ENCORE2	27533
PRPF4-BGHLV37-41D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1953					GRCh38	V40	PRPF4-BGHLV37-41D/Aligned.sortedByCoord.out.bam		ENCORE2	27561
PRPF4-BGHLV37-41D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1953					GRCh38	V40	PRPF4-BGHLV37-41D/Aligned.sortedByCoord.out.bam		ENCORE2	27589
PRPF4-BGHLV37-41D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1953					GRCh38	V40	PRPF4-BGHLV37-41D_CAGATC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BGHLV37-41D_CAGATC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27617
PRPF4_BGHLV37-42_ATTCCT_L006_001.R1.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1634	HiSeq2500	100	paired-ended	1				NT_BGHLV37-1_GTCCGC_L005_001.R1.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R1.fastq.gz	ENCODE3	22041
PRPF4_BGHLV37-42_ATTCCT_L006_001.R2.fastq.gz	ENCODE_DATA/set37/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1634	HiSeq2500	100	paired-ended	2				NT_BGHLV37-1_GTCCGC_L005_001.R2.fastq.gz,NT_BGHLV37-2_GTGAAA_L005_001.R2.fastq.gz	ENCODE3	22057
PRPF4_BGHLV37-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1634					GRCh38	V40	PRPF4_BGHLV37-42_ATTCCT_L006_001.R1.fastq.gz,PRPF4_BGHLV37-42_ATTCCT_L006_001.R2.fastq.gz		ENCORE2	22073
PRPF4_BGHLV37-42_Signal.Unique.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1634					GRCh38	V40	PRPF4_BGHLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	22089
PRPF4_BGHLV37-42_Signal.Unique.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1634					GRCh38	V40	PRPF4_BGHLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	22105
PRPF4_BGHLV37-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1634					GRCh38	V40	PRPF4_BGHLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	22121
PRPF4_BGHLV37-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set37/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1634					GRCh38	V40	PRPF4_BGHLV37-42/Aligned.sortedByCoord.out.bam		ENCORE2	22137
PRPF4_BGHLV37-42_quant.sf	ENCODE_DATA/set37/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1634					GRCh38	V40	PRPF4_BGHLV37-42_ATTCCT_L006_001.R1.fastq.gz,PRPF4_BGHLV37-42_ATTCCT_L006_001.R2.fastq.gz		ENCORE2	22153
PRPF4-BGHLV37-42B_ACTTGA_ACBE67ANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1690	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R1.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R1.fastq.gz	ENCODE3	22285
PRPF4-BGHLV37-42B_ACTTGA_ACBE67ANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set39_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1690	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1B_ACAGTG_ACBE67ANXX_L001_001.R2.fastq.gz,NT-BGHLV37-2B_GCCAAT_ACBE67ANXX_L001_001.R2.fastq.gz	ENCODE3	22309
PRPF4-BGHLV37-42B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1690					GRCh38	V40	PRPF4-BGHLV37-42B_ACTTGA_ACBE67ANXX_L002_001.R1.fastq.gz,PRPF4-BGHLV37-42B_ACTTGA_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22333
PRPF4-BGHLV37-42B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1690					GRCh38	V40	PRPF4-BGHLV37-42B/Aligned.sortedByCoord.out.bam		ENCORE2	22357
PRPF4-BGHLV37-42B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1690					GRCh38	V40	PRPF4-BGHLV37-42B/Aligned.sortedByCoord.out.bam		ENCORE2	22381
PRPF4-BGHLV37-42B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1690					GRCh38	V40	PRPF4-BGHLV37-42B/Aligned.sortedByCoord.out.bam		ENCORE2	22405
PRPF4-BGHLV37-42B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1690					GRCh38	V40	PRPF4-BGHLV37-42B/Aligned.sortedByCoord.out.bam		ENCORE2	22429
PRPF4-BGHLV37-42B_quant.sf	ENCODE_DATA/set39_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1690					GRCh38	V40	PRPF4-BGHLV37-42B_ACTTGA_ACBE67ANXX_L002_001.R1.fastq.gz,PRPF4-BGHLV37-42B_ACTTGA_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22453
PRPF4-BGHLV37-42D_ACTTGA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1954	HiSeq2500	100	paired-ended	1				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27422
PRPF4-BGHLV37-42D_ACTTGA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1954	HiSeq2500	100	paired-ended	2				NT-BGHLV37-1D_ACAGTG_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHLV37-2D_GCCAAT_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27450
PRPF4-BGHLV37-42D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1954					GRCh38	V40	PRPF4-BGHLV37-42D_ACTTGA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BGHLV37-42D_ACTTGA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27478
PRPF4-BGHLV37-42D_Signal.Unique.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1954					GRCh38	V40	PRPF4-BGHLV37-42D/Aligned.sortedByCoord.out.bam		ENCORE2	27506
PRPF4-BGHLV37-42D_Signal.Unique.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1954					GRCh38	V40	PRPF4-BGHLV37-42D/Aligned.sortedByCoord.out.bam		ENCORE2	27534
PRPF4-BGHLV37-42D_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1954					GRCh38	V40	PRPF4-BGHLV37-42D/Aligned.sortedByCoord.out.bam		ENCORE2	27562
PRPF4-BGHLV37-42D_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1954					GRCh38	V40	PRPF4-BGHLV37-42D/Aligned.sortedByCoord.out.bam		ENCORE2	27590
PRPF4-BGHLV37-42D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1954					GRCh38	V40	PRPF4-BGHLV37-42D_ACTTGA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,PRPF4-BGHLV37-42D_ACTTGA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27618