UTP3 RNA-Seq in K562


RBP	UTP3
Cell_Line	K562
Method	shRNA
Exp_Name	UTP3-BGKLV38-K562
ENCODE_series_ID	ENCSR084HQG
Batch_ID	BGKLV38
Pool ID	Pool-181119
Local_Set_Name	set41_spikeins
ENCODE_KD_Exp_ID	ENCSR473KFO
ENCODE_CN_Exp_ID	ENCSR655JYC
Rep1	UTP3-BGKLV38-103D
Rep2	UTP3-BGKLV38-104D
CN1	NT-BGKLV38-1D
CN2	NT-BGKLV38-2D
Rep1_qPCR	78.6
Rep2_qPCR	76.4
Rep1_WB	51.7
Rep2_WB	50.8
Antibody Cat#	A302-067A
Antibody Lot#	A302-067A
Antibody DCC ID	ENCAB872CCU
Status	Released
Project	ENCODE4
ID	884

	BGKLV38-103	BGKLV38-104
idx	874	875
TRCN#_or_BGC#	TRCN0000135598	TRCN0000135598
shRNA_or_gRNA_sequence	GAACTCTTGGAGCTGATAGAA	GAACTCTTGGAGCTGATAGAA
PAM
Name	UTP3	UTP3
Sample_ID	BGKLV38-103	BGKLV38-104
transduction_Date	9/15/16	9/15/16
days
RBP_name	UTP3	UTP3
qPCR_result	78.6	76.4
Ave_qPCR	77.5
RT-qPCR_primer-F	gctgcctgtgctgttacagat
RT-qPCR_primer-R	caagagcctgttcttcagtgc
protein_conc	3106	2761
WB_result	51.7	50.8
Ave_WB	51.2
WB_DONE_date	10/19/16
MW	55kDa
IP	1	1
antibody_Cat#	A302-067A	A302-067A
Antibody DCC ID	ENCAB872CCU	ENCAB872CCU
submitted_to_DCC_date	10/26/16
Rep1_TPM	42.8	0
Rep2_TPM	29.4	0
Action
Library_start_date	11/3/16	11/3/16
repeat_library	5/11/17	5/11/17
Note
ID	971	972

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-104	BGKLV38-104	BGKLV38-104
Sample #			69			70
Sample Name	UTP3-BGKLV38-103	UTP3-BGKLV38-103B	UTP3-BGKLV38-103D	UTP3-BGKLV38-104	UTP3-BGKLV38-104B	UTP3-BGKLV38-104D
Sample_Name_Alias	UTP3_BGKLV38-103	UTP3-BGKLV38-103B		UTP3_BGKLV38-104	UTP3-BGKLV38-104B
Index Well Position	S15	S13	S13	S16	S14	S14
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			288			301
Peak_Molarity			51.40			48.30
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/G5.png	DNA_Library_set39/set2/E6.png	DNA_Library_set41/set1/E8.png	DNA_Library_LV37-38/set1/H5.png	DNA_Library_set39/set2/F6.png	DNA_Library_set41/set1/F8.png
RIN	9.2	9.2	9.2	9.2	9.2	9.2
libSample_RNA_Well	RNA_Library_LV37_38/set1/G3.png	RNA_Library_LV37_38/set1/G3.png	RNA_Library_LV37_38/set1/G3.png	RNA_Library_LV37_38/set1/H3.png	RNA_Library_LV37_38/set1/H3.png	RNA_Library_LV37_38/set1/H3.png
SampleQC_method			TapeStation			TapeStation
SampleQC_date			2022-03-01			2022-03-01
Sample_ID	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-104	BGKLV38-104	BGKLV38-104
RBP	UTP3	UTP3	UTP3	UTP3	UTP3	UTP3
Batch_ID	BGKLV38	BGKLV38	BGKLV38	BGKLV38	BGKLV38	BGKLV38
WB_result	51.700	51.700	51.700	50.800	50.800	50.800
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	3000	3040	3246	3001	3041	3247

Sequencing Information

	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-104	BGKLV38-104	BGKLV38-104
Sample_ID	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-104	BGKLV38-104	BGKLV38-104
Sample Name	UTP3_BGKLV38-103	UTP3-BGKLV38-103B	UTP3-BGKLV38-103D	UTP3_BGKLV38-104	UTP3-BGKLV38-104B	UTP3-BGKLV38-104D
Pool ID	Pool-161129	Pool-170911	Pool-181119	Pool-161129	Pool-170911	Pool-181119
LocalServer_folder	set38	set39_K	set41_spikeins	set38	set39_K	set41_spikeins
total_reads	99,781,210	90,005,652	34,626,318	37,699,984	53,411,444	36,031,860
total_aligned_reads	94,431,094	80,769,796	33,564,588	33,440,640	48,438,272	35,636,100
unique_aligned_reads	86,790,554	73,779,894	30,615,630	28,927,654	44,400,604	32,434,558
percent_uniqueAligned	0.86981	0.81973	0.88417	0.76731	0.83129	0.90016
correlation_replicates	0.777401	0.998814	0.999236	0.777401	0.998814	0.999236
spikein_reads	185,984	100	54,564	510	2	66,394
percent_spikeins	0.00186		0.00158	0.00001		0.00184
original_ReadLength	100	100	100	100	100	100
QC_Status	BadCorrelation	Submitted	Submitted	BadCorrelation	Submitted	Submitted
ID	1649	1695	1959	1650	1696	1960

	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-104	BGKLV38-104
ENCODE_alias	brenton-graveley:UTP3-BGKLV38-B	brenton-graveley:UTP3-BGKLV38-K562_A	brenton-graveley:UTP3-BGKLV38-D	brenton-graveley:L-UTP3-BGKLV38-103D	brenton-graveley:UTP3-BGKLV38-K562	brenton-graveley:UTP3-BGKLV38-103B	brenton-graveley:L-UTP3-BGKLV38-104D	brenton-graveley:UTP3-BGKLV38-104B
ENCODE_accession	ENCSR818TZM	ENCSR565UMT	ENCSR473KFO	ENCLB092PIG	ENCSR084HQG	ENCBS742THM	ENCLB306BLZ	ENCBS532TPY
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	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-103	BGKLV38-104	BGKLV38-104
Sample Name	UTP3-BGKLV38-103B	UTP3-BGKLV38-103B	UTP3-BGKLV38-103D	UTP3-BGKLV38-103D	UTP3-BGKLV38-103D	UTP3-BGKLV38-103B	UTP3-BGKLV38-104D	UTP3-BGKLV38-104B
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-UTP3-BGKLV38-103D.pdf		UTP3-BGKLV38-103B.pdf	L-UTP3-BGKLV38-104D.pdf	UTP3-BGKLV38-104B.pdf
ID	3211	7037	7378	7397	7422	7428	7398	7429

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
UTP3_BGKLV38-103_ATGTCA_L008_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1649	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22180
UTP3_BGKLV38-103_ATGTCA_L008_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1649	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22192
UTP3_BGKLV38-103_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1649					GRCh38	V40	UTP3_BGKLV38-103_ATGTCA_L008_001.R1.fastq.gz,UTP3_BGKLV38-103_ATGTCA_L008_001.R2.fastq.gz		ENCORE2	22204
UTP3_BGKLV38-103_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1649					GRCh38	V40	UTP3_BGKLV38-103/Aligned.sortedByCoord.out.bam		ENCORE2	22216
UTP3_BGKLV38-103_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1649					GRCh38	V40	UTP3_BGKLV38-103/Aligned.sortedByCoord.out.bam		ENCORE2	22228
UTP3_BGKLV38-103_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1649					GRCh38	V40	UTP3_BGKLV38-103/Aligned.sortedByCoord.out.bam		ENCORE2	22240
UTP3_BGKLV38-103_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1649					GRCh38	V40	UTP3_BGKLV38-103/Aligned.sortedByCoord.out.bam		ENCORE2	22252
UTP3_BGKLV38-103_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1649					GRCh38	V40	UTP3_BGKLV38-103_ATGTCA_L008_001.R1.fastq.gz,UTP3_BGKLV38-103_ATGTCA_L008_001.R2.fastq.gz		ENCORE2	22264
UTP3-BGKLV38-103B_AGTCAA_ACBE67ANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1695	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R1.fastq.gz,NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R1.fastq.gz	ENCODE3	22494
UTP3-BGKLV38-103B_AGTCAA_ACBE67ANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1695	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R2.fastq.gz,NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R2.fastq.gz	ENCODE3	22530
UTP3-BGKLV38-103B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1695					GRCh38	V40	UTP3-BGKLV38-103B_AGTCAA_ACBE67ANXX_L002_001.R1.fastq.gz,UTP3-BGKLV38-103B_AGTCAA_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22566
UTP3-BGKLV38-103B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1695					GRCh38	V40	UTP3-BGKLV38-103B/Aligned.sortedByCoord.out.bam		ENCORE2	22602
UTP3-BGKLV38-103B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1695					GRCh38	V40	UTP3-BGKLV38-103B/Aligned.sortedByCoord.out.bam		ENCORE2	22638
UTP3-BGKLV38-103B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1695					GRCh38	V40	UTP3-BGKLV38-103B/Aligned.sortedByCoord.out.bam		ENCORE2	22674
UTP3-BGKLV38-103B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1695					GRCh38	V40	UTP3-BGKLV38-103B/Aligned.sortedByCoord.out.bam		ENCORE2	22710
UTP3-BGKLV38-103B_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1695					GRCh38	V40	UTP3-BGKLV38-103B_AGTCAA_ACBE67ANXX_L002_001.R1.fastq.gz,UTP3-BGKLV38-103B_AGTCAA_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22746
UTP3-BGKLV38-103D_AGTCAA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1959	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27429
UTP3-BGKLV38-103D_AGTCAA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1959	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27457
UTP3-BGKLV38-103D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1959					GRCh38	V40	UTP3-BGKLV38-103D_AGTCAA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,UTP3-BGKLV38-103D_AGTCAA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27485
UTP3-BGKLV38-103D_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	1959					GRCh38	V40	UTP3-BGKLV38-103D/Aligned.sortedByCoord.out.bam		ENCORE2	27513
UTP3-BGKLV38-103D_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	1959					GRCh38	V40	UTP3-BGKLV38-103D/Aligned.sortedByCoord.out.bam		ENCORE2	27541
UTP3-BGKLV38-103D_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	1959					GRCh38	V40	UTP3-BGKLV38-103D/Aligned.sortedByCoord.out.bam		ENCORE2	27569
UTP3-BGKLV38-103D_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	1959					GRCh38	V40	UTP3-BGKLV38-103D/Aligned.sortedByCoord.out.bam		ENCORE2	27597
UTP3-BGKLV38-103D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1959					GRCh38	V40	UTP3-BGKLV38-103D_AGTCAA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,UTP3-BGKLV38-103D_AGTCAA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27625
UTP3_BGKLV38-104_CCGTCC_L008_001.R1.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1650	HiSeq2500	100	paired-ended	1				NT_BGKLV38-1_GATCAG_L007_001.R1.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R1.fastq.gz	ENCODE3	22181
UTP3_BGKLV38-104_CCGTCC_L008_001.R2.fastq.gz	ENCODE_DATA/set38/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1650	HiSeq2500	100	paired-ended	2				NT_BGKLV38-1_GATCAG_L007_001.R2.fastq.gz,NT_BGKLV38-2_TAGCTT_L007_001.R2.fastq.gz	ENCODE3	22193
UTP3_BGKLV38-104_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1650					GRCh38	V40	UTP3_BGKLV38-104_CCGTCC_L008_001.R1.fastq.gz,UTP3_BGKLV38-104_CCGTCC_L008_001.R2.fastq.gz		ENCORE2	22205
UTP3_BGKLV38-104_Signal.Unique.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1650					GRCh38	V40	UTP3_BGKLV38-104/Aligned.sortedByCoord.out.bam		ENCORE2	22217
UTP3_BGKLV38-104_Signal.Unique.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1650					GRCh38	V40	UTP3_BGKLV38-104/Aligned.sortedByCoord.out.bam		ENCORE2	22229
UTP3_BGKLV38-104_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1650					GRCh38	V40	UTP3_BGKLV38-104/Aligned.sortedByCoord.out.bam		ENCORE2	22241
UTP3_BGKLV38-104_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set38/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1650					GRCh38	V40	UTP3_BGKLV38-104/Aligned.sortedByCoord.out.bam		ENCORE2	22253
UTP3_BGKLV38-104_quant.sf	ENCODE_DATA/set38/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1650					GRCh38	V40	UTP3_BGKLV38-104_CCGTCC_L008_001.R1.fastq.gz,UTP3_BGKLV38-104_CCGTCC_L008_001.R2.fastq.gz		ENCORE2	22265
UTP3-BGKLV38-104B_AGTTCC_ACBE67ANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1696	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R1.fastq.gz,NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R1.fastq.gz	ENCODE3	22495
UTP3-BGKLV38-104B_AGTTCC_ACBE67ANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1696	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1B_GGCTAC_ACBE67ANXX_L002_001.R2.fastq.gz,NT-BGKLV38-2B_CTTGTA_ACBE67ANXX_L002_001.R2.fastq.gz	ENCODE3	22531
UTP3-BGKLV38-104B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1696					GRCh38	V40	UTP3-BGKLV38-104B_AGTTCC_ACBE67ANXX_L002_001.R1.fastq.gz,UTP3-BGKLV38-104B_AGTTCC_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22567
UTP3-BGKLV38-104B_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1696					GRCh38	V40	UTP3-BGKLV38-104B/Aligned.sortedByCoord.out.bam		ENCORE2	22603
UTP3-BGKLV38-104B_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1696					GRCh38	V40	UTP3-BGKLV38-104B/Aligned.sortedByCoord.out.bam		ENCORE2	22639
UTP3-BGKLV38-104B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1696					GRCh38	V40	UTP3-BGKLV38-104B/Aligned.sortedByCoord.out.bam		ENCORE2	22675
UTP3-BGKLV38-104B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1696					GRCh38	V40	UTP3-BGKLV38-104B/Aligned.sortedByCoord.out.bam		ENCORE2	22711
UTP3-BGKLV38-104B_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1696					GRCh38	V40	UTP3-BGKLV38-104B_AGTTCC_ACBE67ANXX_L002_001.R1.fastq.gz,UTP3-BGKLV38-104B_AGTTCC_ACBE67ANXX_L002_001.R2.fastq.gz		ENCORE2	22747
UTP3-BGKLV38-104D_AGTTCC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1960	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27430
UTP3-BGKLV38-104D_AGTTCC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41_spikeins/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1960	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1D_GGCTAC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKLV38-2D_CTTGTA_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27458
UTP3-BGKLV38-104D_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41_spikeins/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1960					GRCh38	V40	UTP3-BGKLV38-104D_AGTTCC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,UTP3-BGKLV38-104D_AGTTCC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27486
UTP3-BGKLV38-104D_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	1960					GRCh38	V40	UTP3-BGKLV38-104D/Aligned.sortedByCoord.out.bam		ENCORE2	27514
UTP3-BGKLV38-104D_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	1960					GRCh38	V40	UTP3-BGKLV38-104D/Aligned.sortedByCoord.out.bam		ENCORE2	27542
UTP3-BGKLV38-104D_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	1960					GRCh38	V40	UTP3-BGKLV38-104D/Aligned.sortedByCoord.out.bam		ENCORE2	27570
UTP3-BGKLV38-104D_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	1960					GRCh38	V40	UTP3-BGKLV38-104D/Aligned.sortedByCoord.out.bam		ENCORE2	27598
UTP3-BGKLV38-104D_quant.sf	ENCODE_DATA/set41_spikeins/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1960					GRCh38	V40	UTP3-BGKLV38-104D_AGTTCC_HJMK5BCX2_L001_R1_001.filtered.trimmed.paired.fastq.gz,UTP3-BGKLV38-104D_AGTTCC_HJMK5BCX2_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27626