non-target RNA-Seq in K562

	BGKcLV04-1	BGKcLV04-2
idx	49	50
TRCN#_or_BGC#	BGC#0000000	BGC#0000000
shRNA_or_gRNA_sequence	CAGTCGGGCGTCATCATGAT	CAGTCGGGCGTCATCATGAT
PAM
Name	non -target	non -target
Sample_ID	BGKcLV04-1	BGKcLV04-2
transduction_Date	6/22/16	6/22/16
days	day 6	day 6
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	2434
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	08/15/16	08/15/16
repeat_library	5/11/17	5/11/17
Note
ID	4147	4148

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2
Sample #				71				72
Sample Name	NT-BGKcLV04-1	NT-BGKcLV04-1B	NT-BGKcLV04-1C	NT-BGKcLV04-1D	NT-BGKcLV04-2	NT-BGKcLV04-2B	NT-BGKcLV04-2C	NT-BGKcLV04-2D
Sample_Name_Alias	NT_BGKcLV04-1	NT_BGKcLV04-1B	NT-BGKcLV04-1B	NT-BGKcLV04-1C	NT_BGKcLV04-2	NT_BGKcLV04-2B	NT-BGKcLV04-2B	NT-BGKcLV04-2C
Index Well Position	S05	S03	S15	S15	S06	S04	S16	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-08-15	2016-11-07	2017-05-11	2018-11-19	2016-08-15	2016-11-07	2017-05-11	2018-11-19
Lib_ID	Lib-160815	Lib-161107	Lib-170511	Lib-181119	Lib-160815	Lib-161107	Lib-170511	Lib-181119
Tecan_Location
Tecan
Tecan_date
Size_bp				284				290
Peak_Molarity				66.40				56.40
libSampleQC_DNA_Well	DNA_Library_LV37-38/set1/C2.png	DNA_Library_LV37-38/set1/C2.png		DNA_Library_set41/set1/G8.png	DNA_Library_LV37-38/set1/D2.png	DNA_Library_LV37-38/set1/D2.png		DNA_Library_set41/set1/H8.png
RIN	9.1	9.1		9.1	9.1	9.1		9.1
libSample_RNA_Well	RNA_Library_cLV04-05/set1/E8.png	RNA_Library_cLV04-05/set1/E8.png		RNA_Library_cLV04-05/set1/E8.png	RNA_Library_cLV04-05/set1/F8.png	RNA_Library_cLV04-05/set1/F8.png		RNA_Library_cLV04-05/set1/F8.png
SampleQC_method				TapeStation				TapeStation
SampleQC_date				2022-03-01				2022-03-01
Sample_ID	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2
RBP	NT	NT	NT	NT	NT	NT	NT	NT
Batch_ID	BGKcLV04	BGKcLV04	BGKcLV04	BGKcLV04	BGKcLV04	BGKcLV04	BGKcLV04	BGKcLV04
WB_result	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B	C	D		B	C	D
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE4	ENCODE3	ENCODE3	ENCODE3	ENCODE4
ID	3008	3026	3086	3248	3009	3027	3087	3249

Sequencing Information

	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2
Sample_ID	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2	BGKcLV04-2
Sample Name	NT_BGKcLV04-1	NT_BGKcLV04-1B	NT-BGKcLV04-1B	NT-BGKcLV04-1C	NT_BGKcLV04-2	NT_BGKcLV04-2B	NT-BGKcLV04-2B	NT-BGKcLV04-2C
Pool ID	Pool-161129	Pool-161129	Pool-170911	Pool-181119	Pool-161129	Pool-161129	Pool-170911	Pool-181119
LocalServer_folder	BGKcLV04	BGKcLV04	set39_K	set41_spikeins	BGKcLV04	BGKcLV04	set39_K	set41_spikeins
total_reads	49,006,016	103,000,000	37,614,548	376,190,728	40,750,750	102,000,000	37,294,160	50,310,080
total_aligned_reads	38,456,114	92,100,768	33,013,340	305,645,820	33,081,098	92,858,682	33,137,534	45,075,946
unique_aligned_reads	35,117,870	84,216,478	30,275,004	276,571,958	30,450,406	84,969,752	30,391,608	41,318,546
percent_uniqueAligned	0.71660	0.81764	0.80487	0.73519	0.74724	0.83304	0.81492	0.82128
correlation_replicates	0.997670	0.993950	0.996572	0.994406	0.997670	0.993950	0.996572	0.994406
spikein_reads	71,100	512,196	52	993,378	71,692	462,644	24	137,694
percent_spikeins	0.00145	0.00497		0.00264	0.00176	0.00454		0.00274
original_ReadLength	100	100	100	100	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted	Submitted	Submitted	Submitted	Submitted
ID	1657	1663	1677	1961	1658	1664	1678	1962

	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-2	BGKcLV04-2
ENCODE_alias	brenton-graveley:NT_BGKcLV04	brenton-graveley:NT_BGKcLV04_B	brenton-graveley:NT-BGKcLV04-B	brenton-graveley:NT-BGKcLV04-C	brenton-graveley:L-NT-BGKcLV04-1C	brenton-graveley:NT_BGKcLV04-1	brenton-graveley:L-NT-BGKcLV04-2C	brenton-graveley:NT_BGKcLV04-2
ENCODE_accession	ENCSR828YEB	ENCSR226KWO	ENCSR772DUM	ENCSR005JBU	ENCLB312WPF	ENCBS834BAD	ENCLB977VXZ	ENCBS644QUZ
object_type	experiment	experiment	experiment	experiment	library	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	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-1	BGKcLV04-2	BGKcLV04-2
Sample Name	NT_BGKcLV04-1	NT_BGKcLV04-1B	NT_BGKcLV04-1B	NT-BGKcLV04-1C	NT-BGKcLV04-1C	NT_BGKcLV04-1	NT-BGKcLV04-2C	NT_BGKcLV04-2
Selected	Yes	Yes	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	ENCODE3	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
					LV41_library_protocol_spikeins	cLV04-05_biosample_protocol	LV41_library_protocol_spikeins	cLV04-05_biosample_protocol
protocol_URL					L-NT-BGKcLV04-1C.pdf	NT_BGKcLV04-1.pdf	L-NT-BGKcLV04-2C.pdf	NT_BGKcLV04-2.pdf
ID	3199	3200	3212	7383	7402	7432	7403	7433

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	Project	FILE_ID
NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1677	HiSeq2500	100	paired-ended	1				ENCODE3	22468
NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1677	HiSeq2500	100	paired-ended	2				ENCODE3	22504
NT-BGKcLV04-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1677					GRCh38	V40	NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R2.fastq.gz	ENCORE2	22540
NT-BGKcLV04-1B_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	1677					GRCh38	V40	NT-BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	22576
NT-BGKcLV04-1B_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	1677					GRCh38	V40	NT-BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	22612
NT-BGKcLV04-1B_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	1677					GRCh38	V40	NT-BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	22648
NT-BGKcLV04-1B_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	1677					GRCh38	V40	NT-BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	22684
NT-BGKcLV04-1B_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1677					GRCh38	V40	NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGKcLV04-1B_ATGTCA_ACBE67ANXX_L003_001.R2.fastq.gz	ENCORE2	22720
NT_BGKcLV04-1_ACAGTG_L004_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1657	HiSeq2500	100	paired-ended	1				ENCODE3	23058
NT_BGKcLV04-1B_TTAGGC_L004_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1663	HiSeq2500	100	paired-ended	1				ENCODE3	23059
NT_BGKcLV04-1_ACAGTG_L004_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1657	HiSeq2500	100	paired-ended	2				ENCODE3	23068
NT_BGKcLV04-1B_TTAGGC_L004_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1663	HiSeq2500	100	paired-ended	2				ENCODE3	23069
NT_BGKcLV04-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1657					GRCh38	V40	NT_BGKcLV04-1_ACAGTG_L004_001.R1.fastq.gz,NT_BGKcLV04-1_ACAGTG_L004_001.R2.fastq.gz	ENCORE2	23078
NT_BGKcLV04-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1663					GRCh38	V40	NT_BGKcLV04-1B_TTAGGC_L004_001.R1.fastq.gz,NT_BGKcLV04-1B_TTAGGC_L004_001.R2.fastq.gz	ENCORE2	23079
NT_BGKcLV04-1B_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1663					GRCh38	V40	NT_BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23088
NT_BGKcLV04-1_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1657					GRCh38	V40	NT_BGKcLV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	23089
NT_BGKcLV04-1B_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1663					GRCh38	V40	NT_BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23098
NT_BGKcLV04-1_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1657					GRCh38	V40	NT_BGKcLV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	23099
NT_BGKcLV04-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1663					GRCh38	V40	NT_BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23108
NT_BGKcLV04-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1657					GRCh38	V40	NT_BGKcLV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	23109
NT_BGKcLV04-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1663					GRCh38	V40	NT_BGKcLV04-1B/Aligned.sortedByCoord.out.bam	ENCORE2	23118
NT_BGKcLV04-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1657					GRCh38	V40	NT_BGKcLV04-1/Aligned.sortedByCoord.out.bam	ENCORE2	23119
NT_BGKcLV04-1B_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1663					GRCh38	V40	NT_BGKcLV04-1B_TTAGGC_L004_001.R1.fastq.gz,NT_BGKcLV04-1B_TTAGGC_L004_001.R2.fastq.gz	ENCORE2	23128
NT_BGKcLV04-1_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1657					GRCh38	V40	NT_BGKcLV04-1_ACAGTG_L004_001.R1.fastq.gz,NT_BGKcLV04-1_ACAGTG_L004_001.R2.fastq.gz	ENCORE2	23129
NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1678	HiSeq2500	100	paired-ended	1				ENCODE3	22469
NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1678	HiSeq2500	100	paired-ended	2				ENCODE3	22505
NT-BGKcLV04-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1678					GRCh38	V40	NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R2.fastq.gz	ENCORE2	22541
NT-BGKcLV04-2B_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	1678					GRCh38	V40	NT-BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	22577
NT-BGKcLV04-2B_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	1678					GRCh38	V40	NT-BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	22613
NT-BGKcLV04-2B_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	1678					GRCh38	V40	NT-BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	22649
NT-BGKcLV04-2B_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	1678					GRCh38	V40	NT-BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	22685
NT-BGKcLV04-2B_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1678					GRCh38	V40	NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R1.fastq.gz,NT-BGKcLV04-2B_CCGTCC_ACBE67ANXX_L003_001.R2.fastq.gz	ENCORE2	22721
NT_BGKcLV04-2B_TGACCA_L004_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1664	HiSeq2500	100	paired-ended	1				ENCODE3	23060
NT_BGKcLV04-2_GCCAAT_L004_001.R1.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1658	HiSeq2500	100	paired-ended	1				ENCODE3	23061
NT_BGKcLV04-2B_TGACCA_L004_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1664	HiSeq2500	100	paired-ended	2				ENCODE3	23070
NT_BGKcLV04-2_GCCAAT_L004_001.R2.fastq.gz	ENCODE_DATA/BGKcLV04/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1658	HiSeq2500	100	paired-ended	2				ENCODE3	23071
NT_BGKcLV04-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1664					GRCh38	V40	NT_BGKcLV04-2B_TGACCA_L004_001.R1.fastq.gz,NT_BGKcLV04-2B_TGACCA_L004_001.R2.fastq.gz	ENCORE2	23080
NT_BGKcLV04-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1658					GRCh38	V40	NT_BGKcLV04-2_GCCAAT_L004_001.R1.fastq.gz,NT_BGKcLV04-2_GCCAAT_L004_001.R2.fastq.gz	ENCORE2	23081
NT_BGKcLV04-2B_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1664					GRCh38	V40	NT_BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23090
NT_BGKcLV04-2_Signal.Unique.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1658					GRCh38	V40	NT_BGKcLV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	23091
NT_BGKcLV04-2B_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1664					GRCh38	V40	NT_BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23100
NT_BGKcLV04-2_Signal.Unique.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1658					GRCh38	V40	NT_BGKcLV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	23101
NT_BGKcLV04-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1664					GRCh38	V40	NT_BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23110
NT_BGKcLV04-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1658					GRCh38	V40	NT_BGKcLV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	23111
NT_BGKcLV04-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1664					GRCh38	V40	NT_BGKcLV04-2B/Aligned.sortedByCoord.out.bam	ENCORE2	23120
NT_BGKcLV04-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/BGKcLV04/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1658					GRCh38	V40	NT_BGKcLV04-2/Aligned.sortedByCoord.out.bam	ENCORE2	23121
NT_BGKcLV04-2B_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1664					GRCh38	V40	NT_BGKcLV04-2B_TGACCA_L004_001.R1.fastq.gz,NT_BGKcLV04-2B_TGACCA_L004_001.R2.fastq.gz	ENCORE2	23130
NT_BGKcLV04-2_quant.sf	ENCODE_DATA/BGKcLV04/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1658					GRCh38	V40	NT_BGKcLV04-2_GCCAAT_L004_001.R1.fastq.gz,NT_BGKcLV04-2_GCCAAT_L004_001.R2.fastq.gz	ENCORE2	23131