non-target RNA-Seq in K562

	BGKLV19-1	BGKLV19-2
idx	208	209
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV19-1	BGKLV19-2
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	4343
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
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	227	228

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-1	BGKLV19-1	BGKLV19-1	BGKLV19-2	BGKLV19-2	BGKLV19-2
Sample #
Sample Name	NT-BGKLV19-1	NT-BGKLV19-1B	NT-BGKLV19-1C	NT-BGKLV19-2	NT-BGKLV19-2B	NT-BGKLV19-2C
Sample_Name_Alias	NT_BGKLV19_1A	NT_BGKLV19_1B	NT_BGKLV19-1B_repeat	NT_BGKLV19_2A	NT_BGKLV19_2B	NT_BGKLV19-2B_repeat
Index Well Position	S15	S01	S20	S16	S02	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-03	2015-09-28	2014-10-02	2014-10-03	2015-09-28
Lib_ID	Lib-141002	Lib-141003	Lib-150928	Lib-141002	Lib-141003	Lib-150928
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/G5.png	DNA_Library_LV18-19/set1/A7.png	DNA_Library_LV27/set2/C1.png	DNA_Library_LV18-19/set1/H5.png	DNA_Library_LV18-19/set1/B7.png	DNA_Library_LV27/set2/D1.png
RIN	9.7	9.7	9.7	9.3	9.3	9.3
libSample_RNA_Well	RNA_Library_LV18-19/set1/E12.png	RNA_Library_LV18-19/set1/E12.png	RNA_Library_LV18-19/set1/E12.png	RNA_Library_LV18-19/set1/F12.png	RNA_Library_LV18-19/set1/F12.png	RNA_Library_LV18-19/set1/F12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-1	BGKLV19-1	BGKLV19-1	BGKLV19-2	BGKLV19-2	BGKLV19-2
RBP	NT	NT	NT	NT	NT	NT
Batch_ID	BGKLV19	BGKLV19	BGKLV19	BGKLV19	BGKLV19	BGKLV19
WB_result	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
Repeat_Library_Suffix		B	C		B	C
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2346	2368	2650	2347	2369	2651

Sequencing Information

	BGKLV19-1	BGKLV19-1	BGKLV19-1	BGKLV19-2	BGKLV19-2	BGKLV19-2
Sample_ID	BGKLV19-1	BGKLV19-1	BGKLV19-1	BGKLV19-2	BGKLV19-2	BGKLV19-2
Sample Name	NT_BGKLV19_1A	NT_BGKLV19_1B	NT_BGKLV19-1B_repeat	NT_BGKLV19_2A	NT_BGKLV19_2B	NT_BGKLV19-2B_repeat
Pool ID	Pool-141010	Pool-141015	Pool-151201	Pool-141010	Pool-141015	Pool-151201
LocalServer_folder	set19	set19	set19	set19	set19	set19
total_reads	50,840,000	32,500,000	67,843,944	39,640,000	42,260,000	84,072,712
total_aligned_reads	47,461,676	29,707,520	64,329,634	36,672,696	38,524,254	78,984,490
unique_aligned_reads	43,556,018	27,216,608	59,107,504	33,589,000	35,226,426	72,226,644
percent_uniqueAligned	0.85673	0.83743	0.87123	0.84735	0.83356	0.85910
correlation_replicates	0.997100	0.997100	0.998788	0.994242	0.994242	0.998788
spikein_reads	193,614	160,092	817,602	191,772	135,124	755,592
percent_spikeins	0.00381	0.00493	0.01205	0.00484	0.00320	0.00899
original_ReadLength	100	100	101	100	100	101
QC_Status	Submitted	Submitted	Submitted	Submitted	Submitted	Submitted
ID	988	1010	1292	989	1011	1293

	BGKLV19-1	BGKLV19-1	BGKLV19-1
ENCODE_alias	brenton-graveley:NT_BGKLV19-A	brenton-graveley:NT_BGKLV19-B	brenton-graveley:NT_BGKLV19-B_repeat
ENCODE_accession	ENCSR245BNJ	ENCSR661HEL	ENCSR092WKG
object_type	experiment	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV19-1	BGKLV19-1	BGKLV19-1
Sample Name	NT_BGKLV19_1A	NT_BGKLV19_1B	NT_BGKLV19-1B_repeat
Selected	Yes	Yes	Yes
Status	Released	Released	Released
Status_Date	2014-12-05	2014-12-05	2016-01-14
Project	ENCODE3	ENCODE3	ENCODE3

protocol_URL
ID	2890	2902	3038

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_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1010	HiSeq2000	100	paired-ended	1				ENCODE3	15123
NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1010	HiSeq2000	100	paired-ended	2				ENCODE3	15181
NT_BGKLV19_1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1010					GRCh38	V40	NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz	ENCORE2	15239
NT_BGKLV19-1B_repeat_1.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1292	HiSeq2000	100	paired-ended	1				ENCODE3	15272
NT_BGKLV19-1B_repeat_2.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1292	HiSeq2000	100	paired-ended	2				ENCODE3	15273
NT_BGKLV19-1B_repeat_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1292					GRCh38	V40	NT_BGKLV19-1B_repeat_1.fastq.gz,NT_BGKLV19-1B_repeat_2.fastq.gz	ENCORE2	15279
NT_BGKLV19-1B_repeat_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1010					GRCh38	V40	NT_BGKLV19_1B/Aligned.sortedByCoord.out.bam	ENCORE2	15310
NT_BGKLV19_1B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1292					GRCh38	V40	NT_BGKLV19-1B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15311
NT_BGKLV19-1B_repeat_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1010					GRCh38	V40	NT_BGKLV19_1B/Aligned.sortedByCoord.out.bam	ENCORE2	15368
NT_BGKLV19_1B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1292					GRCh38	V40	NT_BGKLV19-1B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15369
NT_BGKLV19-1B_repeat_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1010					GRCh38	V40	NT_BGKLV19_1B/Aligned.sortedByCoord.out.bam	ENCORE2	15426
NT_BGKLV19_1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1292					GRCh38	V40	NT_BGKLV19-1B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15427
NT_BGKLV19-1B_repeat_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1010					GRCh38	V40	NT_BGKLV19_1B/Aligned.sortedByCoord.out.bam	ENCORE2	15484
NT_BGKLV19_1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1292					GRCh38	V40	NT_BGKLV19-1B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15485
NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	988	HiSeq2000	100	paired-ended	1				ENCODE3	15522
NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	988	HiSeq2000	100	paired-ended	2				ENCODE3	15532
NT_BGKLV19_1A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	988					GRCh38	V40	NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz	ENCORE2	15542
NT_BGKLV19_1A_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	988					GRCh38	V40	NT_BGKLV19_1A/Aligned.sortedByCoord.out.bam	ENCORE2	15552
NT_BGKLV19_1A_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	988					GRCh38	V40	NT_BGKLV19_1A/Aligned.sortedByCoord.out.bam	ENCORE2	15562
NT_BGKLV19_1A_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	988					GRCh38	V40	NT_BGKLV19_1A/Aligned.sortedByCoord.out.bam	ENCORE2	15572
NT_BGKLV19_1A_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	988					GRCh38	V40	NT_BGKLV19_1A/Aligned.sortedByCoord.out.bam	ENCORE2	15582
NT_BGKLV19_1A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	988					GRCh38	V40	NT_BGKLV19_1A_ATGTCA_L001_R1_001.fastq.gz,NT_BGKLV19_1A_ATGTCA_L001_R2_001.fastq.gz	ENCORE2	16380
NT_BGKLV19_1B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1010					GRCh38	V40	NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz	ENCORE2	16381
NT_BGKLV19-1B_repeat_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1292					GRCh38	V40	NT_BGKLV19-1B_repeat_1.fastq.gz,NT_BGKLV19-1B_repeat_2.fastq.gz	ENCORE2	16382
NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1011	HiSeq2000	100	paired-ended	1				ENCODE3	15126
NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1011	HiSeq2000	100	paired-ended	2				ENCODE3	15184
NT_BGKLV19_2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1011					GRCh38	V40	NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCORE2	15242
NT_BGKLV19-2B_repeat_1.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1293	HiSeq2000	100	paired-ended	1				ENCODE3	15271
NT_BGKLV19-2B_repeat_2.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1293	HiSeq2000	100	paired-ended	2				ENCODE3	15274
NT_BGKLV19-2B_repeat_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1293					GRCh38	V40	NT_BGKLV19-2B_repeat_1.fastq.gz,NT_BGKLV19-2B_repeat_2.fastq.gz	ENCORE2	15280
NT_BGKLV19-2B_repeat_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1011					GRCh38	V40	NT_BGKLV19_2B/Aligned.sortedByCoord.out.bam	ENCORE2	15313
NT_BGKLV19_2B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1293					GRCh38	V40	NT_BGKLV19-2B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15314
NT_BGKLV19-2B_repeat_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1011					GRCh38	V40	NT_BGKLV19_2B/Aligned.sortedByCoord.out.bam	ENCORE2	15371
NT_BGKLV19_2B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1293					GRCh38	V40	NT_BGKLV19-2B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15372
NT_BGKLV19-2B_repeat_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1011					GRCh38	V40	NT_BGKLV19_2B/Aligned.sortedByCoord.out.bam	ENCORE2	15429
NT_BGKLV19_2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1293					GRCh38	V40	NT_BGKLV19-2B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15430
NT_BGKLV19-2B_repeat_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1011					GRCh38	V40	NT_BGKLV19_2B/Aligned.sortedByCoord.out.bam	ENCORE2	15487
NT_BGKLV19_2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1293					GRCh38	V40	NT_BGKLV19-2B_repeat/Aligned.sortedByCoord.out.bam	ENCORE2	15488
NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	989	HiSeq2000	100	paired-ended	1				ENCODE3	15523
NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	989	HiSeq2000	100	paired-ended	2				ENCODE3	15533
NT_BGKLV19_2A_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	989					GRCh38	V40	NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCORE2	15543
NT_BGKLV19_2A_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	989					GRCh38	V40	NT_BGKLV19_2A/Aligned.sortedByCoord.out.bam	ENCORE2	15553
NT_BGKLV19_2A_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	989					GRCh38	V40	NT_BGKLV19_2A/Aligned.sortedByCoord.out.bam	ENCORE2	15563
NT_BGKLV19_2A_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	989					GRCh38	V40	NT_BGKLV19_2A/Aligned.sortedByCoord.out.bam	ENCORE2	15573
NT_BGKLV19_2A_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	989					GRCh38	V40	NT_BGKLV19_2A/Aligned.sortedByCoord.out.bam	ENCORE2	15583
NT_BGKLV19_2A_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	989					GRCh38	V40	NT_BGKLV19_2A_CCGTCC_L001_R1_001.fastq.gz,NT_BGKLV19_2A_CCGTCC_L001_R2_001.fastq.gz	ENCORE2	16383
NT_BGKLV19_2B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1011					GRCh38	V40	NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCORE2	16384
NT_BGKLV19-2B_repeat_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1293					GRCh38	V40	NT_BGKLV19-2B_repeat_1.fastq.gz,NT_BGKLV19-2B_repeat_2.fastq.gz	ENCORE2	16385