non-target RNA-Seq in K562

	BGKLV24-1	BGKLV24-2
idx	338	339
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV24-1	BGKLV24-2
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3411	0
WB_result		4964.9
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	5/22/2015	5/22/2015
repeat_library
Note
ID	379	380

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-1	BGKLV24-1	BGKLV24-1	BGKLV24-2	BGKLV24-2	BGKLV24-2
Sample #
Sample Name	NT-BGKLV24-1	NT-BGKLV24-1B	NT-BGKLV24-1C	NT-BGKLV24-2	NT-BGKLV24-2B	NT-BGKLV24-2C
Sample_Name_Alias	non-target_BGKLV24_1_17594	non-target_BGKLV24_1B	NT_BGKLV24-1C	non-target_BGKLV24_2_17595	non-target_BGKLV24_2B	NT_BGKLV24-2C
Index Well Position	S18	S01	S03	S19	S02	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-22	2015-09-02	2016-03-10	2015-05-22	2015-09-02	2016-03-10
Lib_ID	Lib-150522	Lib-150902	Lib-160310	Lib-150522	Lib-150902	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/B1.png	DNA_Library_LV24-25-26/set1/A5.png	DNA_Library_LV33-34-25B-32/set1/A11.png	DNA_Library_LV21-24/set1/C1.png	DNA_Library_LV24-25-26/set1/B5.png	DNA_Library_LV33-34-25B-32/set1/B11.png
RIN	9.7	9.7	9.7	9.8	9.8	9.8
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E12.png	RNA_Library_LV19-21-24/set1/E12.png	RNA_Library_LV19-21-24/set1/E12.png	RNA_Library_LV19-21-24/set1/F12.png	RNA_Library_LV19-21-24/set1/F12.png	RNA_Library_LV19-21-24/set1/F12.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-1	BGKLV24-1	BGKLV24-1	BGKLV24-2	BGKLV24-2	BGKLV24-2
RBP	NT	NT	NT	NT	NT	NT
Batch_ID	BGKLV24	BGKLV24	BGKLV24	BGKLV24	BGKLV24	BGKLV24
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	2560	2580	2880	2561	2581	2881

Sequencing Information

	BGKLV24-1	BGKLV24-1	BGKLV24-1	BGKLV24-2	BGKLV24-2	BGKLV24-2
Sample_ID	BGKLV24-1	BGKLV24-1	BGKLV24-1	BGKLV24-2	BGKLV24-2	BGKLV24-2
Sample Name	non-target_BGKLV24_1_17594	non-target_BGKLV24_1B	NT_BGKLV24-1C	non-target_BGKLV24_2_17595	non-target_BGKLV24_2B	NT_BGKLV24-2C
Pool ID	Pool-150615	Pool-151101	Pool-160425	Pool-150615	Pool-151101	Pool-160425
LocalServer_folder	set24	set24_2	set24	set24	set24_2	set24
total_reads	34,070,000	77,489,178	104,383,072	29,500,000	79,325,808	74,087,364
total_aligned_reads	31,183,192	69,944,132	72,111,238	27,419,260	75,916,894	50,632,004
unique_aligned_reads	28,693,042	63,599,558	65,832,740	25,144,392	69,182,118	46,192,544
percent_uniqueAligned	0.84218	0.82075	0.63068	0.85235	0.87213	0.62349
correlation_replicates	0.998201	0.996354	0.999260	0.998201	0.996354	0.999260
spikein_reads	151,096	255,492	174,842	131,724	261,202	114,116
percent_spikeins	0.00443	0.00330	0.00168	0.00447	0.00329	0.00154
original_ReadLength	100	100	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted	Submitted	Submitted
ID	1094	1222	1529	1095	1223	1530

	BGKLV24-1	BGKLV24-1	BGKLV24-1
ENCODE_alias	brenton-graveley:non-target_BGKLV24	brenton-graveley:non-target_BGKLV24_B	brenton-graveley:NT_BGKLV24C
ENCODE_accession	ENCSR667PLJ	ENCSR419JMU	ENCSR154OBA
object_type	experiment	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-1	BGKLV24-1	BGKLV24-1
Sample Name	non-target_BGKLV24_1_17594	non-target_BGKLV24_1B	NT_BGKLV24-1C
Selected	Yes	Yes	Yes
Status	Released	Released	Released
Status_Date	2015-08-13	2015-12-02	2016-05-25
Project	ENCODE3	ENCODE3	ENCODE3

protocol_URL
ID	2987	2995	3141

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
non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1094	HiSeq2000	100	paired-ended	1				ENCODE3	17206
NT_BGKLV24-1C_TTAGGC_L006_001.R1.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1529	HiSeq2000	100	paired-ended	1				ENCODE3	17208
non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1094	HiSeq2000	100	paired-ended	2				ENCODE3	17242
NT_BGKLV24-1C_TTAGGC_L006_001.R2.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1529	HiSeq2000	100	paired-ended	2				ENCODE3	17244
non-target_BGKLV24_1_17594_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1094					GRCh38	V40	non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz	ENCORE2	17278
NT_BGKLV24-1C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1529					GRCh38	V40	NT_BGKLV24-1C_TTAGGC_L006_001.R1.fastq.gz,NT_BGKLV24-1C_TTAGGC_L006_001.R2.fastq.gz	ENCORE2	17280
non-target_BGKLV24_1_17594_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1094					GRCh38	V40	non-target_BGKLV24_1_17594/Aligned.sortedByCoord.out.bam	ENCORE2	17314
NT_BGKLV24-1C_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1529					GRCh38	V40	NT_BGKLV24-1C/Aligned.sortedByCoord.out.bam	ENCORE2	17316
non-target_BGKLV24_1_17594_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1094					GRCh38	V40	non-target_BGKLV24_1_17594/Aligned.sortedByCoord.out.bam	ENCORE2	17350
NT_BGKLV24-1C_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1529					GRCh38	V40	NT_BGKLV24-1C/Aligned.sortedByCoord.out.bam	ENCORE2	17352
non-target_BGKLV24_1_17594_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1094					GRCh38	V40	non-target_BGKLV24_1_17594/Aligned.sortedByCoord.out.bam	ENCORE2	17386
NT_BGKLV24-1C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1529					GRCh38	V40	NT_BGKLV24-1C/Aligned.sortedByCoord.out.bam	ENCORE2	17388
non-target_BGKLV24_1_17594_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1094					GRCh38	V40	non-target_BGKLV24_1_17594/Aligned.sortedByCoord.out.bam	ENCORE2	17422
NT_BGKLV24-1C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1529					GRCh38	V40	NT_BGKLV24-1C/Aligned.sortedByCoord.out.bam	ENCORE2	17424
non-target_BGKLV24_1_17594_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1094					GRCh38	V40	non-target_BGKLV24_1_17594_GTCCGC_L005_R1_001.fastq.gz,non-target_BGKLV24_1_17594_GTCCGC_L005_R2_001.fastq.gz	ENCORE2	17458
NT_BGKLV24-1C_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1529					GRCh38	V40	NT_BGKLV24-1C_TTAGGC_L006_001.R1.fastq.gz,NT_BGKLV24-1C_TTAGGC_L006_001.R2.fastq.gz	ENCORE2	17460
non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1222	HiSeq2000	100	paired-ended	1				ENCODE3	17478
non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1222	HiSeq2000	100	paired-ended	2				ENCODE3	17502
non-target_BGKLV24_1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1222					GRCh38	V40	non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz	ENCORE2	17526
non-target_BGKLV24_1B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1222					GRCh38	V40	non-target_BGKLV24_1B/Aligned.sortedByCoord.out.bam	ENCORE2	17550
non-target_BGKLV24_1B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1222					GRCh38	V40	non-target_BGKLV24_1B/Aligned.sortedByCoord.out.bam	ENCORE2	17574
non-target_BGKLV24_1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1222					GRCh38	V40	non-target_BGKLV24_1B/Aligned.sortedByCoord.out.bam	ENCORE2	17598
non-target_BGKLV24_1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1222					GRCh38	V40	non-target_BGKLV24_1B/Aligned.sortedByCoord.out.bam	ENCORE2	17622
non-target_BGKLV24_1B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1222					GRCh38	V40	non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz	ENCORE2	17646
non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1095	HiSeq2000	100	paired-ended	1				ENCODE3	17207
NT_BGKLV24-2C_TGACCA_L006_001.R1.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1530	HiSeq2000	100	paired-ended	1				ENCODE3	17209
non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1095	HiSeq2000	100	paired-ended	2				ENCODE3	17243
NT_BGKLV24-2C_TGACCA_L006_001.R2.fastq.gz	ENCODE_DATA/set24/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1530	HiSeq2000	100	paired-ended	2				ENCODE3	17245
non-target_BGKLV24_2_17595_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1095					GRCh38	V40	non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCORE2	17279
NT_BGKLV24-2C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1530					GRCh38	V40	NT_BGKLV24-2C_TGACCA_L006_001.R1.fastq.gz,NT_BGKLV24-2C_TGACCA_L006_001.R2.fastq.gz	ENCORE2	17281
non-target_BGKLV24_2_17595_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1095					GRCh38	V40	non-target_BGKLV24_2_17595/Aligned.sortedByCoord.out.bam	ENCORE2	17315
NT_BGKLV24-2C_Signal.Unique.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1530					GRCh38	V40	NT_BGKLV24-2C/Aligned.sortedByCoord.out.bam	ENCORE2	17317
non-target_BGKLV24_2_17595_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1095					GRCh38	V40	non-target_BGKLV24_2_17595/Aligned.sortedByCoord.out.bam	ENCORE2	17351
NT_BGKLV24-2C_Signal.Unique.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1530					GRCh38	V40	NT_BGKLV24-2C/Aligned.sortedByCoord.out.bam	ENCORE2	17353
non-target_BGKLV24_2_17595_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1095					GRCh38	V40	non-target_BGKLV24_2_17595/Aligned.sortedByCoord.out.bam	ENCORE2	17387
NT_BGKLV24-2C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1530					GRCh38	V40	NT_BGKLV24-2C/Aligned.sortedByCoord.out.bam	ENCORE2	17389
non-target_BGKLV24_2_17595_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1095					GRCh38	V40	non-target_BGKLV24_2_17595/Aligned.sortedByCoord.out.bam	ENCORE2	17423
NT_BGKLV24-2C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1530					GRCh38	V40	NT_BGKLV24-2C/Aligned.sortedByCoord.out.bam	ENCORE2	17425
non-target_BGKLV24_2_17595_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1095					GRCh38	V40	non-target_BGKLV24_2_17595_GTGAAA_L005_R1_001.fastq.gz,non-target_BGKLV24_2_17595_GTGAAA_L005_R2_001.fastq.gz	ENCORE2	17459
NT_BGKLV24-2C_quant.sf	ENCODE_DATA/set24/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1530					GRCh38	V40	NT_BGKLV24-2C_TGACCA_L006_001.R1.fastq.gz,NT_BGKLV24-2C_TGACCA_L006_001.R2.fastq.gz	ENCORE2	17461
non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1223	HiSeq2000	100	paired-ended	1				ENCODE3	17479
non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1223	HiSeq2000	100	paired-ended	2				ENCODE3	17503
non-target_BGKLV24_2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1223					GRCh38	V40	non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCORE2	17527
non-target_BGKLV24_2B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1223					GRCh38	V40	non-target_BGKLV24_2B/Aligned.sortedByCoord.out.bam	ENCORE2	17551
non-target_BGKLV24_2B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1223					GRCh38	V40	non-target_BGKLV24_2B/Aligned.sortedByCoord.out.bam	ENCORE2	17575
non-target_BGKLV24_2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1223					GRCh38	V40	non-target_BGKLV24_2B/Aligned.sortedByCoord.out.bam	ENCORE2	17599
non-target_BGKLV24_2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1223					GRCh38	V40	non-target_BGKLV24_2B/Aligned.sortedByCoord.out.bam	ENCORE2	17623
non-target_BGKLV24_2B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1223					GRCh38	V40	non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCORE2	17647