non-target RNA-Seq in K562

	BGKLV21-1	BGKLV21-2
idx	272	273
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGKLV21-1	BGKLV21-2
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	4420
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	5/19/2015	5/19/2015
repeat_library
Note
ID	297	298

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV21-1	BGKLV21-1	BGKLV21-2	BGKLV21-2
Sample_ID	BGKLV21-1	BGKLV21-1	BGKLV21-2	BGKLV21-2
Sample Name	non-target_BGKLV21_1	NT_BGKLV21-1B	non-target_BGKLV21_2	NT_BGKLV21-2B
Sample Name	non-target_BGKLV21_1	NT_BGKLV21-1B	non-target_BGKLV21_2	NT_BGKLV21-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	Released	Released	Released
Status_date	2015-08-14	2016-03-07	2015-08-14	2016-03-07
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note
ID	762	1135	763	1136

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-1	BGKLV21-1	BGKLV21-2	BGKLV21-2
Sample #
Sample Name	NT-BGKLV21-1	NT-BGKLV21-1B	NT-BGKLV21-2	NT-BGKLV21-2B
Sample_Name_Alias	non-target_BGKLV21_1	NT_BGKLV21-1B	non-target_BGKLV21_2	NT_BGKLV21-2B
Index Well Position	S01	S07	S02	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2016-02-04	2015-05-19	2016-02-04
Lib_ID	Lib-150519	Lib-160204	Lib-150519	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/A5.png	DNA_Library_LV31-21B/set1/G7.png	DNA_Library_LV21-24/set1/B5.png	DNA_Library_LV31-21B/set1/H7.png
RIN	9.8	9.8	10.0	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C7.png	RNA_Library_LV19-21-24/set1/C7.png	RNA_Library_LV19-21-24/set2/A2.png	RNA_Library_LV19-21-24/set2/A2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-1	BGKLV21-1	BGKLV21-2	BGKLV21-2
RBP	NT	NT	NT	NT
Batch_ID	BGKLV21	BGKLV21	BGKLV21	BGKLV21
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2448	2832	2449	2833

Sequencing Information

	BGKLV21-1	BGKLV21-1	BGKLV21-2	BGKLV21-2
Sample_ID	BGKLV21-1	BGKLV21-1	BGKLV21-2	BGKLV21-2
Sample Name	non-target_BGKLV21_1	NT_BGKLV21-1B	non-target_BGKLV21_2	NT_BGKLV21-2B
Pool ID	Pool-150615	Pool-160229	Pool-150615	Pool-160229
LocalServer_folder	set21	set21	set21	set21
total_reads	44,490,000	61,608,202	50,940,000	65,292,736
total_aligned_reads	41,205,810	57,128,564	46,474,376	61,586,678
unique_aligned_reads	37,837,006	51,955,228	42,489,206	56,297,930
percent_uniqueAligned	0.85046	0.84332	0.83410	0.86224
correlation_replicates	0.992352	0.997543	0.992352	0.997543
spikein_reads	254,776	343,400	316,220	381,024
percent_spikeins	0.00573	0.00557	0.00621	0.00584
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	1054	1481	1055	1482

Data Submission Information

	BGKLV21-1	BGKLV21-1
ENCODE_alias	brenton-graveley:non-target_BGKLV21	brenton-graveley:NT_BGKLV21-B
ENCODE_accession	ENCSR572FFX	ENCSR438MDN
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-1	BGKLV21-1
Sample Name	non-target_BGKLV21_1	NT_BGKLV21-1B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2016-03-07
Project	ENCODE3	ENCODE3

protocol_URL
ID	2967	3100

File Information

Search:

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_BGKLV21_1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1054					GRCh38	V40	non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz	ENCORE2	16030
non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1054	HiSeq2000	100	paired-ended	1				ENCODE3	15942
non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1054	HiSeq2000	100	paired-ended	2				ENCODE3	15986
non-target_BGKLV21_1_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1054					GRCh38	V40	non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz	ENCORE2	16250
non-target_BGKLV21_1_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1054					GRCh38	V40	non-target_BGKLV21_1/Aligned.sortedByCoord.out.bam	ENCORE2	16074
non-target_BGKLV21_1_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1054					GRCh38	V40	non-target_BGKLV21_1/Aligned.sortedByCoord.out.bam	ENCORE2	16118
non-target_BGKLV21_1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1054					GRCh38	V40	non-target_BGKLV21_1/Aligned.sortedByCoord.out.bam	ENCORE2	16162
non-target_BGKLV21_1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1054					GRCh38	V40	non-target_BGKLV21_1/Aligned.sortedByCoord.out.bam	ENCORE2	16206
non-target_BGKLV21_2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1055					GRCh38	V40	non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCORE2	16031
non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1055	HiSeq2000	100	paired-ended	1				ENCODE3	15943
non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1055	HiSeq2000	100	paired-ended	2				ENCODE3	15987
non-target_BGKLV21_2_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1055					GRCh38	V40	non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCORE2	16251
non-target_BGKLV21_2_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1055					GRCh38	V40	non-target_BGKLV21_2/Aligned.sortedByCoord.out.bam	ENCORE2	16075
non-target_BGKLV21_2_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1055					GRCh38	V40	non-target_BGKLV21_2/Aligned.sortedByCoord.out.bam	ENCORE2	16119
non-target_BGKLV21_2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1055					GRCh38	V40	non-target_BGKLV21_2/Aligned.sortedByCoord.out.bam	ENCORE2	16163
non-target_BGKLV21_2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1055					GRCh38	V40	non-target_BGKLV21_2/Aligned.sortedByCoord.out.bam	ENCORE2	16207
NT_BGKLV21-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1481					GRCh38	V40	NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz	ENCORE2	16032
NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1481	HiSeq2000	100	paired-ended	1				ENCODE3	15944
NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1481	HiSeq2000	100	paired-ended	2				ENCODE3	15988
NT_BGKLV21-1B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1481					GRCh38	V40	NT_BGKLV21-1B_CAGATC_L007_001.R1.fastq.gz,NT_BGKLV21-1B_CAGATC_L007_001.R2.fastq.gz	ENCORE2	16252
NT_BGKLV21-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1481					GRCh38	V40	NT_BGKLV21-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16076
NT_BGKLV21-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1481					GRCh38	V40	NT_BGKLV21-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16120
NT_BGKLV21-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1481					GRCh38	V40	NT_BGKLV21-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16164
NT_BGKLV21-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1481					GRCh38	V40	NT_BGKLV21-1B/Aligned.sortedByCoord.out.bam	ENCORE2	16208
NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1482	HiSeq2000	100	paired-ended	1				ENCODE3	15945
NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1482	HiSeq2000	100	paired-ended	2				ENCODE3	15989
NT_BGKLV21-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1482					GRCh38	V40	NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCORE2	16033
NT_BGKLV21-2B_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1482					GRCh38	V40	NT_BGKLV21-2B_ACTTGA_L007_001.R1.fastq.gz,NT_BGKLV21-2B_ACTTGA_L007_001.R2.fastq.gz	ENCORE2	16253
NT_BGKLV21-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1482					GRCh38	V40	NT_BGKLV21-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16077
NT_BGKLV21-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1482					GRCh38	V40	NT_BGKLV21-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16121
NT_BGKLV21-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1482					GRCh38	V40	NT_BGKLV21-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16165
NT_BGKLV21-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1482					GRCh38	V40	NT_BGKLV21-2B/Aligned.sortedByCoord.out.bam	ENCORE2	16209

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